diff --git a/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownHit.cs b/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownHit.cs index d675f753..2b877ec0 100644 --- a/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownHit.cs +++ b/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownHit.cs @@ -106,9 +106,9 @@ public double Score get { return h.score; } } - public string PFR + public string PFR_accession { - get { return h.pfr; } + get { return h.pfr_accession; } } #endregion Public Properties @@ -154,6 +154,7 @@ private static string header(string property_name) if (property_name == nameof(retention_time)) return "Retention Time"; if (property_name == nameof(pscore)) return "P-Score"; if (property_name == nameof(ptm_description)) return "PTM Description"; + if (property_name == nameof(PFR_accession)) return "PFR Accession"; return null; } diff --git a/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownProteoform.cs b/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownProteoform.cs index ad921d71..a08d1e83 100755 --- a/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownProteoform.cs +++ b/ProteoformSuiteGUI/DisplayObjects/DisplayTopDownProteoform.cs @@ -109,9 +109,9 @@ public int Observations get { return t.topdown_hits.Count; } } - public string PFR + public string PFR_accession { - get { return t.pfr; } + get { return t.pfr_accession; } } public string family_id @@ -170,6 +170,7 @@ public static string header(string name) if (name == nameof(manual_id)) return "Best Hit Info"; if (name == nameof(family_id)) return "Family ID"; if (name == nameof(mass_error)) return "Mass Error"; + if (name == nameof(PFR_accession)) return "PFR Accession"; return null; } diff --git a/ProteoformSuiteGUI/ExperimentTheoreticalComparison.Designer.cs b/ProteoformSuiteGUI/ExperimentTheoreticalComparison.Designer.cs index 888ffffa..52afdd25 100644 --- a/ProteoformSuiteGUI/ExperimentTheoreticalComparison.Designer.cs +++ b/ProteoformSuiteGUI/ExperimentTheoreticalComparison.Designer.cs @@ -363,7 +363,6 @@ private void InitializeComponent() this.label12.Size = new System.Drawing.Size(118, 13); this.label12.TabIndex = 3; this.label12.Text = "ET Relation Table Filter"; - this.label12.Click += new System.EventHandler(this.label12_Click); // // tb_relationTableFilter // diff --git a/ProteoformSuiteGUI/ExperimentTheoreticalComparison.cs b/ProteoformSuiteGUI/ExperimentTheoreticalComparison.cs index a96238c1..3df5877d 100644 --- a/ProteoformSuiteGUI/ExperimentTheoreticalComparison.cs +++ b/ProteoformSuiteGUI/ExperimentTheoreticalComparison.cs @@ -477,10 +477,5 @@ private void ct_ET_peakList_MouseClick(object sender, MouseEventArgs e) } #endregion Tooltip Private Methods - - private void label12_Click(object sender, EventArgs e) - { - - } } } diff --git a/ProteoformSuiteGUI/TopDown.cs b/ProteoformSuiteGUI/TopDown.cs index 0b9e4799..11a861d4 100755 --- a/ProteoformSuiteGUI/TopDown.cs +++ b/ProteoformSuiteGUI/TopDown.cs @@ -52,7 +52,7 @@ public void FillTablesAndCharts() mods = Sweet.lollipop.topdown_proteoforms.SelectMany(p => p.topdown_ptm_set.ptm_combination).Select(m => m.modification.id).Distinct().ToList(); tb_tdProteoforms.Text = Sweet.lollipop.topdown_proteoforms.Count.ToString(); tb_td_hits.Text = Sweet.lollipop.top_down_hits.Count.ToString(); - tb_unique_PFRs.Text = Sweet.lollipop.topdown_proteoforms.Select(p => p.pfr).Distinct().Count().ToString(); + tb_unique_PFRs.Text = Sweet.lollipop.topdown_proteoforms.Select(p => p.pfr_accession).Distinct().Count().ToString(); } public void RunTheGamut(bool full_run) diff --git a/ProteoformSuiteInternal/Calibration.cs b/ProteoformSuiteInternal/Calibration.cs index 154a40c2..6478cbde 100755 --- a/ProteoformSuiteInternal/Calibration.cs +++ b/ProteoformSuiteInternal/Calibration.cs @@ -193,8 +193,11 @@ private DataPointAquisitionResults GetDataPoints() { //look around theoretical mass of topdown hit identified proteoforms - 10 ppm and 5 minutes same br, tr, fraction, condition (same file!) //if neucode labled, look for the light component mass (loaded in...) - List potential_matches = Sweet.lollipop.calibration_components.Where(c => c.input_file.lt_condition == raw_file.lt_condition && (Sweet.lollipop.neucode_labeled || c.input_file.biological_replicate == raw_file.biological_replicate) && c.input_file.fraction == raw_file.fraction - && c.input_file.technical_replicate == raw_file.technical_replicate).ToList(); + List potential_matches = Sweet.lollipop.calibration_components. + Where(c => c.input_file.lt_condition == raw_file.lt_condition + && (Sweet.lollipop.neucode_labeled || c.input_file.biological_replicate == raw_file.biological_replicate) + && c.input_file.fraction == raw_file.fraction + && c.input_file.technical_replicate == raw_file.technical_replicate).ToList(); if (potential_matches.Count > 0) matching_component = potential_matches.Where(c => Math.Abs(c.charge_states.OrderByDescending(s => s.intensity).First().mz_centroid.ToMass(c.charge_states.OrderByDescending(s => s.intensity).First().charge_count) - identification.theoretical_mass) * 1e6 / c.charge_states.OrderByDescending(s => s.intensity).First().mz_centroid.ToMass(c.charge_states.OrderByDescending(s => s.intensity).First().charge_count) < 10 @@ -211,14 +214,12 @@ private DataPointAquisitionResults GetDataPoints() rt = myMsDataFile.GetOneBasedScan(scanNumber + 1).RetentionTime; } proteinCharge = matching_component.charge_states.OrderByDescending(c => c.intensity).First().charge_count; - } - else - { - //if top-down file, needs to be hit from same techrep (exact same raw file...) - if (identification.technical_replicate != raw_file.technical_replicate) continue; - } + } + else if(identification.technical_replicate != raw_file.technical_replicate) continue; + - var SequenceWithChemicalFormulas = identification.GetSequenceWithChemicalFormula(); + var SequenceWithChemicalFormulas = identification.GetSequenceWithChemicalFormula + (); if (SequenceWithChemicalFormulas == null) { continue; diff --git a/ProteoformSuiteInternal/ComponentReader.cs b/ProteoformSuiteInternal/ComponentReader.cs index 3ae24267..d5cd2849 100644 --- a/ProteoformSuiteInternal/ComponentReader.cs +++ b/ProteoformSuiteInternal/ComponentReader.cs @@ -37,7 +37,7 @@ public List read_components_from_xlsx(InputFile file, bool remove_mis int charge_row_index = 0; string scan_range = ""; List> cells = ExcelReader.get_cell_strings(file, false); - for (int i = 0; i < cells.Count(); i++) + for (int i = 0; i < cells.Count; i++) { if (i == 0) continue; //skip component header List cellStrings = cells[i]; diff --git a/ProteoformSuiteInternal/Lollipop.cs b/ProteoformSuiteInternal/Lollipop.cs index 8f479ff5..ce76f7c1 100644 --- a/ProteoformSuiteInternal/Lollipop.cs +++ b/ProteoformSuiteInternal/Lollipop.cs @@ -362,10 +362,10 @@ public List aggregate_td_hits(List top_down_hits, //get topdown hits that meet criteria List remaining_td_hits = top_down_hits.Where(h => h.score >= min_score_td && ((biomarker && h.tdResultType == TopDownResultType.Biomarker) || (tight_abs_mass && h.tdResultType == TopDownResultType.TightAbsoluteMass))).OrderByDescending(h => h.score).ThenBy(h => h.pscore).ThenBy(h => h.reported_mass).ToList(); - List PFRs = remaining_td_hits.Select(h => h.pfr).Distinct().ToList(); - Parallel.ForEach(PFRs, pfr => + List unique_proteoform_ids = remaining_td_hits.Select(h => h.pfr_accession).Distinct().ToList(); + Parallel.ForEach(unique_proteoform_ids, pfr => { - List hits_by_pfr = remaining_td_hits.Where(h => h.pfr == pfr).ToList(); + List hits_by_pfr = remaining_td_hits.Where(h => h.pfr_accession == pfr).ToList(); List first_aggregation = new List(); //aggregate to td hit w/ highest c-score as root - 1st average for retention time while (hits_by_pfr.Count > 0) @@ -400,7 +400,7 @@ public List aggregate_td_hits(List top_down_hits, //convert unlabeled mass to neucode light mass based on lysine count (used for topdown identifications) public double get_neucode_mass(double unlabeled_mass, int lysine_count) { - return (unlabeled_mass - lysine_count * 128.094963 + lysine_count * 136.109162); + return unlabeled_mass - lysine_count * 128.094963 + lysine_count * 136.109162; } #endregion TOPDOWN @@ -452,7 +452,7 @@ public List aggregate_proteoforms(bool two_pass_validati { community.experimental_proteoforms = Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Select(e => e.topdown_id ? new TopDownProteoform(e as TopDownProteoform) : new ExperimentalProteoform(e)).ToArray(); } - if(get_files(input_files, Purpose.Quantification).Count() > 0) + if (get_files(input_files, Purpose.Quantification).Count() > 0) { assignQuantificationComponents(vetted_proteoforms, raw_quantification_components); } @@ -506,7 +506,7 @@ public void assign_best_components_for_manual_validation(IEnumerable add_topdown_proteoforms(List vetted_proteoforms, List topdown_proteoforms) { - foreach (TopDownProteoform topdown in topdown_proteoforms.Where(t => t.accepted).OrderByDescending(t => t.topdown_hits.Max(h => h.score)).ThenBy(t => t.topdown_hits.Min(h => h.pscore)).ThenBy(t => t.topdown_hits.Count()).ThenBy(t => t.agg_mass)) + foreach (TopDownProteoform topdown in topdown_proteoforms.Where(t => t.accepted).OrderByDescending(t => t.topdown_hits.Max(h => h.score)).ThenBy(t => t.topdown_hits.Min(h => h.pscore)).ThenBy(t => t.topdown_hits.Count).ThenBy(t => t.agg_mass)) { double mass = topdown.modified_mass; List all_td_relations = new List(); @@ -1171,7 +1171,12 @@ public string calibrate_files() //determine component and td hit shifts determine_shifts(raw_file); //calibrate component xlsx files - foreach (InputFile f in input_files.Where(f => f.lt_condition == raw_file.lt_condition && f.purpose == Purpose.CalibrationIdentification && f.biological_replicate == raw_file.biological_replicate && f.fraction == raw_file.fraction && f.technical_replicate == raw_file.technical_replicate)) Calibration.calibrate_components_in_xlsx(f); + foreach (InputFile f in input_files.Where(f => f.lt_condition == raw_file.lt_condition && f.purpose == Purpose.CalibrationIdentification + && f.biological_replicate == raw_file.biological_replicate && f.fraction == raw_file.fraction + && f.technical_replicate == raw_file.technical_replicate)) + { + Calibration.calibrate_components_in_xlsx(f); + } } else filenames_did_not_calibrate.Add(raw_file.filename); } @@ -1180,7 +1185,8 @@ public string calibrate_files() } if (calibrate_td_files) { - foreach (InputFile file in input_files.Where(f => f.purpose == Purpose.CalibrationTopDown && td_hits_calibration.Any(h => h.file == f && td_hit_correction.ContainsKey(new Tuple(h.filename, h.ms2ScanNumber, h.reported_mass))))) + foreach (InputFile file in input_files.Where(f => f.purpose == Purpose.CalibrationTopDown && + td_hits_calibration.Any(h => h.file == f && td_hit_correction.ContainsKey(new Tuple(h.filename, h.ms2ScanNumber, h.reported_mass))))) { Calibration.calibrate_td_hits_file(file); } diff --git a/ProteoformSuiteInternal/ProteinSequenceGroup.cs b/ProteoformSuiteInternal/ProteinSequenceGroup.cs index 98b0032f..1b18e7dd 100644 --- a/ProteoformSuiteInternal/ProteinSequenceGroup.cs +++ b/ProteoformSuiteInternal/ProteinSequenceGroup.cs @@ -6,7 +6,7 @@ namespace ProteoformSuiteInternal { public class ProteinSequenceGroup : ProteinWithGoTerms { - public List proteinWithGoTermList; + public List proteinWithGoTermList = new List(); public ProteinSequenceGroup(IEnumerable proteins_with_contaminants_first) : base(proteins_with_contaminants_first.First().BaseSequence, proteins_with_contaminants_first.First().Accession + "_" + proteins_with_contaminants_first.Count() + "G", diff --git a/ProteoformSuiteInternal/ProteinWithGoTerms.cs b/ProteoformSuiteInternal/ProteinWithGoTerms.cs index 18c238d7..4ae83493 100644 --- a/ProteoformSuiteInternal/ProteinWithGoTerms.cs +++ b/ProteoformSuiteInternal/ProteinWithGoTerms.cs @@ -9,7 +9,7 @@ public class ProteinWithGoTerms : Protein { public List AccessionList { get; set; } public List GoTerms { get; set; } - public bool topdown_protein; + public bool topdown_protein { get; set; } public ProteinWithGoTerms(string sequence, string accession, List> gene_names, IDictionary> oneBasedModifications, List proteolysisProducts, string name, string full_name, bool isDecoy, bool isContaminant, IEnumerable databaseReferences, IEnumerable goTerms) : base(sequence, accession, gene_names: gene_names, oneBasedModifications: oneBasedModifications, proteolysisProducts: proteolysisProducts, name: name, full_name: full_name, isDecoy: isDecoy, isContaminant: isContaminant, databaseReferences: databaseReferences.ToList()) diff --git a/ProteoformSuiteInternal/Proteoform.cs b/ProteoformSuiteInternal/Proteoform.cs index b33e40c3..d73a56e8 100644 --- a/ProteoformSuiteInternal/Proteoform.cs +++ b/ProteoformSuiteInternal/Proteoform.cs @@ -253,7 +253,10 @@ private void assign_pf_identity(ExperimentalProteoform e, PtmSet set, Proteoform e.begin--; remove.Add(mod); } - foreach (var ptm in remove) e.ptm_set.ptm_combination.Remove(ptm); + foreach (var ptm in remove) + { + e.ptm_set.ptm_combination.Remove(ptm); + } e.ptm_set = new PtmSet(e.ptm_set.ptm_combination); } else @@ -265,7 +268,7 @@ private void assign_pf_identity(ExperimentalProteoform e, PtmSet set, Proteoform if (e.gene_name == null) e.gene_name = this.gene_name; - else if(!e.topdown_id) + else if (!e.topdown_id) e.gene_name.gene_names.Concat(this.gene_name.gene_names); } diff --git a/ProteoformSuiteInternal/ProteoformCommunity.cs b/ProteoformSuiteInternal/ProteoformCommunity.cs index 628be5ca..873c746e 100644 --- a/ProteoformSuiteInternal/ProteoformCommunity.cs +++ b/ProteoformSuiteInternal/ProteoformCommunity.cs @@ -77,7 +77,7 @@ public List relate(ExperimentalProteoform[] pfs1, Proteoform { pf1.ptm_set = null; pf1.linked_proteoform_references = null; - if(pf1 as TopDownProteoform == null) pf1.gene_name = null; + if (pf1 as TopDownProteoform == null) pf1.gene_name = null; } if (limit_et_relations && (relation_type == ProteoformComparison.ExperimentalTheoretical || relation_type == ProteoformComparison.ExperimentalDecoy)) @@ -354,7 +354,7 @@ public void clear_families() p.family = null; p.ptm_set = new PtmSet(new List()); p.linked_proteoform_references = null; - if(p as TopDownProteoform == null) p.gene_name = null; + if (p as TopDownProteoform == null) p.gene_name = null; } foreach (Proteoform p in theoretical_proteoforms) p.family = null; } diff --git a/ProteoformSuiteInternal/ProteoformFamily.cs b/ProteoformSuiteInternal/ProteoformFamily.cs index 5cf0a0e5..8d0d11f0 100644 --- a/ProteoformSuiteInternal/ProteoformFamily.cs +++ b/ProteoformSuiteInternal/ProteoformFamily.cs @@ -84,7 +84,7 @@ select f public void identify_experimentals() { HashSet identified_experimentals = new HashSet(); - foreach(TheoreticalProteoform t in theoretical_proteoforms) + foreach (TheoreticalProteoform t in theoretical_proteoforms) { lock (identified_experimentals) foreach (ExperimentalProteoform e in t.identify_connected_experimentals(Sweet.lollipop.theoretical_database.all_possible_ptmsets, Sweet.lollipop.theoretical_database.all_mods_with_mass)) @@ -100,7 +100,7 @@ public void identify_experimentals() { last_identified_count = identified_experimentals.Count; HashSet tmp_new_experimentals = new HashSet(); - foreach(ExperimentalProteoform id_experimental in newly_identified_experimentals) + foreach (ExperimentalProteoform id_experimental in newly_identified_experimentals) { lock (identified_experimentals) lock (tmp_new_experimentals) foreach (ExperimentalProteoform new_e in id_experimental.identify_connected_experimentals(Sweet.lollipop.theoretical_database.all_possible_ptmsets, Sweet.lollipop.theoretical_database.all_mods_with_mass)) diff --git a/ProteoformSuiteInternal/ResultsSummaryGenerator.cs b/ProteoformSuiteInternal/ResultsSummaryGenerator.cs index 4f581e4d..92501452 100644 --- a/ProteoformSuiteInternal/ResultsSummaryGenerator.cs +++ b/ProteoformSuiteInternal/ResultsSummaryGenerator.cs @@ -241,7 +241,7 @@ public static string proteoform_families_report() List experimental_ids = Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Where(e => !e.topdown_id && e.linked_proteoform_references != null && (Sweet.lollipop.count_adducts_as_identifications || !e.adduct)) .Select(p => String.Join(",", (p.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(e => e.AccessionList.Select(a => a.Split('_')[0])).Distinct()) + "_" + p.begin + "_" + p.end + "_" + String.Join(", ", p.ptm_set.ptm_combination.Select(ptm => Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(ptm.modification, out UnlocalizedModification x) ? x.id : ptm.modification.id).OrderBy(m => m))).ToList(); report += experimental_ids.Distinct().Count() + "\tUnique Intact-Mass Experimental Proteoforms Identifications" + Environment.NewLine; - int unique_td = Sweet.lollipop.topdown_proteoforms.Select(p => p.pfr).Distinct().Count(); + int unique_td = Sweet.lollipop.topdown_proteoforms.Select(p => p.pfr_accession).Distinct().Count(); report += unique_td + "\tUnique Top-Down Proteoforms Identifications (TDPortal)" + Environment.NewLine; List topdown_ids = Sweet.lollipop.topdown_proteoforms .Select(p => p.accession.Split('_')[0].Split('-')[0] + "_" + p.topdown_begin + "_" + p.topdown_end + "_" + String.Join(", ", p.topdown_ptm_set.ptm_combination.Select(ptm => Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(ptm.modification, out UnlocalizedModification x) ? x.id : ptm.modification.id).OrderBy(m => m))).ToList(); @@ -468,10 +468,10 @@ public static DataTable experimental_results_dataframe(TusherAnalysis analysis) public static DataTable topdown_results_dataframe() { DataTable results = new DataTable(); - results.Columns.Add("PFR", typeof(string)); - results.Columns.Add("Theoretiecal Accession", typeof(string)); + results.Columns.Add("PFR Accession", typeof(string)); + results.Columns.Add("Theoretical Accession", typeof(string)); results.Columns.Add("Top-Down Full Accession", typeof(string)); - results.Columns.Add("Top-Down Accession", typeof(string)); + results.Columns.Add("Top-Down Accession", typeof(string)); results.Columns.Add("Theoretical Description", typeof(string)); results.Columns.Add("Theoretical Begin and End", typeof(string)); results.Columns.Add("Top-Down Begin and End", typeof(string)); @@ -493,7 +493,7 @@ public static DataTable topdown_results_dataframe() foreach (TopDownProteoform td in Sweet.lollipop.topdown_proteoforms) { results.Rows.Add( - td.pfr, + td.pfr_accession, td.linked_proteoform_references == null ? "N/A" : (td.linked_proteoform_references.First() as TheoreticalProteoform).accession, td.accession, td.accession.Split('_')[0], diff --git a/ProteoformSuiteInternal/StatisticalAnalysis/Log2FoldChangeAnalysis.cs b/ProteoformSuiteInternal/StatisticalAnalysis/Log2FoldChangeAnalysis.cs index 02091e6d..be7a46a4 100644 --- a/ProteoformSuiteInternal/StatisticalAnalysis/Log2FoldChangeAnalysis.cs +++ b/ProteoformSuiteInternal/StatisticalAnalysis/Log2FoldChangeAnalysis.cs @@ -50,14 +50,16 @@ public void compute_proteoform_statistics(List satisfact QuantitativeDistributions.defineBackgroundIntensityDistribution(Sweet.lollipop.quantBioFracCombos, Sweet.lollipop.satisfactoryProteoforms, Sweet.lollipop.condition_count, Sweet.lollipop.backgroundShift, Sweet.lollipop.backgroundWidth); // Use those values to impute missing ones - foreach(var pf in Sweet.lollipop.satisfactoryProteoforms) pf.quant.Log2FoldChangeValues.impute_biorep_intensities(pf.quant.Log2FoldChangeValues.numeratorOriginalIntensities.Concat(pf.quant.Log2FoldChangeValues.denominatorOriginalIntensities).ToList(), conditionsBioReps, numerator_condition, denominator_condition, induced_condition, QuantitativeDistributions.bkgdAverageIntensity, QuantitativeDistributions.bkgdStDev, sKnot_minFoldChange, Sweet.lollipop.useRandomSeed_quant, Sweet.lollipop.seeded); + foreach (var pf in Sweet.lollipop.satisfactoryProteoforms) + { + pf.quant.Log2FoldChangeValues.impute_biorep_intensities(pf.quant.Log2FoldChangeValues.numeratorOriginalIntensities.Concat(pf.quant.Log2FoldChangeValues.denominatorOriginalIntensities).ToList(), conditionsBioReps, numerator_condition, denominator_condition, induced_condition, QuantitativeDistributions.bkgdAverageIntensity, QuantitativeDistributions.bkgdStDev, sKnot_minFoldChange, Sweet.lollipop.useRandomSeed_quant, Sweet.lollipop.seeded); + } QuantitativeDistributions.defineSelectObservedWithImputedIntensityDistribution(Sweet.lollipop.satisfactoryProteoforms.SelectMany(pf => pf.quant.Log2FoldChangeValues.allIntensities.Values), QuantitativeDistributions.logSelectIntensityWithImputationHistogram); // Calculate log2 fold changes Parallel.ForEach(Sweet.lollipop.satisfactoryProteoforms, pf => { pf.quant.Log2FoldChangeValues.calcluate_statistics(Sweet.lollipop.numerator_condition, Sweet.lollipop.denominator_condition); - MathNet.Numerics.Distributions.StudentT asdf = new MathNet.Numerics.Distributions.StudentT(); int degrees_of_freedom = Sweet.lollipop.conditionsBioReps.Values.SelectMany(x => x).Count() - 2; //degrees of freedom for unpaired 2 samples t test = n1 + n2 - 2 pf.quant.Log2FoldChangeValues.pValue_uncorrected = ExtensionMethods.Student2T(pf.quant.Log2FoldChangeValues.tTestStatistic, degrees_of_freedom); // using a two-tailed test. Null hypothesis is that our value x is equal to the mean. Alternative hypothesis is in either direction. diff --git a/ProteoformSuiteInternal/TheoreticalProteoformDatabase.cs b/ProteoformSuiteInternal/TheoreticalProteoformDatabase.cs index d7012852..f73f9301 100644 --- a/ProteoformSuiteInternal/TheoreticalProteoformDatabase.cs +++ b/ProteoformSuiteInternal/TheoreticalProteoformDatabase.cs @@ -355,7 +355,9 @@ public void add_topdown_sequences() topdown.gene_name = new GeneName(candidate_theoreticals.First().GeneNames); if (!candidate_theoreticals.Any(p => p.BaseSequence == topdown.sequence) && !new_proteins.Any(p => p.AccessionList.Select(a => a.Split('_')[0]).Contains(topdown.accession.Split('_')[0].Split('-')[0]) && p.BaseSequence == topdown.sequence)) { - int count = candidate_theoreticals.Count(t => t.ProteolysisProducts.First().OneBasedBeginPosition == topdown.topdown_begin && t.ProteolysisProducts.First().OneBasedEndPosition == topdown.topdown_end && t.BaseSequence != topdown.sequence) + new_proteins.Count(t => t.AccessionList.Select(a => a.Split('_')[0].Split('-')[0]).Contains(topdown.accession.Split('_')[0]) && t.ProteolysisProducts.First().OneBasedBeginPosition == topdown.topdown_begin && t.ProteolysisProducts.First().OneBasedEndPosition == topdown.topdown_end && t.BaseSequence != topdown.sequence); + int old_proteins_with_same_begin_end_diff_sequence = candidate_theoreticals.Count(t => t.ProteolysisProducts.First().OneBasedBeginPosition == topdown.topdown_begin && t.ProteolysisProducts.First().OneBasedEndPosition == topdown.topdown_end && t.BaseSequence != topdown.sequence); + int new_proteins_with_same_being_end_diff_sequence = new_proteins.Count(t => t.AccessionList.Select(a => a.Split('_')[0].Split('-')[0]).Contains(topdown.accession.Split('_')[0]) && t.ProteolysisProducts.First().OneBasedBeginPosition == topdown.topdown_begin && t.ProteolysisProducts.First().OneBasedEndPosition == topdown.topdown_end && t.BaseSequence != topdown.sequence); + int count = old_proteins_with_same_begin_end_diff_sequence + new_proteins_with_same_being_end_diff_sequence; ProteinWithGoTerms p = new ProteinWithGoTerms(topdown.sequence, topdown.accession.Split('_')[0].Split('-')[0] + "_" + topdown.topdown_begin + "frag" + topdown.topdown_end + (count > 0 ? "_" + count : ""), candidate_theoreticals.First().GeneNames.ToList(), new Dictionary>(), new List() { new ProteolysisProduct(topdown.topdown_begin, topdown.topdown_end, "full") }, candidate_theoreticals.First().Name, candidate_theoreticals.First().FullName, false, false, candidate_theoreticals.First().DatabaseReferences, candidate_theoreticals.First().GoTerms); p.topdown_protein = true; //add the ptm's of the top-down proteoform @@ -530,8 +532,8 @@ private void process_decoys(TheoreticalProteoform[] entries) sb.Append(proteoform.sequence); } string giantProtein = sb.ToString(); - TheoreticalProteoform[] shuffled_proteoforms = new TheoreticalProteoform[entries.Count()]; - Array.Copy(entries, shuffled_proteoforms, entries.Count()); + TheoreticalProteoform[] shuffled_proteoforms = new TheoreticalProteoform[entries.Length]; + Array.Copy(entries, shuffled_proteoforms, entries.Length); Random decoy_rng = Sweet.lollipop.useRandomSeed_decoys ? new Random(decoyNumber + Sweet.lollipop.randomSeed_decoys) : new Random(); // each decoy database needs to have a new random number generator decoy_rng.Shuffle(shuffled_proteoforms); //randomize order of protein array int prevLength = 0; diff --git a/ProteoformSuiteInternal/TopDownHit.cs b/ProteoformSuiteInternal/TopDownHit.cs index 2c7df16a..ca78cd2a 100755 --- a/ProteoformSuiteInternal/TopDownHit.cs +++ b/ProteoformSuiteInternal/TopDownHit.cs @@ -26,7 +26,7 @@ public class TopDownHit public double score { get; set; }//C-score public TopDownResultType tdResultType { get; set; } public InputFile file { get; set; } - public string pfr { get; set; } + public string pfr_accession { get; set; } //for mass calibration public string biological_replicate { get; set; } = ""; @@ -40,7 +40,7 @@ public class TopDownHit public TopDownHit(Dictionary aaIsotopeMassList, InputFile file, TopDownResultType tdResultType, string accession, string pfr, string uniprot_id, string name, string sequence, int begin, int end, List modifications, double reported_mass, double theoretical_mass, int scan, double retention_time, string filename, double pscore, double score) { - this.pfr = pfr; + this.pfr_accession = pfr; this.file = file; this.tdResultType = tdResultType; this.accession = accession; @@ -72,7 +72,7 @@ private double CalculateProteoformMass(string pForm, Dictionary aa List aaMasses = new List(); for (int i = 0; i < pForm.Length; i++) { - if(aaIsotopeMassList.ContainsKey(aminoAcids[i])) aaMasses.Add(aaIsotopeMassList[aminoAcids[i]]); + if (aaIsotopeMassList.ContainsKey(aminoAcids[i])) aaMasses.Add(aaIsotopeMassList[aminoAcids[i]]); } return proteoformMass + aaMasses.Sum(); } diff --git a/ProteoformSuiteInternal/TopDownProteoform.cs b/ProteoformSuiteInternal/TopDownProteoform.cs index 577d7d47..6a5182e6 100755 --- a/ProteoformSuiteInternal/TopDownProteoform.cs +++ b/ProteoformSuiteInternal/TopDownProteoform.cs @@ -8,7 +8,7 @@ namespace ProteoformSuiteInternal public class TopDownProteoform : ExperimentalProteoform { public string uniprot_id { get; set; } - public string pfr { get; set; } + public string pfr_accession { get; set; } public string name { get; set; } public string sequence { get; set; } public int topdown_begin { get; set; } //position one based @@ -43,7 +43,7 @@ public TopDownProteoform(string accession, List hits) : base(accessi { TopDownHit root = hits[0]; this.name = root.name; - this.pfr = root.pfr; + this.pfr_accession = root.pfr_accession; this.topdown_ptm_set = new PtmSet(root.ptm_list); this.uniprot_id = root.uniprot_id; this.sequence = root.sequence; @@ -77,7 +77,7 @@ public TopDownProteoform(TopDownProteoform t) : base(t.accession, null, true) this.lysine_count = t.lysine_count; this.accepted = t.accepted; this.uniprot_id = t.uniprot_id; - this.pfr = t.pfr; + this.pfr_accession = t.pfr_accession; this.agg_intensity = t.agg_intensity; this.topdown_id = t.topdown_id; this.agg_mass = t.agg_mass; diff --git a/ProteoformSuiteInternal/TopDownReader.cs b/ProteoformSuiteInternal/TopDownReader.cs index 8b15ef53..bac980cb 100755 --- a/ProteoformSuiteInternal/TopDownReader.cs +++ b/ProteoformSuiteInternal/TopDownReader.cs @@ -99,7 +99,10 @@ public List ReadTDFile(InputFile file) } id = "PSI-MOD:" + psimod; } - if (mod != null) ptm_list.Add(new Ptm(position, mod)); + if (mod != null) + { + ptm_list.Add(new Ptm(position, mod)); + } else { lock (topdown_ptms) diff --git a/Test/TestTopDown.cs b/Test/TestTopDown.cs index e761a29d..0525682d 100644 --- a/Test/TestTopDown.cs +++ b/Test/TestTopDown.cs @@ -22,7 +22,7 @@ public void TestSimpleAggregation() t.score = (10 + Convert.ToDouble(i)); t.ms2_retention_time = 50d; t.ptm_list = new List(); - t.pfr = "12345"; + t.pfr_accession = "12345"; t.sequence = "SEQUENCE"; t.tdResultType = TopDownResultType.TightAbsoluteMass; tdhList.Add(t); @@ -45,13 +45,13 @@ public void TestSimpleAggregation() //Test no aggregation different pfr tdhList[1].ms2_retention_time = tdhList[0].ms2_retention_time; - tdhList[1].pfr = "12346"; + tdhList[1].pfr_accession = "12346"; Sweet.lollipop.top_down_hits = tdhList; Sweet.lollipop.topdown_proteoforms = Sweet.lollipop.aggregate_td_hits(Sweet.lollipop.top_down_hits, Sweet.lollipop.min_score_td, Sweet.lollipop.biomarker, Sweet.lollipop.tight_abs_mass); Assert.AreEqual(2, Sweet.lollipop.topdown_proteoforms.Count()); //both topdown hits should aggregate to a single proteoform //if hit score below threshold, don't aggregate - tdhList[1].pfr = "12345"; + tdhList[1].pfr_accession = "12345"; tdhList[1].score = 1; Sweet.lollipop.min_score_td = 3; Sweet.lollipop.top_down_hits = tdhList; @@ -107,12 +107,12 @@ public void TestTopdownReader() Assert.AreEqual(7, Sweet.lollipop.top_down_hits.Count); Assert.AreEqual("RESID:AA929292 at S", Sweet.lollipop.topdownReader.topdown_ptms.OrderByDescending(p => p).First()); Assert.AreEqual(7, Sweet.lollipop.top_down_hits.Sum(h => h.ptm_list.Count)); - Assert.AreEqual(10894.157, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr).First().theoretical_mass, 3)); - Assert.AreEqual(10894.130, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr).First().reported_mass, 3)); + Assert.AreEqual(10894.157, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); + Assert.AreEqual(10894.130, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr_accession).First().reported_mass, 3)); Sweet.lollipop.topdown_proteoforms = Sweet.lollipop.aggregate_td_hits(Sweet.lollipop.top_down_hits, Sweet.lollipop.min_score_td, Sweet.lollipop.biomarker, Sweet.lollipop.tight_abs_mass); Assert.AreEqual(4, Sweet.lollipop.topdown_proteoforms.Count()); - Assert.AreEqual(10894.157, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr).First().theoretical_mass, 3)); - Assert.AreEqual(10894.130, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr).First().agg_mass, 3)); + Assert.AreEqual(10894.157, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); + Assert.AreEqual(10894.130, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr_accession).First().agg_mass, 3)); //neucode labeled Sweet.lollipop = new Lollipop(); @@ -129,12 +129,12 @@ public void TestTopdownReader() Assert.AreEqual(2, Sweet.lollipop.topdownReader.topdown_ptms.Count); Assert.AreEqual("RESID:AA929292 at S", Sweet.lollipop.topdownReader.topdown_ptms.OrderByDescending(p => p).First()); Assert.AreEqual(7, Sweet.lollipop.top_down_hits.Sum(h => h.ptm_list.Count)); - Assert.AreEqual(10934.228, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr).First().theoretical_mass, 3)); - Assert.AreEqual(10934.201, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr).First().reported_mass, 3)); + Assert.AreEqual(10934.228, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); + Assert.AreEqual(10934.201, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr_accession).First().reported_mass, 3)); Sweet.lollipop.topdown_proteoforms = Sweet.lollipop.aggregate_td_hits(Sweet.lollipop.top_down_hits, Sweet.lollipop.min_score_td, Sweet.lollipop.biomarker, Sweet.lollipop.tight_abs_mass); Assert.AreEqual(4, Sweet.lollipop.topdown_proteoforms.Count()); - Assert.AreEqual(10934.228, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr).First().theoretical_mass, 3)); - Assert.AreEqual(10934.201, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr).First().agg_mass, 3)); + Assert.AreEqual(10934.228, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); + Assert.AreEqual(10934.201, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr_accession).First().agg_mass, 3)); //carbamidomethylated Sweet.lollipop = new Lollipop(); @@ -151,10 +151,10 @@ public void TestTopdownReader() Assert.AreEqual(2, Sweet.lollipop.topdownReader.topdown_ptms.Count); Assert.AreEqual("RESID:AA929292 at S", Sweet.lollipop.topdownReader.topdown_ptms.OrderByDescending(p => p).First()); Assert.AreEqual(7, Sweet.lollipop.top_down_hits.Sum(h => h.ptm_list.Count)); - Assert.AreEqual(10951.178, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr).First().theoretical_mass, 3)); + Assert.AreEqual(10951.178, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); Sweet.lollipop.topdown_proteoforms = Sweet.lollipop.aggregate_td_hits(Sweet.lollipop.top_down_hits, Sweet.lollipop.min_score_td, Sweet.lollipop.biomarker, Sweet.lollipop.tight_abs_mass); Assert.AreEqual(4, Sweet.lollipop.topdown_proteoforms.Count()); - Assert.AreEqual(10951.178, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr).First().theoretical_mass, 3)); + Assert.AreEqual(10951.178, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); //carbamidomethylated and neucode labeled Sweet.lollipop = new Lollipop(); @@ -171,10 +171,10 @@ public void TestTopdownReader() Assert.AreEqual(2, Sweet.lollipop.topdownReader.topdown_ptms.Count); Assert.AreEqual("RESID:AA929292 at S", Sweet.lollipop.topdownReader.topdown_ptms.OrderByDescending(p => p).First()); Assert.AreEqual(7, Sweet.lollipop.top_down_hits.Sum(h => h.ptm_list.Count)); - Assert.AreEqual(10991.249, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr).First().theoretical_mass, 3)); + Assert.AreEqual(10991.249, Math.Round(Sweet.lollipop.top_down_hits.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); Sweet.lollipop.topdown_proteoforms = Sweet.lollipop.aggregate_td_hits(Sweet.lollipop.top_down_hits, Sweet.lollipop.min_score_td, Sweet.lollipop.biomarker, Sweet.lollipop.tight_abs_mass); Assert.AreEqual(4, Sweet.lollipop.topdown_proteoforms.Count()); - Assert.AreEqual(10991.249, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr).First().theoretical_mass, 3)); + Assert.AreEqual(10991.249, Math.Round(Sweet.lollipop.topdown_proteoforms.OrderBy(h => h.pfr_accession).First().theoretical_mass, 3)); } @@ -316,7 +316,7 @@ public void TestCopyTopDown() hit.theoretical_mass = 1000; hit.reported_mass = 1000; hit.ms2_retention_time = 10; - hit.pfr = "PFR"; + hit.pfr_accession = "PFR"; TopDownProteoform td1 = new TopDownProteoform("accession", new List() { hit }); TopDownProteoform td2 = new TopDownProteoform(td1); Assert.AreNotEqual(td1, td2); diff --git a/wq b/wq deleted file mode 100644 index 369a20f0..00000000 --- a/wq +++ /dev/null @@ -1,8197 +0,0 @@ -commit 21b507d7c2cd7b6fcf1fc66e80285d7024ce8b17 (HEAD -> TD_BU_integration, origin/TD_BU_integration) -Author: unknown -Date: Thu Jan 25 10:04:48 2018 -0600 - - EE from TD nodes - -commit ae0712ae324ab3b0590f2d22c948e505af99a5e6 -Author: unknown -Date: Mon Jan 22 17:23:26 2018 -0600 - - more tests - -commit e09dd6aeda007afaf4506d27c28e83ee1457baaa -Author: unknown -Date: Mon Jan 22 14:22:32 2018 -0600 - - elements.dat added - -commit 691ae4599d454e1f954a8b37107b8ff906325e16 -Author: unknown -Date: Mon Jan 22 13:52:40 2018 -0600 - - nuget packages updates - -commit 5ee15e2d05ce6d0b43a216e516608c1e40cdf33e -Author: unknown -Date: Mon Jan 22 13:16:07 2018 -0600 - - tests - -commit 1eff2b4dcd25790b9ef49229a93fa69997d0fb20 -Author: unknown -Date: Thu Jan 18 16:53:52 2018 -0600 - - quantification log2 - -commit bffb77f3c81ca9e2806f64c3308832944adbb211 -Author: unknown -Date: Tue Jan 16 11:36:00 2018 -0600 - - quant gui - -commit 9b764500eb4f15c071000ace14dadc35f0b51c0b -Author: unknown -Date: Mon Jan 15 09:57:49 2018 -0600 - - fixes - -commit 624ae29cca1d7cee2c194611c15474c34e3fdcc8 -Author: unknown -Date: Fri Jan 12 12:34:57 2018 -0600 - - remove flashlfq - -commit 2229e1bdabc31269d8d58ec0f8802effe8c55923 -Merge: aa0846b 9650a15 -Author: unknown -Date: Fri Jan 12 11:08:40 2018 -0600 - - merge from upstream - -commit aa0846bd29f4663bcccf3e0eff16a9242e65bbf5 -Author: unknown -Date: Thu Jan 11 18:47:04 2018 -0600 - - calibration bug fixes and neucode td - -commit dbe701b18aa06e6491ed813c97f75c731baa3551 -Author: unknown -Date: Wed Jan 10 17:56:03 2018 -0600 - - labelfree quant fixes - -commit 9650a15027bb903350da57bc3150f19db1c414c9 (upstream/master) -Merge: 27648f3 b47497b -Author: Anthony -Date: Wed Dec 20 16:51:56 2017 -0600 - - Merge pull request #482 from smith-chem-wisc/acesnik-patch-2 - - Update README.md - -commit b47497b0d254ba526bb7fa538f5e72b29db0e6c2 -Author: Anthony -Date: Wed Dec 20 16:41:39 2017 -0600 - - Update README.md - -commit 27648f3c911981a6030a00041ec9112511e853be -Merge: 32e1928 fb27839 -Author: Anthony -Date: Fri Dec 15 03:14:57 2017 -0600 - - Merge pull request #481 from acesnik/master - - Update readme - -commit fb27839eec5a9a4273a8bacf343ebef964b43f57 -Author: Anthony -Date: Fri Dec 15 03:08:09 2017 -0600 - - updateReadme - -commit 32e1928e37353b86d5978af7770f43ec44a39f6a -Merge: bd5545f 8011fa3 -Author: Anthony -Date: Fri Dec 15 02:58:42 2017 -0600 - - Merge pull request #479 from acesnik/master - - Bug fixes and nice notifications. - -commit 8011fa3b958cfffb349443cc272e9d2d96dfa506 -Author: Anthony -Date: Fri Dec 15 02:44:04 2017 -0600 - - Fixing families table selector bug; readme updates - -commit 5f734801400f36dec16f3dc6fa10c4ac598ccad2 -Author: Anthony -Date: Fri Dec 15 01:57:56 2017 -0600 - - Fix crash on Build all families before creating them. - -commit 03253a1a248a48fa747d237fe0c9d584a5d06d73 -Author: Anthony -Date: Fri Dec 15 01:37:36 2017 -0600 - - Change only file with the correct purpose, since files could be added to both dataframes - -commit 1cdf84072646f945654038e6f6e0f7d44422ec84 -Author: Anthony -Date: Fri Dec 15 01:32:03 2017 -0600 - - set make db button upon downloading PTM list; fix results report bug - -commit 73957eaeb34eacd5de1fc73475f422844f056544 -Author: Anthony -Date: Fri Dec 15 01:10:30 2017 -0600 - - Allow and use relative paths for results folder and all input files. - -commit ec71d7562c157f6305499d737b8f9315158d109e -Author: Anthony -Date: Thu Dec 14 22:39:44 2017 -0600 - - Notify user when xml is added and they still need a PTM list. Notify user that FASTA isn't enabled, yet. - -commit bd5545f322c79b7369d0eb169b5d6099b5fb6311 -Merge: d2fc670 4988525 -Author: Anthony -Date: Fri Dec 15 02:49:04 2017 -0600 - - Merge pull request #469 from lschaffer2/master - - ptm loss bug fix - -commit d882049e326e5f58240a73f7fcea64375f04e3b2 -Author: unknown -Date: Thu Dec 14 11:04:41 2017 -0600 - - line - -commit 9285da07e0f299bed913c670c1eb3509017c0102 -Author: unknown -Date: Thu Dec 14 11:03:28 2017 -0600 - - test debugging - -commit c2f94e56749d661f5bf80929597c3739fbe397c7 -Author: unknown -Date: Wed Dec 13 13:14:02 2017 -0600 - - add mass error for each id - -commit fbc136e2f414c231bc9587d210d630146f5443ef -Author: unknown -Date: Tue Dec 12 09:20:09 2017 -0600 - - charge state normalize - -commit c8086a5397361aa5efec1a5bc445db2416f3a572 -Author: unknown -Date: Tue Nov 21 16:27:20 2017 -0600 - - quant 2 lines - -commit ede55c1ae192d3cd3d8ab107574715ac56e02396 -Author: unknown -Date: Tue Nov 21 14:10:13 2017 -0600 - - changes - -commit 2ece0a96bd5e9fe3f58076bd0e63c4d7b860befd -Author: unknown -Date: Sun Nov 19 15:17:10 2017 -0600 - - quant and test fixes - -commit 889bf4d0b41bd322050f2bfaf6a75b269c0f51c3 -Author: unknown -Date: Fri Nov 17 13:21:44 2017 -0600 - - quant - -commit ccaf333ff232c5f4cd408dbd3b94519a923f6ab3 -Author: unknown -Date: Tue Oct 31 16:20:41 2017 -0500 - - hm - -commit cc3ee78d08e33a082f3a7615726dac7fce39e5fe -Author: unknown -Date: Tue Oct 31 16:18:28 2017 -0500 - - method - -commit d6e64bf98df24d82a8fb3dc47ada2535d60c9fdf -Author: unknown -Date: Tue Oct 31 16:03:09 2017 -0500 - - ok - -commit e576f11ae579eb4b5a2d6e9a4d3d428178d9f72f -Author: unknown -Date: Tue Oct 31 15:32:16 2017 -0500 - - uninstall reinstall - -commit fa7b0ad7ed01568cf029d3f1f740dcd8452e6ebd -Author: unknown -Date: Tue Oct 31 15:13:08 2017 -0500 - - unit update - -commit 06d14bc46e727eb128f62cc34ef1d6c5b42ea9cf -Author: unknown -Date: Tue Oct 31 14:56:29 2017 -0500 - - make decoys from theoretical proteoforms not proteins - -commit 8bd703f229ef8be28d0343db771dbd7c44804485 -Author: unknown -Date: Tue Oct 31 12:37:59 2017 -0500 - - signal to noise for decon setting - -commit db385bceb57051a143c26e97f18590dcd9b20ea7 -Author: unknown -Date: Mon Oct 30 17:25:51 2017 -0500 - - gui fixes - -commit 9ac1acfd6c9f05e25d487f69ab53da73536c5d1b -Author: unknown -Date: Mon Oct 30 15:32:51 2017 -0500 - - flash fix - -commit 81f0b7e36967cfa0e6c1af975119f4e521f8f630 -Author: unknown -Date: Mon Oct 30 14:21:35 2017 -0500 - - remove test code - -commit 73f9331b2e4fe3746cb30c4b5d881a4c5b7f13d6 -Author: unknown -Date: Mon Oct 30 10:48:22 2017 -0500 - - move flash flq to component - -commit c4e696eff053b9972809c8c504803ed4e56b778d -Author: unknown -Date: Fri Oct 27 16:56:37 2017 -0500 - - fixes - -commit 3b5231f28e5768cf68aebd3cd84a62a0432be3e3 -Author: unknown -Date: Fri Oct 27 10:44:12 2017 -0500 - - write calibrated mzml - -commit 05bc883621652fa6b09acc60f87b4cfc2bbf9e0a -Author: unknown -Date: Tue Oct 24 17:23:07 2017 -0500 - - decon updates - -commit 9dae4cb2749ade9c794325db6533d07cee5a74fd -Author: unknown -Date: Tue Oct 24 12:53:13 2017 -0500 - - deconvolution - -commit 0b2a98c54f80ce4c2be340bebf59ea722c06d0ea -Author: unknown -Date: Thu Oct 19 13:35:49 2017 -0500 - - flash flq - -commit 8d5d4f1b4bef475f6d470c016c67ff98858ab8e1 -Author: unknown -Date: Thu Oct 19 09:46:46 2017 -0500 - - flash lfq changes - -commit 4988525cfde01c0a07b7d496e1ba16438a5e884d (origin/master, origin/HEAD, master) -Author: unknown -Date: Wed Oct 18 12:01:03 2017 -0500 - - ptm loss bug fix - -commit 606621daf81f8535d517bd163c5c18433cbfee20 -Author: unknown -Date: Tue Oct 17 14:27:58 2017 -0500 - - flashlfq - -commit 864a992a79335c4b527d10c8ca207131ca14d279 -Author: unknown -Date: Mon Oct 16 14:42:36 2017 -0500 - - don't need to have same biorep if calibrating neucode - -commit 456d977351cef5bfea573402cbc89d5e616dd3bf -Author: unknown -Date: Mon Oct 16 14:36:20 2017 -0500 - - calibration condition specified - -commit 70e45c1f710ec3200cbead8899007bdb819322a4 (upstream/td_release, td_release) -Author: unknown -Date: Thu Oct 12 17:15:51 2017 -0500 - - display exp proteoform - -commit c8c033b79af714cff7847385385e9a3d6e58a8f5 -Author: unknown -Date: Thu Oct 12 15:32:17 2017 -0500 - - last small changes - -commit d4937d2bd9ae53d195f39e1ae0dc3caa421c4cfe -Author: unknown -Date: Thu Oct 12 11:01:28 2017 -0500 - - took out contam lines - -commit 61e384501ad93dfca923b8e5f0a0df472eee2945 -Author: unknown -Date: Wed Oct 11 22:27:04 2017 -0500 - - search box on id page bug - -commit 2f50a7f2fbf17e912f95f9fe1c15a3bf63022481 -Author: unknown -Date: Tue Oct 10 18:05:01 2017 -0500 - - bug fixes - -commit d426e8031658870aa683c0779e8c731fc441c0a2 -Author: unknown -Date: Mon Oct 9 12:21:43 2017 -0500 - - method file - -commit cdddef9a5a56ffbfa1b28e68f07297042c7103ff -Author: unknown -Date: Mon Oct 9 11:18:25 2017 -0500 - - vignette files - -commit bed7332b2faff9e818881ac94d07ce0108424ac6 -Author: unknown -Date: Thu Oct 5 16:14:27 2017 -0500 - - families in vignette - -commit da3d073121bac1ef9efc48c7c507b9978d0ca320 -Author: unknown -Date: Fri Sep 29 12:04:28 2017 -0500 - - dashses in accession - -commit 506575b8ead447b36a892eea733a23e918f5e917 -Author: unknown -Date: Wed Sep 27 15:07:15 2017 -0500 - - change unmodified type - -commit 68cc46c556707ad6646552901ecefe2024f27b3f -Author: unknown -Date: Tue Sep 26 15:04:46 2017 -0500 - - normalize - -commit 0942465cb639861f1a736de0eece894cca67b653 -Author: unknown -Date: Fri Sep 22 17:27:11 2017 -0500 - - mzlib update and ptm/td fixes - -commit fc732b333217e5eacaf8ed2c679a7e3dc1f27a2c -Author: unknown -Date: Wed Sep 20 16:50:27 2017 -0500 - - comma separate ptm names for easier comparison - -commit 9531b98d9b18b22eb5e9fb50efb69ffd500fe3f3 -Author: unknown -Date: Wed Sep 20 13:01:57 2017 -0500 - - comment out more bu stuff - -commit 8ff814a852999825ea36a9c2a0745d2040042440 -Merge: 733943a d2fc670 -Author: unknown -Date: Wed Sep 20 11:26:10 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/ProteoformSuite into TD_BU_integration - -commit 733943a6f92382486e29451718dbf773b09a294e -Author: unknown -Date: Wed Sep 20 11:21:25 2017 -0500 - - more tests, removed topdown theoretical combos - -commit ff74046d2058428bb950d28cdd231f67abca9a25 -Author: unknown -Date: Mon Sep 18 18:23:01 2017 -0500 - - vignettes - -commit 495d2b8a4c2fc3d81bdeb0d1557af55e784e9f91 -Author: unknown -Date: Thu Sep 14 19:49:21 2017 -0500 - - commented out BU code - -commit 747dc1cb3aeadfe3d76a245f1d32c2feaa9c6966 -Author: unknown -Date: Thu Sep 14 19:29:02 2017 -0500 - - test fixes - -commit 7beb06ca14ba31949e4c198e1aafe3119d43437e -Author: unknown -Date: Fri Sep 8 14:26:17 2017 -0500 - - bug fixes - - topdown begin/end - - begin/end fixes - - random forest calibration... - - GUI polishes and cali bug fix - - delete test files - - remove my vignettes - - gzipd databases in vignettes - -commit d2fc6708c03aee23f752b6b44c3ed3254f95409f -Merge: fd6c871 06ec317 -Author: Anthony -Date: Tue Sep 12 12:07:59 2017 -0500 - - Merge pull request #467 from acesnik/master - - Update README.md with tutorial video - -commit 06ec317078f19980696959ab89df6167411b05b8 -Merge: 15ef660 fd6c871 -Author: Anthony -Date: Tue Sep 12 12:03:54 2017 -0500 - - Merge branch 'master' into master - -commit 15ef660a09509ada82490538f523f2b7ab7e531f -Author: Anthony -Date: Tue Sep 12 11:50:11 2017 -0500 - - Update README.md - -commit fd6c8713faec1b730e67ecb12fd7c023fa366c5f -Merge: 03cddbc 47558af -Author: Anthony -Date: Mon Sep 11 20:53:04 2017 -0500 - - Merge pull request #466 from smith-chem-wisc/acesnik-patch-1 - - Update README.md - -commit 47558af1d8e505d695e8b4da98809e3e0b0ec141 (upstream/acesnik-patch-1) -Author: Anthony -Date: Mon Sep 11 20:48:35 2017 -0500 - - Update README.md - -commit 03cddbcb217c42e782d3c67fd25f7ccd2f148fb4 -Merge: 3d63c34 0c623e2 -Author: Anthony -Date: Mon Sep 11 20:08:17 2017 -0500 - - Merge pull request #465 from acesnik/master - - edits to readme - -commit 0c623e2f42040938a63c3a8bd0e6dfcc9bb9d3be -Author: Anthony -Date: Sat Sep 9 20:10:33 2017 -0500 - - remove the download option, since it's just for the whole codebase, not the actual release. - -commit f493f26f3622103b9ff80eba2a754d92d829ac53 -Merge: 09aa243 3d63c34 -Author: Anthony -Date: Sat Sep 9 20:09:46 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/ProteoformSuite - -commit 09aa243f37794958f8436dba4cf324bb1cfd0c25 -Author: Anthony -Date: Sat Sep 9 20:06:01 2017 -0500 - - Update README.md - -commit 3d63c34eca92f776cbf4d9bc53a4372f5077f5dd -Merge: c74384a 807afdd -Author: Anthony -Date: Sat Sep 9 19:51:07 2017 -0500 - - Merge pull request #464 from smith-chem-wisc/acesnik-patch-2 - - Update _config.yml - -commit 807afddbacf0491cb83cc8eb5ecd2411e5fa1fd7 -Author: Anthony -Date: Sat Sep 9 19:47:42 2017 -0500 - - Update _config.yml - -commit c74384ab7fc379950f0f13487ae725b19a110697 -Merge: 466c22e 75a9759 -Author: Anthony -Date: Sat Sep 9 19:41:49 2017 -0500 - - Merge pull request #463 from smith-chem-wisc/acesnik-patch-1 - - Create _config.yml - -commit 75a975961dc6facbd95c0b9cf11554f1db148e23 -Author: Anthony -Date: Sat Sep 9 19:38:51 2017 -0500 - - Create _config.yml - -commit 466c22eb09a790d33fe9bed83ac1f49cbb966f90 -Merge: 735189c 45eaf43 -Author: Anthony -Date: Fri Sep 8 18:49:16 2017 -0500 - - Merge pull request #462 from acesnik/master - - cleanup - -commit 45eaf438ab10659ef3e6cbb4eecd68751c52cc87 -Author: Anthony -Date: Fri Sep 8 17:42:29 2017 -0500 - - remove docs - -commit b48d1ef82df75d4dca2cd0a43a863c3abe4001c3 -Author: Anthony -Date: Fri Sep 8 17:31:34 2017 -0500 - - asdf - -commit 7f1c8ee2eea713cd04166690e90a1445cdc6aac8 -Author: unknown -Date: Wed Sep 6 16:22:19 2017 -0500 - - vignettes - -commit b7f47e98250ea61c9a78baf8a57bb1c0f04bb6ef -Author: unknown -Date: Wed Sep 6 16:08:56 2017 -0500 - - OK - -commit 90f763d8cf7d2e872036d37501df1970097adf7d -Author: unknown -Date: Wed Sep 6 10:22:58 2017 -0500 - - td accession and quant table crash fix - -commit dff3624ac54b8510a726e8ff6d4abe5197e7a5ef -Author: unknown -Date: Tue Sep 5 09:47:38 2017 -0500 - - ambiguous of same path length to theoretical - -commit fa3ef0d5bb213172dc6202af23772e38b98e030d -Merge: a5513ff 735189c -Author: unknown -Date: Tue Sep 5 09:44:12 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/ProteoformSuite into TD_BU_integration - -commit a5513ff1df1891b50411c85a354d5eb8db7cf672 -Author: unknown -Date: Tue Sep 5 09:43:58 2017 -0500 - - seed for calibration - -commit 735189c670062cf6298f953032878c3b054a5569 -Merge: ea9471d 3de1610 -Author: Anthony -Date: Mon Sep 4 14:26:51 2017 -0500 - - Merge pull request #459 from acesnik/master - - Vignette - -commit 3de1610a376d429572a8b428625cdaef961b71f1 -Author: Anthony -Date: Mon Sep 4 14:20:47 2017 -0500 - - vignette changes - -commit e9feb06aa4fda494a8f190b932c29e7fc37993c8 -Author: Anthony -Date: Mon Sep 4 14:16:24 2017 -0500 - - add vignette - -commit ea9471ddf74931e9dad1d70b0a2aac17d14e67c6 -Merge: 2cf7e1b af7dcd4 -Author: Anthony -Date: Fri Sep 1 16:28:19 2017 -0500 - - Merge pull request #458 from smith-chem-wisc/acesnik-patch-2 - - Create _config.yml - -commit 15f99f9d4c624264cee4c6a7b213a94279d1bf8d -Merge: 8638014 2cf7e1b -Author: unknown -Date: Fri Sep 1 15:12:18 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/ProteoformSuite into TD_BU_integration - -commit 8638014aeb5b57ce32ca9c75c120ffca1fba9dbf -Author: unknown -Date: Fri Sep 1 15:00:54 2017 -0500 - - small fixes - -commit af7dcd43e4b5d8579ee0da8af38643cd5eefa3e0 -Author: Anthony -Date: Fri Sep 1 14:20:23 2017 -0500 - - Create _config.yml - -commit 2cf7e1bb0ed4d3f44a5835f4aba752e0f3f7c52e -Merge: d84f604 f2b5b31 -Author: Anthony -Date: Fri Sep 1 14:00:27 2017 -0500 - - Merge pull request #457 from smith-chem-wisc/acesnik-patch-1 - - Create main.md - -commit f2b5b3101d0a23f95702b5bc515330c942f70e97 -Author: Anthony -Date: Fri Sep 1 13:57:36 2017 -0500 - - Create main.md - -commit d84f604bf602e276c3b6b00c2c8941b35fd0218a -Merge: cf73a47 65e2536 -Author: Anthony -Date: Fri Sep 1 13:39:27 2017 -0500 - - Merge pull request #456 from acesnik/master - - add docs folder - -commit 65e2536e063d176a38e8fbb0581c77f5b6178b91 -Author: Anthony -Date: Fri Sep 1 13:36:18 2017 -0500 - - add docs folder - -commit 07fffb9a7ba74c191e1f130241d3213b99142522 -Author: unknown -Date: Thu Aug 31 13:01:37 2017 -0500 - - TD reader ptm fixes - -commit 6b695b1f6de3bbd9029aab22ad5ffe7c461990d5 -Author: unknown -Date: Wed Aug 30 10:00:46 2017 -0500 - - test fix - -commit e04bb4c370a4733eb7b5c495f98966d2f021dd01 -Author: unknown -Date: Tue Aug 29 19:07:03 2017 -0500 - - td relation bug fix, triple phospho lower ranking - -commit c6a685cdf5e63b0adac0f9fb470032fa0d9e06dc -Author: unknown -Date: Tue Aug 29 12:00:36 2017 -0500 - - added additional tests - -commit 83e859ea81da0e16ccae8fc4af4cfc1a3f3ab2ce -Author: unknown -Date: Tue Aug 29 10:27:15 2017 -0500 - - neucode with topdown, can check results against other td file - -commit 17a00aba012d47e88cbb0297707ccfa6b5412337 -Author: unknown -Date: Mon Aug 28 19:23:19 2017 -0500 - - remove duplicate usings - -commit 9767dd86c143d50beabb4c889bbee8c9fd66da22 -Merge: 07a9a72 cf73a47 -Author: unknown -Date: Mon Aug 28 19:20:09 2017 -0500 - - merge upstream and fixed up tests - -commit 07a9a72c19b1b1edbc945163e45dd04c679bdaf6 -Author: unknown -Date: Mon Aug 28 09:24:22 2017 -0500 - - fixes - -commit cf73a47cd8584be0ab5c4fece7b1d4761c477e76 (tag: 0.2.7) -Merge: 1321e7a 328fcd7 -Author: Anthony -Date: Thu Aug 24 12:32:36 2017 -0500 - - Merge pull request #451 from acesnik/master - - add unlocalized mod table to full export - -commit 328fcd7c2d17bd92e392dfe484a8f7a12c6de9a4 -Author: Anthony -Date: Thu Aug 24 12:20:40 2017 -0500 - - add unlocalized mod table to full export - -commit 1321e7a7c4f8fbfab8be0e213125d6f6c6b8548c -Merge: 5ea6486 4d9868b -Author: Anthony -Date: Thu Aug 17 16:59:15 2017 -0500 - - Merge pull request #448 from acesnik/master - - Export go tables, too. Don't crash with exporting empty datatables. - -commit 4d9868b55bdd551cf57b8ef62dc8759fc885cd21 -Author: Anthony -Date: Thu Aug 17 14:36:20 2017 -0500 - - Export go tables, too. Don't crash with exporting empty datatables. - -commit b0eeeb52216434d413b8868f9df9877ba4c66179 -Author: unknown -Date: Thu Aug 17 14:31:10 2017 -0500 - - topdown restructure - -commit d3f24961e68d9f0265f3caf7eb2a589d7283892c -Author: unknown -Date: Wed Aug 16 17:49:57 2017 -0500 - - restructure topdown proteoforms - -commit 5ea6486d64fe2c4eaaa6d2d04d732b99f94784d2 (tag: 0.2.6) -Merge: 8410235 9020354 -Author: Anthony -Date: Wed Aug 16 16:29:03 2017 -0500 - - Merge pull request #447 from acesnik/master - - Use DataTables for exporting to Excel instead of DGVs - -commit 9020354f6993f4a4d806e451cd53a03a771b34c0 -Author: Anthony -Date: Wed Aug 16 16:25:47 2017 -0500 - - slight speedup - -commit a7a83e9e12811b5df4e5e7d39d68515c6e08e919 -Author: Anthony -Date: Wed Aug 16 15:25:49 2017 -0500 - - Fixes - -commit b38ba4c27397d32f7cfd5501efe2bc4916733074 -Author: Anthony -Date: Wed Aug 16 12:42:40 2017 -0500 - - use datatables for exporting tables instead of DGVs - -commit 982e8ffb288d33681cfd0283ab96844d9630a56d -Author: unknown -Date: Wed Aug 16 11:32:25 2017 -0500 - - fixes - -commit 6e8953e5073f985a1e4d683c84140dd8d2953d41 -Author: Anthony -Date: Wed Aug 16 10:52:11 2017 -0500 - - finished the datatable formatting - -commit 015ab6d0a22df732acdcce497c9bd3d6cbda11a1 -Author: Anthony -Date: Tue Aug 15 20:53:07 2017 -0500 - - Starting on exporting datatables to excel - -commit 33512c57d466276972436cc949c103cb4020b3ad -Author: Anthony -Date: Tue Aug 15 18:01:14 2017 -0500 - - Value missed monoisotopic higher. Move raw component figs of merit into component reader, so they're not loaded as presets - -commit a610ff2772b4c88da1fa591ebfbc14a9fdf961bb -Author: unknown -Date: Tue Aug 15 10:53:50 2017 -0500 - - added back button, package line error - -commit 3c9cd4c1e7caa5711287b655fd68a6d7c8dea7cc -Author: unknown -Date: Tue Aug 15 09:54:17 2017 -0500 - - graph thresholds - -commit bb3f2c358178faf9994202d01328343c759e9e39 -Merge: f67269d 8410235 -Author: unknown -Date: Tue Aug 15 09:41:15 2017 -0500 - - merge upstream fixes - -commit f67269d10f3804a1791037a85d40c843bc87b7c0 -Author: unknown -Date: Tue Aug 15 09:28:52 2017 -0500 - - mzlib update - -commit 841023585bf074bd6ba01957a784b371a07ccca7 (tag: 0.2.5) -Merge: 5947209 3d1d302 -Author: Anthony -Date: Mon Aug 14 23:10:51 2017 -0500 - - Merge pull request #444 from acesnik/master - - bug fix in making intensity dataframes - -commit 3d1d302f114977f698c8cf4179c82c13ab534fdb -Author: Anthony -Date: Mon Aug 14 23:02:52 2017 -0500 - - bug fix in making intensity dataframes - -commit 59472094592e1f4154ade468538adc49a7c60e3c (tag: 0.2.4) -Merge: fce37dd 9c6573a -Author: Anthony -Date: Mon Aug 14 20:59:28 2017 -0500 - - Merge pull request #443 from acesnik/master - - Bug fix for identifying amino acid loss; simplified identification code slightly; tests for identifying proteoforms - -commit 9c6573ad7f1349ff36f211e0114f32b48e20715c -Author: Anthony -Date: Mon Aug 14 20:43:15 2017 -0500 - - Bug fix for identifying amino acid loss; simplified identification code slightly; tests for identifying proteoforms - -commit 087e59f931c509031e84bedaa3727e82ce478f31 -Merge: 73bd10a fce37dd -Author: unknown -Date: Mon Aug 14 16:17:13 2017 -0500 - - pull upstream - -commit 73bd10ab78a032c658e3f53418aa2d7ff66f5dc9 -Author: unknown -Date: Mon Aug 14 16:14:27 2017 -0500 - - gene name - -commit 44a2eacace003cc69f133bea6e7c08bc9650adbe -Author: unknown -Date: Mon Aug 14 15:24:13 2017 -0500 - - id experimental fixes - -commit fce37dde7f2a6084b8cab42f159ac6319b995d78 -Merge: 1106d45 9506629 -Author: Anthony -Date: Mon Aug 14 12:19:35 2017 -0500 - - Merge pull request #441 from acesnik/master - - update quant checkboxes with presets - -commit 9506629f246146d920456dd14619ee570299d5b4 -Author: Anthony -Date: Mon Aug 14 11:45:30 2017 -0500 - - update quant checkboxes with presets - -commit d0270bb77ea66242598b183aef968f3f1d862249 -Author: unknown -Date: Sun Aug 13 13:35:48 2017 -0500 - - change - -commit 155181907a87be344ff67638d04339311bfb38bc -Author: unknown -Date: Sun Aug 13 13:33:40 2017 -0500 - - one line - -commit 25c179efc8182ee09d61f0480473d5cdbc13e4bd -Author: unknown -Date: Sun Aug 13 13:28:48 2017 -0500 - - added back inclusion list, proteoforms id'd in specific order each time - -commit 3190b2b80de7351b8ceb1ccca6f67ac0bc6bc97d -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sat Aug 12 11:51:59 2017 -0500 - - GUI changes - -commit fae4686e0af2c479d99816f078d1d8e67255cfc1 -Merge: 21a04d6 1106d45 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sat Aug 12 11:13:02 2017 -0500 - - merge upstream aggregatable changes - -commit 21a04d633112db156e99317c88412d8904b156b2 -Author: unknown -Date: Fri Aug 11 18:06:45 2017 -0500 - - gene merge fixes - -commit 1106d45973bc678c1b12b912e5df2e2b627c705a -Merge: de8ef81 bbc10e6 -Author: Anthony -Date: Fri Aug 11 14:25:21 2017 -0500 - - Merge pull request #434 from acesnik/master - - Update icon, fold change allowances in establishing significance - -commit bbc10e6cb47e32bbda35e1cba9d29393ee728b61 -Author: Anthony -Date: Fri Aug 11 14:08:57 2017 -0500 - - change preset kill to warning - -commit 22a6f6600c6f9baffdf03514b5b1631fd0d9a0ac -Author: Anthony -Date: Fri Aug 11 13:24:33 2017 -0500 - - biorepintensity table tests - -commit ca9d81d7f53a53eac6c752500a749950eee50845 -Author: Anthony -Date: Fri Aug 11 11:47:23 2017 -0500 - - test fixes, except for biorepintensity table - -commit 5c928659d26a109f463b7c090af8dc7aa8c28718 -Author: Anthony -Date: Thu Aug 10 17:39:23 2017 -0500 - - Changing over to IAggregatable instead of extending Component for NeuCodePair - -commit 27c3ffdb2587a8b3e4e7228bac4d89bfed403f13 -Author: Anthony -Date: Thu Aug 10 16:05:06 2017 -0500 - - cytoscape for new quantification results, new quantification datagridview - -commit b6317dc75976efbdd73844e2747a4bef23c2f6c1 -Author: Anthony -Date: Mon Aug 7 20:43:14 2017 -0500 - - Added allowance of fold change, added allowance of fold change in count of biological replicates, updated icon, export correct cytoscape scripts - -commit 13f65c4549546df9ab24ea2667f48a19bc47acc2 (tag: 0.3.0) -Merge: d46edc8 de8ef81 -Author: unknown -Date: Thu Aug 10 18:08:33 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/ProteoformSuite into TD_BU_integration - -commit de8ef81f2a2aca461c90f72133e06e5a042f1caa -Merge: d9d78c0 53a259f -Author: Leah Schaffer -Date: Thu Aug 10 18:08:20 2017 -0500 - - Merge pull request #439 from lschaffer2/master - - method fixes - -commit 53a259febf93d2c816bab8c65b1bbb944170a799 -Author: unknown -Date: Thu Aug 10 17:47:23 2017 -0500 - - remove clear saved methods - -commit a2abb17ec9a85d3f214cf5684798aa13c28ae9d2 -Author: unknown -Date: Thu Aug 10 17:37:57 2017 -0500 - - move one line - -commit 3016d1e623b1f498562240c4c514884d398660ad -Author: unknown -Date: Thu Aug 10 17:35:28 2017 -0500 - - methods peaks update specific to comparison type - -commit c27e91e5b3f86383ce787a3ddf9b07453f10d63f -Author: unknown -Date: Thu Aug 10 16:54:56 2017 -0500 - - clear methods - -commit d46edc8adb1a0b8766098d61834daff872ac0dcc -Author: unknown -Date: Thu Aug 10 16:23:51 2017 -0500 - - line added back in - -commit 34e896b217403dde708bd615935a16f7bd234104 -Merge: ffb4db8 d9d78c0 -Author: unknown -Date: Thu Aug 10 15:31:27 2017 -0500 - - pull component fixes from upstream - -commit d9d78c0b282190f2c97bee77f275763673aa6eed -Merge: 3d224d2 8793f01 -Author: Leah Schaffer -Date: Thu Aug 10 15:30:19 2017 -0500 - - Merge pull request #438 from lschaffer2/master - - components figures of merit - -commit 8793f01b65e0490ce776c88475a198ece5e77985 -Merge: 590cb78 3d224d2 -Author: unknown -Date: Thu Aug 10 15:10:58 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/ProteoformSuite - -commit 590cb7884b6f2cac9df8c4a0e13ea4a24b2b7f08 -Author: unknown -Date: Thu Aug 10 15:09:37 2017 -0500 - - components figures of merit - -commit ffb4db81d6bcc92fc4553778d28fa4378eac826f -Author: unknown -Date: Thu Aug 10 14:36:52 2017 -0500 - - stuff - -commit d0b9ac2972e5757a2c11f0f4f04fa0be2de00f4c -Merge: 5b9ba9c 3d224d2 -Author: unknown -Date: Thu Aug 10 12:58:59 2017 -0500 - - merge upstream - -commit 5b9ba9c4857184476357334b7ab1184739abc73a -Author: unknown -Date: Thu Aug 10 12:56:48 2017 -0500 - - small td fixes - -commit 3d224d2d43114d5e7f4cde726bd6621f4be0833c -Merge: af67d74 335d059 -Author: Leah Schaffer -Date: Thu Aug 10 12:55:35 2017 -0500 - - Merge pull request #435 from lschaffer2/master - - mass shift and load method fixes - -commit 048e7e08196a109285b64de20fb73d82763ca998 -Author: unknown -Date: Thu Aug 10 10:41:29 2017 -0500 - - GUI and packages - -commit 1c9631fbb9b738c4d482441acf99ab9d092c53dc -Author: unknown -Date: Wed Aug 9 18:24:30 2017 -0500 - - git issues - -commit 7e3d247b91684c39f04a80cda2c78407bc723e73 -Author: unknown -Date: Wed Aug 9 18:07:18 2017 -0500 - - restart appveyor - -commit bd513d4a5dbbf1c6c4a91483bccc43c7dcb87449 -Author: unknown -Date: Wed Aug 9 17:34:07 2017 -0500 - - fix - -commit 335d059b387ada0a3a22d16f992212f400b1a5f0 -Author: unknown -Date: Wed Aug 9 17:07:46 2017 -0500 - - revert - -commit 82f1bcfa72851a62799a95563e66a86cc5a8eba6 -Author: unknown -Date: Wed Aug 9 16:57:31 2017 -0500 - - warning messages - -commit 5bb628f31e6b866b8965c6727c3ec014c694fb30 -Author: unknown -Date: Wed Aug 9 14:28:04 2017 -0500 - - changes - -commit 6a409390b4b10b00c11a38fe3a62b8551613af12 -Author: unknown -Date: Wed Aug 9 12:56:11 2017 -0500 - - clear actions - -commit 20dfbec75737acb9e01b1078e06a0ca2df657cc9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Aug 8 18:35:23 2017 -0500 - - mass shift and load method fixes - - fix tests - -commit c17c74a0b098be97dcae3c9c64cca61c113734c3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Aug 8 13:22:22 2017 -0500 - - fixes - -commit fb34239f57d7c6c059daf9511b3a352e250fc19a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Aug 7 18:16:16 2017 -0500 - - calibration rework - -commit a4f2a70efadefe7b9b0a9c80583a92938330a8ca -Merge: f6066ac af67d74 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Aug 7 11:48:01 2017 -0500 - - merge upstream - -commit f6066acfa45a8b29a87642fecb2dfba5bdec54d3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Aug 7 10:14:22 2017 -0500 - - mzlib update - -commit 8c58e0c380b6d21744c49267a3cc8efe1c92acba -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Aug 7 10:11:35 2017 -0500 - - GUI updates - -commit af67d740dee43594f5543bfca9d8b085ecf0f703 (tag: 0.2.3) -Merge: f5f8641 8252d02 -Author: Anthony -Date: Fri Aug 4 16:47:24 2017 -0500 - - Merge pull request #433 from acesnik/master - - Seeded random for imputation; persistent decoy bug fix; speedups for decoy databases - -commit 8252d02ab2ed1a76d1f1210c885e7dc549147885 -Author: Anthony -Date: Fri Aug 4 13:40:37 2017 -0500 - - fix buggy edit thing - -commit 6e37e4cc6def8e2e46b564c041cc916e1e4ddd45 -Author: Anthony -Date: Fri Aug 4 13:38:55 2017 -0500 - - test for decoy crash - -commit ef21316b4ebb58959f601a83e0a593805edf5ff5 -Author: Anthony -Date: Fri Aug 4 13:10:17 2017 -0500 - - Change ptmcombos back to static - -commit 0c582584761fa04aadc2940417a83e3f687406d3 -Author: Anthony -Date: Fri Aug 4 13:06:12 2017 -0500 - - Relation lookup by lysine count - -commit 0fb40b92d76e181c7596986c3f920769b8649a65 -Author: Anthony -Date: Fri Aug 4 12:12:13 2017 -0500 - - speedups - -commit aa0efb79483cf719c8ffe07b16fdb0d39ae6a50a -Author: Anthony -Date: Fri Aug 4 11:30:32 2017 -0500 - - updated mzlib; improved ldr user input validation - -commit fdf5a578d434ffe18a9ab14d1fb92412d27ba0db -Merge: 81b6a40 f5f8641 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Aug 4 11:25:58 2017 -0500 - - merge from upstream - -commit 70b83be45be3829ab60e156666983baa40e55811 -Author: Anthony -Date: Fri Aug 4 10:26:57 2017 -0500 - - trying to speed up decoys - -commit 0cf9c3a6d46da99ebddde97802b96731de02519d -Author: Anthony -Date: Thu Aug 3 00:07:21 2017 -0500 - - seeded random possible for imputation; use unrounded intensities for distribution statistics - -commit bb4de2e2e5ee311a3cc549526bddc892842180cc -Author: Anthony -Date: Wed Aug 2 22:15:09 2017 -0500 - - Fixed big where preset min num of obs wasn't kept - -commit ded4acec13c448665b9591d489e8f1f945e0c8d4 -Author: Anthony -Date: Wed Aug 2 20:43:08 2017 -0500 - - more fixes - -commit 3bf929144843a81007a62cf11eb0a0aa61ec7654 -Author: Anthony -Date: Wed Aug 2 19:08:08 2017 -0500 - - test and bug fixes - -commit e30b7837c715f7a87a02619036e8ee1bf81da547 -Author: Anthony -Date: Wed Aug 2 12:30:20 2017 -0500 - - Added fold change cutoff for tusher analysis, like in paper - -commit f5f8641189cb689c46bd1e358025b50f3d58bf88 -Merge: ac5d757 3d5ad80 -Author: Anthony -Date: Fri Aug 4 10:14:17 2017 -0500 - - Merge pull request #429 from lschaffer2/master - - GUI bug fixes and scroll bars if small screen - -commit 3d5ad8065c00b5fae8df6c1a3b52ca94b0a06a7b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Aug 4 09:55:36 2017 -0500 - - clear GUI methods - -commit c6fca98ef37b2a5ec920b318ab7725cc30c6a8d7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Aug 2 12:52:11 2017 -0500 - - gui fixes - -commit d37399b75cf32228cc3c64c29e3246813dc0bc32 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Aug 2 10:54:55 2017 -0500 - - add scroll bars if screen or window size smaller than form size - -commit 81b6a40eff556a96500eee75324f229eaf66e6bc -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Aug 2 10:45:45 2017 -0500 - - changes - -commit ac5d7572d4a9ade637b00785be8d1bfe7bce0320 (tag: 0.2.2) -Merge: 08bfa0e 3d41fd5 -Author: Anthony -Date: Tue Aug 1 14:50:18 2017 -0500 - - Merge pull request #426 from acesnik/master - - Quantification changes - -commit f06dd29d94f5a8024a6590b76c986472efb22a6f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Aug 1 11:34:24 2017 -0500 - - BU reader fixes - -commit d243431680dd2c32a8122933f08789278999569d -Merge: c9b4e63 08bfa0e -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Aug 1 09:41:03 2017 -0500 - - merge upstream - -commit 3d41fd53ac5555d4b1f3e51007ef5dd47ad91d40 -Author: Anthony -Date: Tue Aug 1 03:29:13 2017 -0500 - - updated mzlib - -commit b08ccd49c1d73231222d67fb25787cb548660354 -Author: Anthony -Date: Tue Aug 1 03:27:32 2017 -0500 - - removed a few things - -commit b390e650e7acfc82fd07c3559576a9b13e595f3a -Author: Anthony -Date: Tue Aug 1 03:22:01 2017 -0500 - - test fixes - -commit c8c9526b2dd2722c3b08891a2a5677566cfd8d72 -Author: Anthony -Date: Tue Aug 1 02:34:00 2017 -0500 - - Get interesting families for specific analysis. - -commit d446b96937f03a1ba68b1cecee9de1bb843e88c0 -Author: Anthony -Date: Tue Aug 1 01:30:39 2017 -0500 - - Extensive changes and refactoring to enable second tusher analysis. - -commit 4e872b0ceccd852a397c5fec602b4cdf88e831a0 -Author: Anthony -Date: Mon Jul 31 17:58:18 2017 -0500 - - Implemented new tusher analysis - -commit ef8b614de66ecce300eba49a71c8af4246925477 -Author: Anthony -Date: Mon Jul 31 17:24:15 2017 -0500 - - refactoring quantification - -commit d7042414106ca89216a3d8571316e2e82480b85d -Author: Anthony -Date: Mon Jul 31 13:04:01 2017 -0500 - - Split the overlap of mass tolerances to prevent quant components being added to both lt and hv lists. - -commit 32fecb29790602c64ee1f598fcd901c71627fd6b -Author: Anthony -Date: Fri Jul 28 14:11:50 2017 -0500 - - normalize - -commit 67325aa69608d16a2949af84ddbdc17abde47cea -Author: Anthony -Date: Fri Jul 28 14:05:26 2017 -0500 - - more - -commit 03468ea0fe26dec8e084a2f71b6ccf2250a0d6ca -Author: Anthony -Date: Wed Jul 26 15:24:31 2017 -0500 - - quant - -commit ff73311eb18b4f8bb55bb597e49e3de8699796ac -Author: Anthony -Date: Fri Jul 21 18:53:45 2017 -0500 - - Full tests of logFC quant methods - -commit 87a1d59fe63dfefe691298648dd1df6d2b454063 -Author: Anthony -Date: Thu Jul 20 11:12:18 2017 -0500 - - Theoretical database fix for small screens - -commit 49504dc7d6fa83a97120c96ef12f50e5d73253ff -Author: Anthony -Date: Wed Jul 19 18:42:28 2017 -0500 - - Log2FC statistics - -commit 91b1f8e799ef6d05b7bb39c7fe1fce39997df4df -Author: Anthony -Date: Mon Jul 17 17:26:38 2017 -0500 - - Keep individual fraction and tech-rep intensity sums during quantification; also keep biorep/techrep/fraction labels as strings, not int - -commit 08bfa0ec6d4adeab42eb779f2d5d049788df887e -Merge: 20ea171 f12181e -Author: Anthony -Date: Tue Aug 1 01:33:31 2017 -0500 - - Merge pull request #427 from lschaffer2/master - - repeating families bug fix - -commit c9b4e63917552c06487f42463093b76f6d4dae1d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 20:59:00 2017 -0500 - - revert - -commit f605f70c06c2c758718ded3429b402059a70dba4 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 20:24:42 2017 -0500 - - ptm combos - -commit 24ce2d1bd55056593ba5471db85b33deb376d2b6 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 18:28:59 2017 -0500 - - small test - -commit 0e8d6afe58c1a616e7d5779421a367dc57baaf4b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 18:14:32 2017 -0500 - - GUI fixes - -commit f12181eff8934de7e613336f0857c96d7c857a17 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 17:18:06 2017 -0500 - - repeating familie - -commit 55bd5f2ab289d6549302488534b606b51f13182b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 17:15:27 2017 -0500 - - repeat node bug - -commit ed07411f6c581b35575a630c7ebc1e0d30d66bb3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 31 11:44:49 2017 -0500 - - td tests and bug fixes - -commit dcfe8e8510ebe40e891c48f930b8f5fdf8558930 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jul 27 20:36:29 2017 -0500 - - removed code used to test - -commit 9000eef78a001958737853afab464dc7bee3e869 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jul 27 20:31:09 2017 -0500 - - bug fixes with topdown and theoresticals - -commit dbb3b883e43b0b49b078deee79865eca1862c6b7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 18:00:47 2017 -0500 - - remove unnecessary fields - -commit 01a163bd2259f3cecfc372852a232c6aa2194dec -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 17:31:11 2017 -0500 - - more tests for calibration - -commit 8c11df99366a33b636adbe802c2a4aa020bc13e7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 14:56:36 2017 -0500 - - delete unnecessary lines - -commit 1260f60498b3e632640db4fc2156627a23c6cb43 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 14:47:28 2017 -0500 - - reinstalled closedxml - -commit ee4937fb9756c46d795a05331579f2286432877c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 13:53:41 2017 -0500 - - ok - -commit ff8855b63de570f533e35acac6a6cd9fdb3ac8f9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 13:45:59 2017 -0500 - - test - -commit 5092689548121d198d29b286f352fd5419f0e218 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 13:40:19 2017 -0500 - - try again - -commit c93d6a798188d48d9785e571b3800e38487f0dc9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 13:23:26 2017 -0500 - - rerun tests - -commit 6c419163b9c724fae434a41398b4c92e721a1760 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 25 12:42:00 2017 -0500 - - cali tests - -commit 9e735f756bb317b946095643a0600f8eec8c9f7c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 24 17:49:48 2017 -0500 - - calibration - -commit 65efb6a7bff5ba19d6d542d67ac5be9c87b84e07 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 24 16:25:12 2017 -0500 - - test - -commit 60444943b792f4fb44b0dcb5c6505c77b061a405 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 24 15:34:33 2017 -0500 - - calibration tests start - -commit 76fa4d10ecca9009513182e78b6ef4b166559229 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 16:44:21 2017 -0500 - - filename change to match upstream - -commit c1c759fb3a0ec677bec0c90006d2b74787865053 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 16:16:56 2017 -0500 - - remove unnecessary code - -commit 98e81d29ed588f1b538631e3bf375c650d079d5b -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 15:34:57 2017 -0500 - - test for making hit chemical formula with sequence and PTMs - -commit 98f92e2eaf51c7fbb5642d3a4e8275df2bc0e99e -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 11:59:00 2017 -0500 - - couple more tdreader tests - -commit 62f20a401818c6ef6cfb00ad0f8094f3bd77fb17 -Merge: 6839866 20ea171 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 11:42:34 2017 -0500 - - merge conflicts - -commit 683986678d81bdc574ebaf8e46d9c08f0e77c175 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 11:38:08 2017 -0500 - - topdown reader test - -commit 20ea171603c83ed708f013023b5f7b6f4f97906e -Merge: e90ebce ce7a295 -Author: Anthony -Date: Thu Jul 20 11:16:43 2017 -0500 - - Merge pull request #421 from lschaffer2/master - - shift masses small fixes in ET GUI - -commit 0b4ba655f7efc3b0bad1c97d2860a05ddb956c2a -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jul 20 09:12:39 2017 -0500 - - cytoscape test - -commit 42a6930729597ed22d85f04d4cb1929d374ef541 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:56:48 2017 -0500 - - inclusion list - -commit ce7a29586b5d8873051e6d68bb945f1a4072a1a9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:54:09 2017 -0500 - - inclusion list change - -commit de8a7cfcff369c38068c70bef632ca1ca74627b7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:50:26 2017 -0500 - - cleanup msscan - -commit d62e62c26eac12e37f3b02b1d9b80bbfe8a911ee -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:39:31 2017 -0500 - - removed small changes - -commit 33fc567812d9ac2493cad1944ac56330a3ec1077 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:38:43 2017 -0500 - - BU test - -commit a6b3f387cdebe56cbfaa7396881b7faed9e5974d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:22:56 2017 -0500 - - bu tests - -commit cc5856ef86b6529c0a757f43a933ea708a5da931 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 18:21:20 2017 -0500 - - BU reader tests - -commit d6863dd915d98a844469445523ffd550de96aac6 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 17:22:21 2017 -0500 - - remove disulfide bonds constructor - -commit 04c44188b1b23b2e6e26c61c51d4bedc59d9f1ef -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 17:05:31 2017 -0500 - - moved disulfid to separate branch - -commit 0a96511adf908c7420e0e512c08ffe8c04047428 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 15:36:03 2017 -0500 - - td family tests - -commit bf60e3b42d7bc2403bcdc98554f63656ddce4bb8 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 11:41:39 2017 -0500 - - TD relation test - -commit ffb1b4c1b4f4a65455695049b73e5c6ae0bdd3d1 -Merge: 48823e3 e90ebce -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 09:58:39 2017 -0500 - - pull upstream - -commit 48823e328f1d733a98ee8cd9f1affcc4f9867283 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 19 09:57:35 2017 -0500 - - small change - -commit 5ebe6e4e668322f820be0bfc4dfca5fab0daaa4f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 18 13:43:34 2017 -0500 - - bool for shifting masses in clear method - -commit 285bad49e402eb66686bb895e925c368fe2d3d2d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 18 13:41:56 2017 -0500 - - Mass shift fix - -commit 95a660c7b1fc4185caf89e7fa19ab6683590a3b0 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 17 21:02:43 2017 -0500 - - fixes - -commit e90ebce94ee7d4af6c9a2032a698c60ea8e35b78 -Merge: a507ae1 7b440ac -Author: Anthony -Date: Thu Jul 13 18:58:26 2017 -0500 - - Merge pull request #419 from acesnik/master - - full quantification test - -commit 7b440acfb94f65534705ff2d8cc086ab766c0d37 -Author: Anthony -Date: Thu Jul 13 18:54:23 2017 -0500 - - rough test of quant summary - -commit ba15feea9a01a82be30ae6e84054060caae7aa9e -Author: Anthony -Date: Thu Jul 13 18:49:13 2017 -0500 - - test reevaluating quant statistics - -commit 26a57e590a4db4e5d94de1b8c7a32f783ca34392 -Author: Anthony -Date: Thu Jul 13 18:44:20 2017 -0500 - - removed old test; added the excel workup for the minimal quantification example. - -commit b33b73a12639bd6913612e8edcdac6ddb850f5c9 -Author: Anthony -Date: Thu Jul 13 18:33:39 2017 -0500 - - full quantification test - -commit a507ae1fdb4421e08137874fbbb44845b66885e6 -Merge: 2dc9035 b610f23 -Author: Anthony -Date: Wed Jul 12 19:05:05 2017 -0500 - - Merge pull request #418 from acesnik/master - - Hard-code 2 in for all possible ptmsets, since that's different from … - -commit 77a2b0329353c99b2b3f4c3621683633752f6a99 -Merge: 17795e7 2dc9035 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 12 18:36:01 2017 -0500 - - pull upstream - -commit b610f23245e2b4fc5a273ba68bdac46fa57a5546 -Author: Anthony -Date: Wed Jul 12 17:58:49 2017 -0500 - - Hard-code 2 in for all possible ptmsets, since that's different from max ptms for theoretical proteoforms - -commit 17795e763488bd37985dbfb1792ef299fb096369 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 12 17:15:24 2017 -0500 - - calibration fixes - -commit 2dc9035f13d447fb042adf310357d112da77cd55 -Merge: 73c6f5c f31d739 -Author: Anthony -Date: Wed Jul 12 15:02:18 2017 -0500 - - Merge pull request #417 from acesnik/master - - Tests - -commit f31d7395b3d812aa9f79ea4fc1b49c6776ad3af4 -Author: Anthony -Date: Wed Jul 12 14:59:54 2017 -0500 - - more tests - -commit 888fd56780a2a76a2a27847f500ce0d863a846f7 -Author: Anthony -Date: Wed Jul 12 14:36:46 2017 -0500 - - asdf - -commit 388f633c47f7fdb9ad7305478d1a5eaca8c408b2 -Author: Anthony -Date: Wed Jul 12 14:34:45 2017 -0500 - - some tests - -commit 73c6f5c7db6a61f70ee19e57e846b4e71d9faccf -Merge: 38a656a b260644 -Author: Anthony -Date: Wed Jul 12 13:50:58 2017 -0500 - - Merge pull request #416 from acesnik/master - - 4x speedup - -commit b260644dc2ad237a374c137738d69e92cf9c78a4 -Author: Anthony -Date: Wed Jul 12 13:42:36 2017 -0500 - - updated mzlib - -commit f61ef76220dbd5134e150e1fbf8a71fed2c26839 -Author: Anthony -Date: Wed Jul 12 13:07:40 2017 -0500 - - space - -commit 1c28791c121ca99707e532225fa230ff73b0f211 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 12 12:06:41 2017 -0500 - - debugged calibration across files - -commit d0822576eba2d5827657b35190d993f9a68528f7 -Author: Anthony -Date: Tue Jul 11 20:53:50 2017 -0500 - - space - -commit 5e99ba72ecf572f3834416061a6eee88acdb5fcd -Author: Anthony -Date: Tue Jul 11 20:47:27 2017 -0500 - - test fixes again - -commit 0bdebf48c5700a05762d452fce443209cc3fbcd8 -Author: Anthony -Date: Tue Jul 11 20:38:20 2017 -0500 - - test fixes - -commit 28a6f740c146ec5176318b20305f728bc8173327 -Author: Anthony -Date: Tue Jul 11 20:34:59 2017 -0500 - - speedups - -commit 40741fd8367f3aec73f1483245dac61b7bd69add -Author: Anthony -Date: Tue Jul 11 16:30:22 2017 -0500 - - cell validation for load files - -commit a3ff4a92e8ff7e062c696b1599bff60abcc60d2a -Author: Anthony -Date: Tue Jul 11 15:44:59 2017 -0500 - - keep bkgd width and shift from presets - -commit dd08047823704afbb1f4ed150a91df3e82c4bd2c -Author: Anthony -Date: Tue Jul 11 15:23:12 2017 -0500 - - Fixed setting biorep from preset - -commit 38a656a4b7f569c4eafb082bcb9c88fab78ebf80 -Merge: 9b4a4a4 8ea5c61 -Author: Anthony -Date: Tue Jul 11 12:36:07 2017 -0500 - - Merge pull request #415 from acesnik/master - - Rename SaveState -> Sweet; record user actions and include in report - -commit 8ea5c61cbf26da5ea5410556a66ed346f81c11f8 -Author: Anthony -Date: Tue Jul 11 12:26:02 2017 -0500 - - save presets with results dump - -commit 20699be6360f1f78630067a783ecad5f70ae5b52 -Author: Anthony -Date: Tue Jul 11 11:44:38 2017 -0500 - - Tested preset actions - -commit 470f70c2cee963f1e3a45762ea2e637045f5afd4 -Author: Anthony -Date: Tue Jul 11 09:49:59 2017 -0500 - - Change multiple dgv items with right click - -commit deb25a96ad1fa01a05d41d65f9dbd9d51bc4015a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 10 17:18:56 2017 -0500 - - fix disulfide input - -commit 0d74b147e1600b847558b9d34b35bdd3203cfb43 -Author: Anthony -Date: Mon Jul 10 14:19:12 2017 -0500 - - Rename SaveState -> Sweet; record user actions and include in report - -commit 9b4a4a4f355faf3a82a1f14004b137ea5b2eb391 -Merge: f8ebca1 71d395b -Author: Anthony -Date: Fri Jul 7 18:21:37 2017 -0500 - - Merge pull request #414 from acesnik/master - - Compare conditions rather than labels; permutation change; fdr change; imputation fix - -commit 71d395bf6d6e03c50386099278b02ec5fb5f927f -Author: Anthony -Date: Fri Jul 7 18:15:50 2017 -0500 - - save input file dataframes, too - -commit bee2ada0f79aaa35be9df009336da022be6efbcd -Author: Anthony -Date: Fri Jul 7 16:33:44 2017 -0500 - - lots from excel work - -commit d837966ca9a4637a217d6a4b502d20ad01b3f364 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jul 6 17:07:57 2017 -0500 - - disulfide - -commit 704f715982d3cdcb26071c3ff5bd152097cfcaf3 -Author: Anthony -Date: Thu Jul 6 14:06:00 2017 -0500 - - Sort permutations before calculating dE(i) - -commit 695bb719999ee8fd36cd3c32d7b452a29a89b268 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jul 6 13:53:37 2017 -0500 - - td identification ptm sorted out - -commit b12e7087317245f97fa3bc6a7d987bccce6c07c9 -Author: Anthony -Date: Thu Jul 6 12:18:05 2017 -0500 - - Permute within bioreps, not condition - -commit 18ddd0b9c245740d4974f57b74c8e64d5edddc55 -Author: Anthony -Date: Wed Jul 5 13:09:16 2017 -0500 - - Fixed bug that caused obs vs scatter to crash - -commit 94be0a557604310c5993e5955da799e6edbf5bfc -Author: Anthony -Date: Wed Jul 5 12:40:50 2017 -0500 - - Fixed bug in permuted stdev calculation. - -commit 55f1a6c1290a4144868b8d137e991c43006171b9 -Author: Anthony -Date: Mon Jul 3 18:29:31 2017 -0500 - - log stdev should be calculated with average of logs, not log of average intensity - -commit 55f7e6578d5c0d79f177fefdbfd3aa67132f4f9c -Author: Anthony -Date: Mon Jul 3 18:10:05 2017 -0500 - - Save biorep intensity dataframes; use stdev function each time permuted test statistic is calculated. - -commit c54436579f2f0e4133f66e60a1b8221496fde3bb -Author: Anthony -Date: Mon Jul 3 15:18:08 2017 -0500 - - Option to perform Tusher calculations from linear intensities - -commit 3e704624bf2aeef7b5936c3e062937e65e845897 -Author: Anthony -Date: Fri Jun 30 16:41:58 2017 -0500 - - displaying all observed intensities; test fixing - -commit 626183d2503638fa0b98d7f6bb6629795138d418 -Author: Anthony -Date: Fri Jun 30 14:20:39 2017 -0500 - - Fix imputed intensity calculation. - -commit f69043c78bb1ef1f69601508317b4cafccc2586b -Author: Anthony -Date: Thu Jun 29 18:45:17 2017 -0500 - - Balanced permutation from first principles. Fixed histogram creation with imputation. - -commit c488783b11bb50f27432daed18271074dd3ab2d9 -Author: Anthony -Date: Wed Jun 28 17:54:11 2017 -0500 - - Corrected FDR calculations; lots of new functionality for quant form. - -commit c1bd91e02313e49c1fcb1d984e54117de2431de5 -Author: Anthony -Date: Tue Jun 27 13:28:41 2017 -0500 - - Allow user to look at quantative components and neucode pairs in agg prots - -commit 53ea45cb2b2f91e1317f09b1996dafcbcd1a054b -Author: Anthony -Date: Mon Jun 26 23:34:46 2017 -0500 - - Sum across labeling in calculating biorepintensities - -commit 8c4f6633f7c0d2262d50fdc63bd51cf6613158c3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 5 18:42:54 2017 -0500 - - fix up td relations and BU PSM readin - -commit b84696e7e446b9224a6e9060f2901abed3284aed -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 5 10:45:38 2017 -0500 - - mzlib update - -commit 18cc334a327419b241185bc50e519183ae42464f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 5 10:16:50 2017 -0500 - - can include or not include td nodes in fams - -commit 94b1e2078b02fe2ecbcae652cdd9342d955bc684 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jul 5 09:42:08 2017 -0500 - - cleanup load decon page dgv - -commit 709e01dbf87536ff431b4fe3141e6ac66a944f00 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jul 4 14:56:21 2017 -0500 - - identified experimental page, look at TD and BU overlap - -commit 92d2922925c89b3ee74d0d79c67b8ee720a6d576 -Merge: c1fb120 f8ebca1 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jul 3 14:30:07 2017 -0500 - - mass calibration across files, fixed database disulfide bug - -commit c1fb120f5853b0422ba7207f02a5ee09c1b94696 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jun 29 10:58:06 2017 -0500 - - disulfide bonds - -commit 29b1dd89031de575f4ff7b112e393472bdf16d1a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jun 27 17:20:31 2017 -0500 - - some TD bug fixes, can unaccept relations that dont lead to ID - -commit f8ebca1c187e63f9b79dd6d9f6e012c56676fc6d -Merge: d536587 7b4562b -Author: Anthony -Date: Mon Jun 26 11:13:27 2017 -0500 - - Merge pull request #412 from acesnik/master - - Added avg permuted test statistic to quant dgv; polished quant graphs - -commit 7b4562b482cab0592f22a471292863b50ecb3cd7 -Author: Anthony -Date: Mon Jun 26 10:59:26 2017 -0500 - - Added avg permuted test statistic to quant dgv; polished quant graphs - -commit c6aba68d50ddb1a75afca32931a24eec47d0b82d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Jun 23 15:08:43 2017 -0500 - - prioritize ETD relations with td nodes w/ higher score - -commit d5365874f267fe02743f62148ae7a3c92e60014b (tag: 0.2.1) -Merge: 75ec60e 1e3dc65 -Author: Anthony -Date: Thu Jun 22 12:17:18 2017 -0500 - - Merge pull request #410 from acesnik/master - - Adjustments for higher and lower screen resolutions... - -commit 1e3dc6517cad49282b347983381520276d6bf52e -Author: Anthony -Date: Thu Jun 22 11:48:12 2017 -0500 - - Don't clear when loading ncps - -commit 2554d0e0cca63bb7b7f052f1be36231acfe6af75 -Author: Anthony -Date: Thu Jun 22 11:36:15 2017 -0500 - - Fixed another missing event entry - -commit 00714f580280247345dc159c500f92205e96b07d -Author: Anthony -Date: Thu Jun 22 11:18:06 2017 -0500 - - Make comboboxes readonly where appropriate. Fixed all of the events that got deselected - -commit e8546bffbeb595ae2abd09517ff80df4a1199b51 -Author: Anthony -Date: Thu Jun 22 09:45:01 2017 -0500 - - udpate csproj - -commit 5dfe587d62d56b03a8b59c313624b6c22a6d1b11 -Author: Anthony -Date: Thu Jun 22 09:42:47 2017 -0500 - - reverted some proteoformsweet changes - -commit 3030acb135778a7afa294505eef0b8335ecc4543 -Author: Anthony -Date: Thu Jun 22 09:40:58 2017 -0500 - - Making forms more flexible for screens with different resolutions - -commit 2e2251fd774a816c4de5232df3a37971fd2869bc -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Jun 21 18:49:30 2017 -0500 - - fix with adducts, can see # fragmented or ID'd in other topdown file - -commit 5394a7a6675ede0a05a9cd249c3d37063044f981 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jun 20 15:22:03 2017 -0500 - - bug fix - -commit 536a36bd94324b6e357322eda5fbfe392a72ed66 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jun 20 13:54:26 2017 -0500 - - can choose to omit adducts in counting # experimentals ID'd - -commit f862be821784be095857685d5f8d7322e519ccfc -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jun 20 13:40:08 2017 -0500 - - fix - -commit 21a1dffe411829cf6d92dc03f50deaed9437e0ba -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jun 19 17:00:18 2017 -0500 - - C alklylation for isotopic distribution - -commit 8770925e558d4f6a123fc50c4328b3eb6ea86ad6 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Jun 19 16:29:58 2017 -0500 - - added td filter options - -commit 27d64facd2ae2445ed657b5e059e3126ed6d6597 -Merge: 0ce1324 75ec60e -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Jun 16 17:31:39 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite into TD_BU_integration - -commit 75ec60eecc881c2b6917f40f5914cfe49bf899e8 -Merge: f31790f 7b5b361 -Author: Anthony -Date: Thu Jun 15 14:00:32 2017 -0500 - - Merge pull request #409 from lschaffer2/master - - unequal lysine counts for EF more than tolerance away - -commit 7b5b361fe1f7742d74745327638ca0f8ba41ce5f -Merge: c50c275 f31790f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jun 15 13:55:10 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit c50c27564f4b8893b22883b5d8738ea02703e6f9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jun 15 13:54:36 2017 -0500 - - unequal lysine counts for EF more than tolerance away - -commit 0ce132406a625dc3a82351a813aefee346c0bfe9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Jun 15 13:50:40 2017 -0500 - - calibration - -commit 7350c25e0dbe7b6824cb1702fd606df233b3e7d1 -Merge: 61672cd f31790f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Jun 13 17:41:11 2017 -0500 - - calibration - -commit 61672cd7d52c44ec67e4f45f4e45be4d68e8b6d3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Jun 2 10:53:14 2017 -0500 - - fixes - -commit f31790f3829ee094874f8386503283b658f14d5c -Merge: 62b4754 2ce1c28 -Author: Anthony -Date: Wed May 31 19:23:13 2017 -0500 - - Merge pull request #406 from acesnik/master - - Nomansland tolerance - -commit 2ce1c2812a260263b117da1a279cbfe38106137d -Author: Anthony -Date: Wed May 31 19:19:42 2017 -0500 - - include both combined and exclusive notes for venn diagram - -commit 76dd24b55b227bd9a93f9429509d6f5974188524 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 31 17:23:54 2017 -0500 - - custom adducts - -commit 96c20d4a0433a5e3c585cdcda9e0144ce03922ca -Author: Anthony -Date: Wed May 31 15:45:16 2017 -0500 - - Allow tolerance around sliding nomansland - -commit 0109131d97bc82255dcfcafa557807098ca9eac5 -Merge: 012eea1 62b4754 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 31 15:05:28 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite into TD_BU_integration - -commit 62b47547236bf64f2c09e3f0f6547181091a8e35 -Merge: 5232a35 3ef4f8b -Author: Anthony -Date: Wed May 31 15:02:34 2017 -0500 - - Merge pull request #405 from acesnik/master - - Start nomansland scaling after mass of CH2 or HPO3. Fix subsetting for quant venn diagram. - -commit 012eea15a477789d4e8222ef2897894ec20002cf -Merge: d11dc82 5232a35 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 31 13:56:57 2017 -0500 - - pull upstream - -commit 3ef4f8b88fe80de0185a74b9bb2c84579bc5a89e -Merge: cee927a 5232a35 -Author: Anthony -Date: Wed May 31 13:52:54 2017 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit cee927ac3ba3e66868cc478c5eb0304b7868475a -Author: Anthony -Date: Wed May 31 13:43:04 2017 -0500 - - Start nomansland scaling after mass of CH2 or HPO3. Fix subsetting for quant venn diagram. - -commit d11dc82b1ed7215050c6380dc823bc60b270c210 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 31 10:06:05 2017 -0500 - - linked proteoform references for TD - -commit 3cc4c76194eed5d802c48fb6bbe0aba423fc0a98 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 30 18:02:38 2017 -0500 - - changes - -commit 5232a355392fb5ff2ceb158c38abd344db65bc49 -Merge: 6a8b4ad 5ce8b0e -Author: Anthony -Date: Tue May 30 16:42:24 2017 -0500 - - Merge pull request #404 from acesnik/master - - Proteoform Suite Manual draft - -commit 5ce8b0ea090e2db734d39982ffaa25de01a4ba0b -Author: Anthony -Date: Tue May 30 16:38:49 2017 -0500 - - Proteoform Suite Manual draft - -commit 6a8b4add29d7b7fd9bdf4654b75a6ed776efe468 -Merge: 0148625 c46aee7 -Author: Anthony -Date: Tue May 30 11:54:17 2017 -0500 - - Merge pull request #400 from acesnik/master - - crash fix without quant - -commit c46aee7945de3098c41392dfbaf3b1c9eaa176db -Merge: b13aadd 0148625 -Author: Anthony -Date: Tue May 30 11:48:41 2017 -0500 - - Merge branch 'master' into master - -commit b13aaddeae436f5b22a3044b58991a19d9d6bc07 -Author: Anthony -Date: Tue May 30 11:46:20 2017 -0500 - - crash fix without quant - -commit 01486258dd1d8cd99d8533ed6dc4012ff038e874 (tag: 0.2.0) -Merge: be550b1 67826ad -Author: Anthony -Date: Tue May 30 11:22:00 2017 -0500 - - Merge pull request #399 from acesnik/master - - Modifiable PTM ranks, used in pf assignment. CH2/HPO3 for no-mans-land calculations - -commit 67826ad8e5fe022e173ddfa4b5a901c393b79f15 -Author: Anthony -Date: Sun May 28 18:36:41 2017 -0500 - - fixed # raw components in families; parallelized DGVExcelWriter - -commit 322e439961508b6ada7c048320e3092bea2db8c1 -Author: Anthony -Date: Sun May 28 17:47:31 2017 -0500 - - Revamped figs of merit for families; venn diagram info for quant in results - -commit c9a270696f06cec7c905a4159bffd5f9a607bb39 -Author: Anthony -Date: Sat May 27 19:05:51 2017 -0500 - - typo - -commit 5c73c334ec7508bbc93ed5759ad2cde1d5b83d62 -Author: Anthony -Date: Sat May 27 19:02:33 2017 -0500 - - Added verification components to experimental manual validation info. - -commit 8d202f7859223c4320674d69d395a60b0c998904 -Author: Anthony -Date: Sat May 27 18:42:08 2017 -0500 - - clarified quant detail - -commit 133c5b8890f5b18b308a2766b2167c27b593869f -Author: Anthony -Date: Fri May 26 19:00:02 2017 -0500 - - testing theo database - -commit beeb1c7d8c2199de112871267993f9421eeb44cb -Merge: 5a89a57 be550b1 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri May 26 13:32:51 2017 -0500 - - pull upstream - -commit 5a89a57bac4f1b17d4a65634d94242afb35f2599 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri May 26 10:14:48 2017 -0500 - - calibration - -commit f64bc86c156a9b8deef4e88ce4f08d054263e3e9 -Author: Anthony -Date: Fri May 26 01:55:08 2017 -0500 - - small change to cytoscript - -commit fa2d8a547fbb6512322217be5741a8c882382ee0 -Author: Anthony -Date: Fri May 26 00:44:40 2017 -0500 - - Information for manual validation using most abundant component - -commit bdf147c41b014d3d4cc2d735c471a6d5d5423751 -Author: Anthony -Date: Thu May 25 18:43:53 2017 -0500 - - stff - -commit b50a69e3ac55cbed5a40e0f48f13783e3b2c5841 -Author: Anthony -Date: Thu May 25 18:34:42 2017 -0500 - - Fixed bug in generating all ptm combinations. Save all tables - -commit b8e0ec99b50c46901359a1ca7154bc6f96e9d9ae -Author: Anthony -Date: Thu May 25 14:55:57 2017 -0500 - - Cytoscape color scheme changes - -commit dc5c332932ee4960bc5ffc1937417314ad92b6a7 -Author: Anthony -Date: Wed May 24 18:45:39 2017 -0500 - - Consistent behavior between forms and consistent code usage. updated heuristics for no-mans-land to start at mass of CH2 or HPO3. - -commit a521ede374bb2d89829839924a27328e21027e31 -Author: Anthony -Date: Wed May 24 02:00:14 2017 -0500 - - Fixes, filters, edited heuristics - -commit 2c464634a122eed4475590d9d3d0f0a2def642f4 -Author: Anthony -Date: Wed May 24 00:02:35 2017 -0500 - - testfixes - -commit c70e26fa4694a0f1b4ffb9bfcab22517d2b987c4 -Author: Anthony -Date: Tue May 23 23:42:44 2017 -0500 - - Allow loss of multiple PTMs. Allow requirement for proteoform without a specific mod (e.g. ammonia loss) - -commit 134add4b62dc3d0547a1c672de6da3ccaaa95b33 -Author: Anthony -Date: Tue May 23 22:59:29 2017 -0500 - - Raw ET histogram - -commit 87bbe56665303b993955a6a449e3bd8b880a6deb -Author: Anthony -Date: Tue May 23 18:38:50 2017 -0500 - - Modifiable PTM ranks; noMansLand is now based on CH2 and HPO3 models - -commit f40dafbf565af96379fe1167a6785899a6927bf3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon May 22 18:29:02 2017 -0500 - - better calibration with MM code - -commit 7bc9a7605f67fd0a425758060c8649625ce50dd7 -Author: Anthony -Date: Mon May 22 12:58:55 2017 -0500 - - use unloc mods for deltamasspeak possible assignments; include unidentified families in results counts; update unlocalized mod table on full run - -commit be550b186ebfe97812c4afd3f6302b8925cd04e7 -Merge: 4c39e82 c20d52e -Author: Anthony -Date: Mon May 22 11:23:13 2017 -0500 - - Merge pull request #397 from acesnik/master - - Unlocalized Modification and custom mod names - -commit c20d52e842519a66a95bd67f31788ae0a7ac3428 -Author: Anthony -Date: Mon May 22 11:05:59 2017 -0500 - - testfixes - -commit 591b822205cc0a46251031a944d901ba6f8ffaae -Author: Anthony -Date: Sat May 20 18:20:16 2017 -0500 - - Unlocalized Modification and custom mod names - -commit 4c39e82bee5b0fa9a10a8b47996eee647398cccc -Merge: faf400b f312e17 -Author: Anthony -Date: Sat May 20 15:33:48 2017 -0500 - - Merge pull request #396 from lschaffer2/master - - use ptmset dictionary look up for faster EE - -commit 3dab74b83fb52c3032133ee2c4b09059fcb0c7d0 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 18 19:14:00 2017 -0500 - - tests for match files - -commit b58bfe5cca291549d655b1f65982b829ae76a2a9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 18 19:01:24 2017 -0500 - - unnecessary test - -commit d9a31e024ef518fc51259bfefbfd7e7e210d689a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 18 18:58:07 2017 -0500 - - test fixes - -commit f312e1735cc0d1646cf1015c0245eb39d857c34c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 18 18:50:46 2017 -0500 - - display num T proteoforms if database loaded in with raw components - -commit 4a9270cb1094b9eb786a234211caa4e93583c804 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 18 18:48:51 2017 -0500 - - speed up EE with lookup - -commit 839d840710125d3f1073588a339a38b626386ab3 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 18 18:04:41 2017 -0500 - - auto peak acceptance with .txt list of delta masses - -commit 8cb5d0f6f9122ba3437f7e6404b3b754a8059e35 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 10 18:15:46 2017 -0500 - - can have more than one peak in window looking for averagine peaks within 0.005 mz units - -commit 5ed52e26ee49634b9a3e72c58cc7037f2ae66c17 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 10 17:56:39 2017 -0500 - - look for # peaks left/right of averagine peak for each charge state - -commit c2e3405c258baf4468865045075e57b4acfd0610 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 10 11:20:09 2017 -0500 - - can have large agg RT window & make sure don't add component repeats - -commit 414ccd4906d631693c3bc4098c9edfaaffcdf12b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 10 09:50:21 2017 -0500 - - can filter by max charge state signal to noise - -commit 47b84a633a30823ee688238d7ca62e4e44e687c1 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed May 10 09:34:34 2017 -0500 - - delete unused buttons - -commit c36406cccf4ea7cc8f33a52a83cb5989e9267bce -Merge: e03f82d faf400b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 9 19:48:08 2017 -0500 - - pull upstream - -commit e03f82d4b9b03a4f8b1b470ecd022eff8ecd7c45 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 9 19:41:40 2017 -0500 - - remove rel abundance (meaningless) and added S/N to excel sheet when calibrating - -commit 038d5bf25d1cd11b3414340a71e61d8b95a7f6dd -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 9 15:08:52 2017 -0500 - - added back in min relative abundance E filter - -commit c12e6102509d64576187a609cd25501085658a79 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 9 14:58:59 2017 -0500 - - don't include ETD pairs in determining FDR - -commit 26e1968c3372b4e6b8e51c3e43ac28ae8842a1fb -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 9 09:37:12 2017 -0500 - - td code cleanup - -commit faf400b5079f381843d9ef8e20394de84f8ff37e (tag: 0.1.16) -Merge: feb4f10 3cca14d -Author: Anthony -Date: Mon May 8 16:50:11 2017 -0500 - - Merge pull request #392 from acesnik/master - - Changed default cytoscape script colors - -commit 3cca14de709498f7610df60bfe4ba21542eb2e5c -Author: Anthony -Date: Mon May 8 16:38:40 2017 -0500 - - tough double cast test for big rational - -commit 5814c56c6bd33c08ea8386874c3502169598bf10 -Author: Anthony -Date: Mon May 8 16:08:47 2017 -0500 - - Changed default cytoscape script colors - -commit feb4f107494fd0770f9b8a6826db7c6b3aef9acd -Merge: 2dc7bcf 0a485db -Author: Anthony -Date: Mon May 8 15:34:52 2017 -0500 - - Merge pull request #391 from acesnik/master - - small bug fix in results summary cyto scripting - -commit 0a485dbc6d728bbb80806e8cc5ac2eadcedcf590 -Author: Anthony -Date: Mon May 8 15:31:22 2017 -0500 - - small bug fix in results summary cyto scripting - -commit 2dc7bcfbaa9bd845c2254538b92eca7e2e8ce81c -Merge: 177bf89 5736353 -Author: Anthony -Date: Mon May 8 13:47:16 2017 -0500 - - Merge pull request #390 from acesnik/master - - Mass-based spiral in cytoscape - -commit 5736353a76a14229275e83c6ce25593e58fbca15 -Author: Anthony -Date: Mon May 8 13:42:22 2017 -0500 - - Organization in CytoScript - -commit d1abffc9be1888725bffda5b12fc213578b961d2 -Author: Anthony -Date: Mon May 8 13:31:43 2017 -0500 - - Mass-based spiral in cytoscape - -commit 177bf895bb3b8b57bb33d053c91463c9093f3171 -Merge: babab0c f1e136f -Author: Anthony -Date: Fri May 5 15:42:16 2017 -0500 - - Merge pull request #389 from acesnik/master - - Save results during full run - -commit f1e136fbc897a70478dff3a08db00dbe378d48fc -Author: Anthony -Date: Fri May 5 15:33:48 2017 -0500 - - testfix again - -commit 0842eec558bc86cbc14d5c0c82a13f243c2b2271 -Author: Anthony -Date: Fri May 5 15:30:32 2017 -0500 - - testfix - -commit 552d4d507db051c0a2024a09509c491cdf741ef8 -Author: Anthony -Date: Fri May 5 15:26:20 2017 -0500 - - test - -commit 3546929a7f13abf28b23d71ddf383e165b2ecee5 -Author: Anthony -Date: Fri May 5 15:18:18 2017 -0500 - - another fix - -commit 18e5fafb909e5fb81336e2530aa4f92e9f7317e6 -Author: Anthony -Date: Fri May 5 14:57:59 2017 -0500 - - testfix - -commit 94ab2c58407c7173286ebbffc620383ecf1d172e -Author: Anthony -Date: Fri May 5 13:53:37 2017 -0500 - - Save results during full run - -commit c5b40d6529d8746b34eb6d638d3e76718ff7f15d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri May 5 10:00:37 2017 -0500 - - deocy proteoform families for topdown - -commit 348d33b7ac73e18dca7ca09d3fd0c2f64d97712f -Merge: bdeb5ba 6759c79 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 4 17:29:42 2017 -0500 - - Merge branch 'TD_BU_integration' of https://github.com/lschaffer2/proteoform-suite-1 into TD_BU_integration - -commit bdeb5ba1bd16b2cdb2300d431a7ea01b1381fd82 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 4 17:29:09 2017 -0500 - - appveyor errors - -commit 6759c797178452d7b36c660991e9847b791fda5e -Author: Michael Shortreed -Date: Thu May 4 14:16:49 2017 -0500 - - Aggregate TopDown testing - -commit 677ab163d88c7e43b96dfe69c5199b4d56532bea -Merge: dba1012 babab0c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 4 10:20:28 2017 -0500 - - merge upstream - -commit dba1012d9bdf32c26354cc6eaa887b74927348b4 -Merge: 624a5f1 6945fe9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu May 4 09:36:13 2017 -0500 - - mrs changes - -commit 6945fe91c685fa062c375427e1a71e892d0e5c3e -Author: Michael Shortreed -Date: Tue May 2 15:30:41 2017 -0500 - - minor aggratetd tweaks and start test - -commit 624a5f17aa90273e87a1cf37713578e985d38086 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 2 15:30:40 2017 -0500 - - aggregate td hits - -commit c6e516f01be746dcdad9e0ca0681814df855cf68 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 2 12:46:38 2017 -0500 - - package - -commit babab0cfeadef4b59ccff97fb6dc4181ed043e8b -Merge: d2ae172 8bdc8bf -Author: Anthony -Date: Tue May 2 12:42:44 2017 -0500 - - Merge pull request #385 from lschaffer2/master - - decoy proteoform communities - -commit 8bdc8bf1d38add074823cdd899340737bbc0ce54 -Merge: 4d19a76 d2ae172 -Author: Anthony -Date: Tue May 2 12:40:19 2017 -0500 - - Merge branch 'master' into master - -commit 1183313f3f4b8b31dd3a5916c76018eba8f8930e -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 2 12:21:11 2017 -0500 - - display all RTs - -commit 4d19a7676fa188ca1329c7b3c3cfe6b1211b5c78 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 2 12:10:06 2017 -0500 - - fixed test -- need to clear peaks before rerunning accept delta mass peaks - -commit 03a5d26739a9a96b3850e0ee45b53036e12b61fc -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 2 11:55:19 2017 -0500 - - fixed up aggregation, one based positions - -commit 717131c65172be8d28eaecd0913a20622c2ab79f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue May 2 10:45:45 2017 -0500 - - if decoy could be in 2 peaks, choose peak with higher count - -commit 29b1b53d955873cb05ffaf536449172b7c486a1e -Author: Michael Shortreed -Date: Tue May 2 10:26:29 2017 -0500 - - added C-score set min score for aggregated topdown - -commit a5855edd80f84c987cdbc7ff6c6e6c3b465dff95 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon May 1 18:40:25 2017 -0500 - - added testing & small changes - - one line - -commit 6caa641cb4a53c7c67a951f53491c0ed0203076b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon May 1 10:11:29 2017 -0500 - - fixes in topdown reader - -commit 1bb17d34cf781296560c8ad374ba2a61b9842dc0 -Author: Michael Shortreed -Date: Mon May 1 09:33:10 2017 -0500 - - comments in topdown reader - -commit e8c8e189c2a3932b51ea65bbf4bc69e6f6615415 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Sun Apr 30 16:03:43 2017 -0500 - - EE cleared if make new T database --> ptmsets could have changed - -commit 43f22f7928e7e48fd2ff2b32e99b3c4bee96b22f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Sun Apr 30 15:44:55 2017 -0500 - - made fixes to decoy families, fixed tests - -commit d2ae17273f0a77046a21ed906503ed04e2cf9bfd -Merge: 0ac9f79 2cb56d8 -Author: Anthony -Date: Fri Apr 28 14:14:05 2017 -0500 - - Merge pull request #384 from acesnik/master - - Download UniProt ptmlist if only a database is specified without a PTM list - -commit 2cb56d85f1c162ad5a14e4754340189e29f66314 -Author: Anthony -Date: Fri Apr 28 14:11:25 2017 -0500 - - Download UniProt ptmlist if only a database is specified without a PTM list. - -commit 20eb7784ba1868623f296b706b1844836de0b033 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Apr 28 13:07:14 2017 -0500 - - decoy communities to detect identified decoys - -commit 8cb84f352ef2961beda077faf687e3b51c303e65 -Author: Michael Shortreed -Date: Fri Apr 28 12:29:39 2017 -0500 - - some test - -commit 0ac9f79cf34a5f7432d238348f4a8059f082174c -Merge: 80d7974 37d47de -Author: Anthony -Date: Fri Apr 28 11:29:58 2017 -0500 - - Merge pull request #382 from trishorts/master - - added test compress neucode harmonics; deleted unused component reader code - -commit 37d47def0832ff1e6d8c26bd495687ef8347daef -Merge: 51741bc 80d7974 -Author: trishorts -Date: Fri Apr 28 08:59:27 2017 -0500 - - Merge branch 'master' into master - -commit 51741bcecb0c48b62ecb312f0db375b52e35efa8 -Merge: 3fc4bf8 e7ce49e -Author: Michael Shortreed -Date: Fri Apr 28 08:55:36 2017 -0500 - - Merge branch 'master' of https://github.com/trishorts/proteoform-suite - -commit 3fc4bf8a821e0b7b46943a6fc993de6bab6a43c0 -Author: Michael Shortreed -Date: Fri Apr 28 08:53:37 2017 -0500 - - test merge neucode harmonics and delete unused code in component reader - -commit 80d7974ac785427d7a2c0f2343cf24a1fd3f0a40 -Merge: 0095811 5d2656b -Author: Anthony -Date: Thu Apr 27 15:37:20 2017 -0500 - - Merge pull request #379 from lschaffer2/master - - keep protein names if combine sequence - -commit 5d2656b74d03b48b3fd55a61afd3dff38eca662d -Merge: a599a4f 0095811 -Author: Anthony -Date: Thu Apr 27 15:34:37 2017 -0500 - - Merge branch 'master' into master - -commit 00958118a050f2ab82930059557f0edfec7978fe -Merge: 32b92f4 e7ce49e -Author: Anthony -Date: Thu Apr 27 15:34:28 2017 -0500 - - Merge pull request #380 from trishorts/master - - test merge missed monoisotopics and harmonics - -commit e7ce49e1b8a786ad36f34f1786f20825eb7ec25a -Merge: cc884bd 32b92f4 -Author: trishorts -Date: Thu Apr 27 12:56:56 2017 -0500 - - Merge branch 'master' into master - -commit cc884bd1d46f97a5585cd8f869f68a5a014533b6 -Author: Michael Shortreed -Date: Thu Apr 27 12:54:32 2017 -0500 - - test merge missed monoisotopics and harmonics - -commit a599a4f44fa2713e283acfa07410a1d2656367dc -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Apr 27 09:39:04 2017 -0500 - - keep protein names if combine sequence - -commit 32b92f4d2f51616f1a250e67ed6b5ea7385612d0 -Merge: 43c73c3 dae76fe -Author: Anthony -Date: Thu Apr 27 04:27:52 2017 -0500 - - Merge pull request #378 from acesnik/master - - Modified some heuristics for a new (somewhat smaller) GPTMD database - -commit dae76fe0fabaf8f02c75cb7b7049c7fb94060147 -Author: Anthony -Date: Thu Apr 27 04:25:15 2017 -0500 - - Modified some heuristics for a new (somewhat smaller) GPTMD database. Also fixed a few bugs, including clearing families using the clear_families method rather than one that doesn't wipe the experimental identifications. - -commit 88f0458339e5b6b4c97de89901464953e9249a96 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 26 20:08:20 2017 -0500 - - fixed up ttd relations - -commit 43c73c3e6249ed55665f07903f3f8e964db7a6ea -Merge: fb9b218 1ea4fb1 -Author: Anthony -Date: Wed Apr 26 18:04:13 2017 -0500 - - Merge pull request #375 from acesnik/master - - M retention bug fix - -commit 1ea4fb10195ba43ae7c6935d2d2fde4e02f41ab5 -Author: Anthony -Date: Wed Apr 26 18:00:04 2017 -0500 - - M retention bug fix - -commit fb9b2183cef10f1a6737068bf8860c9ba28ba472 (tag: 0.1.15) -Merge: 93994a8 398abd1 -Author: Anthony -Date: Wed Apr 26 17:07:56 2017 -0500 - - Merge pull request #374 from acesnik/master - - ET/EE relation table filters; stepthrough info button - -commit 398abd10ab122e4a104f40d4b04a728d4dad270f -Author: Anthony -Date: Wed Apr 26 17:04:22 2017 -0500 - - test fix - -commit 6bf78089805a321ff601fc9fd7770ce87d522e50 -Author: Anthony -Date: Wed Apr 26 17:00:21 2017 -0500 - - test and bug fix in limiting large ptm sets - -commit 9c87e28fe2d9e663edeeae8cc8aa80732c19cbcc -Author: Anthony -Date: Wed Apr 26 16:36:18 2017 -0500 - - fix - -commit 2aac081f996507aad88d4d5770aca8d072da1e4f -Author: Anthony -Date: Wed Apr 26 16:33:41 2017 -0500 - - Generalize null list of datagridviews. - -commit 1515d8c4dce00c20503e2628b109c873de96b185 -Author: Anthony -Date: Wed Apr 26 16:20:24 2017 -0500 - - Added back step through button and added stripline option for ET - -commit 63c85d32e47177069187ecafb8a6326f0bd1891e -Author: Anthony -Date: Wed Apr 26 15:31:35 2017 -0500 - - ET/EE table filters - -commit 93994a86db359e1a8a8aca9871dc2b8dae9e26ce (tag: 0.1.14) -Merge: 4cb41ed 7108302 -Author: Anthony -Date: Wed Apr 26 16:26:51 2017 -0500 - - Merge pull request #373 from lschaffer2/master - - simplified export excel, added clear list of later data, changed 1 li… - -commit 7108302d7101cf435dc5dfe1db32b498855de27d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 26 15:07:20 2017 -0500 - - fixed tests --> need to set relation to accepted, not just peak - -commit d99825c1ce9db1883fc2b49a04c92a70969d2935 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 26 14:50:49 2017 -0500 - - simplified export excel, added clear list of later data, changed 1 line from peak accepted --> relation accepted - -commit f5ecd51bef98ae2d6b48a8be3e1d304336529eb9 -Merge: 97233d3 4256719 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 26 14:00:53 2017 -0500 - - merge upstream - -commit 4cb41edf7c0fbc8e15a3c1b6724107e300093527 -Merge: 4256719 e8e8042 -Author: Anthony -Date: Wed Apr 26 11:36:57 2017 -0500 - - Merge pull request #371 from lschaffer2/master - - make ptmset evertime, prevents crashes if theo database or PTMs change… - -commit e8e8042b05e835f28119ba5d76d23808989ee6a7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 26 09:38:39 2017 -0500 - - make ptmset evertime, prevents crashes if theo database or PTMs change when loading new T database - -commit 4256719b0a3d908269a3d7b54f0a7594ccb09f5b -Merge: c92042f aa85603 -Author: Anthony -Date: Wed Apr 26 00:30:31 2017 -0500 - - Merge pull request #370 from acesnik/master - - Remove serialization; implemented Leah's bug fixes - -commit aa856035047809b3e12d126127d1bc00f994b603 -Author: acesnik -Date: Wed Apr 26 00:25:28 2017 -0500 - - Fixed decoy stuff. Sketched in ET/EE table control. - -commit 26e8d4e149134676d1c0956982595d269f02d7cd -Author: acesnik -Date: Tue Apr 25 22:22:14 2017 -0500 - - update mzLib and remove one more serialization thing - -commit 13d5f8487a598919f899690ea0ab9da2f7389418 -Author: acesnik -Date: Tue Apr 25 21:55:41 2017 -0500 - - Bye, bye, save & open - -commit 97233d3e23c87b4dc4c8137f57cffcad7a6978ba -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Apr 25 17:27:06 2017 -0500 - - small notch changes - -commit c92042fbc019219db3a3e841fd8d96464677854e -Merge: 4ed77e8 8f38c5d -Author: Anthony -Date: Tue Apr 25 15:18:06 2017 -0500 - - Merge pull request #367 from acesnik/master - - Make Lollipop fields instantiated, rather than static, so they can be serialized easily - -commit 8f38c5d89e04b508d5f072592773118ab2090279 -Author: Anthony -Date: Tue Apr 25 15:14:58 2017 -0500 - - Test fix - -commit 8185be539dcc5aad3c078417c0fdd2cc7782cd40 -Author: Anthony -Date: Tue Apr 25 15:10:52 2017 -0500 - - wrapping up serialization. Performance is poor. - -commit 578d7a6ee6f9de825382a29b1d8b634c430f56b5 -Author: Anthony -Date: Tue Apr 25 13:10:44 2017 -0500 - - TheoreticalDatabase Save/Load now working - -commit b60dedf6ad67e3421bfc6e6ad7e8901352a25458 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Apr 25 11:51:17 2017 -0500 - - PTM fixes for reading in topdown PTMs, also added comments - -commit 4b5a554a1c8797dbd7890d92f64825aec2d94a35 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Apr 25 11:15:32 2017 -0500 - - small fix for matching topdown accessions - -commit 23e7e7e83f66db8a30ec4af3469bade2bb0fa70d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Apr 25 11:13:51 2017 -0500 - - add warnings/fixes for topdown accessions and modifications not in database - -commit f442761df7d0a361d3fd83583f86d01cbec4042b -Author: Anthony -Date: Mon Apr 24 21:35:15 2017 -0500 - - Removing circular references from serialization. - -commit 053eb67d36d4867c87a71d9274e7f6f61f431ca5 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 24 19:18:12 2017 -0500 - - fixed up td cytoscape labels - -commit c208b1dff7b0e72681578c5c29f213b86de97f8b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 24 18:18:25 2017 -0500 - - cleaned up td accessions - -commit c369edaa269208746310e19fa69536d33316b05b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 24 17:30:44 2017 -0500 - - fixed up clearing/topdown in families - -commit 8bdbf23fcba23d7dbe6aab641ccc73af4d304603 -Merge: 19bdff8 4ed77e8 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 24 11:33:08 2017 -0500 - - merge upstream, identify experimentals using topdown proteoforms - -commit 19bdff8c8803e389cf5b426c8711e8642a58577f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 24 09:51:16 2017 -0500 - - display td relations - -commit cd8e00a4b9cdaef349c27287a85a1a2531e499fb -Author: Anthony -Date: Sun Apr 23 20:40:29 2017 -0500 - - stuff - -commit d0b8d5cd7ac4cba5bf01fc94c40741baefe05983 -Author: Anthony -Date: Sun Apr 23 20:21:53 2017 -0500 - - Updated mzLib packages. RAM usage improvements for making TheoreticalDatabase. Can't serialize nested objects well, apparently. - -commit 9271fcdd3b7b27ae18badf52e481af306b373d54 -Author: Anthony -Date: Sun Apr 23 00:50:34 2017 -0500 - - again - -commit 0c4d7e71588badd31833f741508a020ddae351d4 -Author: Anthony -Date: Sun Apr 23 00:48:17 2017 -0500 - - Fix test - -commit 0827475d78c20b38a39fa490ed8ddb064f9df2f9 -Author: Anthony -Date: Sun Apr 23 00:36:38 2017 -0500 - - Require modifications for theoretical database creation. - -commit f700cc51af7ad0639aeea43a1a97806a73fdd0ef -Author: Anthony -Date: Sat Apr 22 22:28:03 2017 -0500 - - slight refactor - -commit 594d834bde9694302f0ae8941e9bdae0c1583488 -Author: Anthony -Date: Sat Apr 22 22:24:07 2017 -0500 - - Break out TheoreticalDatabase code, so we can load in that data from save and load later. - -commit 1dd34cd1d28fc493520ef5d18c24f33754dc8afd -Author: Anthony -Date: Sat Apr 22 21:22:45 2017 -0500 - - Cleanup - -commit dde71d0aeb00d764fe627fcaa7054c53590b9ec3 -Author: Anthony -Date: Sat Apr 22 20:38:41 2017 -0500 - - Improved raw components form. Save & open works with components for demonstration. - -commit 82e0d59fc85663aab4654ca395206e2782fecb36 -Author: Anthony -Date: Sat Apr 22 17:56:05 2017 -0500 - - Disenable save and open for now. - -commit bdf9e029bbdf4c11931c342f0b8779ae9c5e50f7 -Author: Anthony -Date: Sat Apr 22 17:54:59 2017 -0500 - - Make Lollipop fields instantiated, rather than static, so we can serialize the class and save it. - -commit 4ed77e8ff1fc98d2937036aa94de1a321f4f454d -Merge: c4dc791 4dc1021 -Author: Anthony -Date: Fri Apr 21 15:25:10 2017 -0500 - - Merge pull request #366 from acesnik/master - - Stability improvements for quant; simplify ComponentReader by using Lollipop.find_neucode_pairs - -commit 4dc10215b2cc7cbccf5d581d1c47f32514cf785a -Author: Anthony -Date: Fri Apr 21 14:02:54 2017 -0500 - - little changes - -commit 1ccbe3f4760fe168381a345489d66983d5a183b1 -Author: Anthony -Date: Fri Apr 21 13:38:18 2017 -0500 - - Update mzLib. Small witespace edits - -commit 2a7379429ed2e65bb899faee334aa288e98422f3 -Author: Anthony -Date: Fri Apr 21 13:34:23 2017 -0500 - - Change ComponentReader over to using the Lollipop neucode method. - -commit 8dab9bed176829a3a84c4b5c37ba04e333cf6bf8 -Author: Anthony -Date: Thu Apr 20 16:11:05 2017 -0500 - - Stability improvements for quantitation and organization for various pieces of GUI code - -commit b9af8219b577ee5f96219d84f7427efa0c9996f8 -Author: Anthony -Date: Wed Apr 19 18:40:25 2017 -0500 - - Reset quant if redoing biorepintensities. Added option to calculate GO Term enrichment from detected background set. - -commit 0b5fb387fd22a8cdda24749d75e3d47be18d5e3a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Apr 21 11:00:52 2017 -0500 - - can change biorep of id file - -commit 6071571313499bdd3c2b795e3ba046221449d4d0 -Merge: a18416d c4dc791 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Apr 21 09:57:46 2017 -0500 - - merge upstream - -commit c4dc79124289c2e3780aceb6b2b902f75f747ede -Merge: 44dec7a 77c65cf -Author: Anthony -Date: Wed Apr 19 14:49:31 2017 -0500 - - Merge pull request #361 from acesnik/master - - Fixed bug in setting ptm set rank sums in proteoform which caused ET relation inconsistencies - -commit 77c65cf1a68e2c9b301993101edaa3b46003ea45 -Author: Anthony -Date: Wed Apr 19 14:38:45 2017 -0500 - - Community clear tests - -commit ebd5e7579e787871e2e64354f8452c38c119813b -Author: Anthony -Date: Mon Apr 17 14:08:06 2017 -0500 - - Fixed bug in setting ptm set rank sums in proteoform, which was causing ET relation inconsistencies. Also changed peak building heuristic. - -commit 44dec7af607bacb04c108b10c7bcd355a18b13bf -Merge: 5a1c4ff 40d8d4a -Author: Anthony -Date: Wed Apr 19 11:54:01 2017 -0500 - - Merge pull request #360 from lschaffer2/master - - added back in 0.1 level dictionary for ptm sets - -commit 40d8d4a34a8f2d67097734b5deed99c8f97986a2 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 19 09:32:26 2017 -0500 - - added back in 0.1 level dictionary for ptm sets - -commit 5a1c4ff471b2db4020e3db3fd1f5563e2d321185 -Merge: c1b3c99 edb3d65 -Author: Anthony -Date: Tue Apr 18 11:10:08 2017 -0500 - - Merge pull request #356 from lschaffer2/master - - ET speedup for checking ptmsets - -commit edb3d65279e2cd59326b2e5c3289250cf6fecf8d -Merge: 78f857f c1b3c99 -Author: Anthony -Date: Mon Apr 17 15:07:12 2017 -0500 - - Merge branch 'master' into master - -commit c1b3c99d7d48afd0be717efb734d63775e782037 -Merge: 2a07023 dee6660 -Author: Anthony -Date: Mon Apr 17 15:06:43 2017 -0500 - - Merge pull request #358 from trishorts/patch-1 - - Update README.md - -commit dee6660673519cc67e46e5f3e2f8c8872467b642 -Author: Anthony -Date: Mon Apr 17 15:03:21 2017 -0500 - - Update README.md - -commit 78f857fc26bf1f554c6cb8e6315b9afd58c20a8f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 17 15:01:26 2017 -0500 - - need to clear agg proteoforms if shift masses - -commit 735d692460bd7e0aa141ead589649d886b628686 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 17 14:52:44 2017 -0500 - - moved 1 line out of loop - -commit a18416d1bbe4add6c35168e65962ab615708c622 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 17 14:47:27 2017 -0500 - - fixed merge conflicts - -commit 1773b86125b6a74259d1f40960d2c5d23dcb499b -Author: Anthony -Date: Mon Apr 17 14:38:09 2017 -0500 - - Update README.md - -commit f74fe153858dabb0116c14a0867ede1f638732c1 -Author: Anthony -Date: Mon Apr 17 14:36:00 2017 -0500 - - Update README.md - -commit b1011fda48045ee20aab5452af4818cde7c53710 -Author: Anthony -Date: Mon Apr 17 14:35:06 2017 -0500 - - Update README.md - -commit 5960c18156fa530b8675b06df4d13a96c6c5ec9e -Author: trishorts -Date: Mon Apr 17 14:32:11 2017 -0500 - - Update README.md - - system requirements - -commit cad8dd7363dd5f6c7cd63548775e73e0904e3f92 -Merge: d252712 2a07023 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 17 12:14:27 2017 -0500 - - small changes to prevent crashes - -commit f8b916dc6d092d225d236d3d908596c594c5d8f1 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 17 12:07:07 2017 -0500 - - fixed up notch search, BU lim search, & auto peak acceptance - -commit 2a070230dc1ebb235b6b4fd09ee43b1f611f86fa -Merge: 5103897 d419ca1 -Author: Anthony -Date: Thu Apr 13 16:35:48 2017 -0500 - - Merge pull request #355 from acesnik/master - - EF bug fix; add variable ox only if checked - -commit d419ca1b10e2f98834abee67ecaf0b2b7a533c87 -Author: Anthony -Date: Thu Apr 13 16:27:16 2017 -0500 - - Clear variable oxidations if remaking the database - -commit d25271256e722db0de7d1b657b7b186c7647de07 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Apr 13 13:06:06 2017 -0500 - - ET speedup for checking ptmsets - -commit f14f28508ad7045eeed11035d1377665163640aa -Author: Anthony -Date: Thu Apr 13 12:23:09 2017 -0500 - - Fixed EF bug found by @lschaffer2 and add variable oxidation to all modifications only if checked. - -commit 3101767c1d0079a0eb3952a18d2277c49b5536b4 -Merge: 76558d0 5103897 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Apr 13 11:57:41 2017 -0500 - - added upstream changes - auto ET id - -commit 76558d0287cf18f12aca3fd0e7c15bf9d2d81822 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 12 10:08:33 2017 -0500 - - mods - -commit 7b1d3c1b907ea191d1886cf4b469bdd4879e43f0 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 12 09:56:59 2017 -0500 - - merge orphans/within family by RT, update mzlib - -commit 510389744ba7efd6dc450972c0426a811f0261b4 -Merge: a4e5b08 d30e9f8 -Author: Anthony -Date: Tue Apr 11 23:25:27 2017 -0500 - - Merge pull request #354 from acesnik/master - - typo fix - -commit d30e9f8c4ef5e4c4ce94efe5c5ab0619d5e50d81 -Merge: d590ee8 a4e5b08 -Author: Anthony -Date: Tue Apr 11 23:23:31 2017 -0500 - - Merge branch 'master' into master - -commit d590ee8e6df3a3d2c5321b83822500682ed2f2b1 -Author: Anthony -Date: Tue Apr 11 23:22:53 2017 -0500 - - typo fix - -commit a4e5b08dfcb2e8a2d13078843e5f04e21460c173 (tag: 0.1.13) -Merge: f848573 31e607d -Author: Anthony -Date: Tue Apr 11 22:48:58 2017 -0500 - - Merge pull request #348 from acesnik/master - - Reworked exp. proteoform identification; variable methionine oxidation; ET improvements - -commit 31e607d9d91e7d0f58fb19e88dfee76820e7a3b9 -Author: Anthony -Date: Tue Apr 11 22:46:53 2017 -0500 - - comments - -commit 55d729e58a5dd536304a133fe9d51c5f5821f4c4 -Author: Anthony -Date: Tue Apr 11 22:46:19 2017 -0500 - - Added a few comments - -commit cecdfc5f0ab4cb60616684e43a8423d1eedac5c5 -Author: Anthony -Date: Tue Apr 11 22:30:44 2017 -0500 - - Tested read_mods and group_by_seq - -commit b8db34e2483dcbbf47d8cf260527b6969a03e543 -Author: Anthony -Date: Tue Apr 11 21:54:27 2017 -0500 - - some reorganization of correction factors; filled out met oxidation tests - -commit 8bc7e8799af2b60d6908def7ab8a1863c64d3d8f -Author: Anthony -Date: Tue Apr 11 21:28:25 2017 -0500 - - fixed remaining tests. tested variable methionine ox. - -commit adf2d6f48794ee4812ed8b860f072750492bf3ec -Author: Anthony -Date: Tue Apr 11 18:04:38 2017 -0500 - - fixed relation tests - -commit 02290d54e021f39495b97fc3cef320b0138d7626 -Author: Anthony -Date: Tue Apr 11 15:17:30 2017 -0500 - - parallelized ef - -commit 79667dc3f3613cbf24ac2263e2b474dcb349bced -Author: Anthony -Date: Tue Apr 11 15:01:12 2017 -0500 - - Test fixing - -commit 767014597871d0b7c2c25d8e121376a6d2d1498c -Author: Anthony -Date: Mon Apr 10 21:21:44 2017 -0500 - - Proteoform family dgv cleanup - -commit 85ee99799885107f0cabe6523c4187c265e43aa9 -Author: Anthony -Date: Mon Apr 10 20:52:43 2017 -0500 - - More DGV improvements. - -commit b1f64b3e50b111998942f93da084cca664ff27a8 -Author: Anthony -Date: Mon Apr 10 18:42:27 2017 -0500 - - Clean up datagridviews - -commit 1be02620fc3bf1bc5ccb55e238cc6d2b47c56c69 -Author: Anthony -Date: Fri Apr 7 18:00:30 2017 -0500 - - Remove MassDifference class to simplify ProteoformRelation. Added missed monoisotopics. - -commit 89186d4e6f48128bfd6c60132398cc9521a841d9 -Author: Anthony -Date: Thu Apr 6 23:57:18 2017 -0500 - - Code cleanup - -commit ae1b6c8713b19a04c43c92bbc784804691f6b592 -Author: Anthony -Date: Thu Apr 6 23:48:20 2017 -0500 - - Display class for proteoform relations - -commit 0272c322c7099b136748b6988df8a15a666c9644 -Author: Anthony -Date: Thu Apr 6 21:30:20 2017 -0500 - - starting to fix tests - -commit 4e5671dca0092b129a4f5fc9936cb771cf994099 -Author: Anthony -Date: Thu Apr 6 18:35:11 2017 -0500 - - Refactor RelationUtil. update mzLib - -commit 42c32584f5536f6b129a2f7b83cfb09f3a9c0d21 -Author: Anthony -Date: Thu Apr 6 18:08:16 2017 -0500 - - Fix missing unmodified connections. Allow variable methionine oxidation. - -commit 0cce00e3c0c80ecdbf28497d83ffeac2ac256ef8 -Author: Anthony -Date: Thu Apr 6 01:09:16 2017 -0500 - - Fixed the [missing isoleucine + ox] bug - -commit d77c63302b41f98e453df53a57b9cf5bba5123f0 -Author: Anthony -Date: Wed Apr 5 23:59:45 2017 -0500 - - Choose best ET pair based on score of candidate relations - -commit 27f74c5ed1d917190158c012565406a89474d061 -Author: Anthony -Date: Tue Apr 4 16:32:06 2017 -0500 - - Bring lots of ET connections are back. Orderby rank after deltaM - -commit fd6a442d0d6cea3d322572d4cd3562a21a052e2b -Author: Anthony -Date: Tue Apr 4 11:53:22 2017 -0500 - - GO term analysis by unique accession - -commit 1f1e30717202ac56f590f6266b47fff3c70d6e5b -Author: Anthony -Date: Tue Apr 4 11:52:31 2017 -0500 - - added in some of Leah's changes - -commit 901359b3bbe5423b2c6835e94b0e20ecb3921e56 -Author: Anthony -Date: Fri Mar 31 11:29:51 2017 -0500 - - Slight change in heuristics - -commit cd76f07ee6891a2ecaeca9d914f22a5af05bf6ba -Author: Anthony -Date: Thu Mar 30 00:05:23 2017 -0500 - - Changing water adduct over to "unlocalized" - -commit ffadefa13787b9f3a72a8eea6c640618bc9dba4e -Author: Anthony -Date: Wed Mar 29 23:57:22 2017 -0500 - - Count all ptm entries in database for ranking, not unique set. Allow ties in ranking. Determine whether ptmset is within EE relation tolerance with the absolute value of the set mass, since the deltaM value only has positie sign there. Reset assignment variables when redoing EE. - -commit e73ef31514571f92605e87813c0ee92bcc4d767c -Author: Anthony -Date: Wed Mar 29 21:47:09 2017 -0500 - - Reworked possible PTM assignment in DeltaMassPeak to streamlineassignment and to have that be more accurate. Fixed issue with expected theoretical sequence by cleaving methionines before constructing expanded protein entries. Get rid of missing mods that can't be degradation. Penalize two-PTM sets. - -commit 765e7aa090d36a5ebbe0d1d1d4dd34ccde4d9b45 -Author: Anthony -Date: Wed Mar 29 13:07:18 2017 -0500 - - Consider multiple ET pairs with the same deltaM_rank - -commit ad6b513e71f052435c76cfeed440a7f1bbe86e05 -Author: Anthony -Date: Wed Mar 29 01:06:40 2017 -0500 - - Consider relations to be PtmSets, and assess the likelihood of those sets as the rank-sum of the modifications - -commit 24e81d33ccfa157b4d92b5a7566bdf69519946ea -Author: Anthony -Date: Tue Mar 28 21:14:34 2017 -0500 - - Make cytoscape load_styling more consistent with script. - -commit 0e894d265ec3da60c4603f58e315cb0a94c022fb -Author: Anthony -Date: Tue Mar 28 20:51:32 2017 -0500 - - Pick ET with ptm_set rank sum of nearest theoreticals. Unmodified gets lowest rank by default. Using linked list for proteoform_reference rather than just the last proteoform, so that EE pairs can be assessed and to simplify accessing theoretical fields. - -commit f8485732ccef24182062688b700b73f195248270 -Merge: cc95026 9f814d7 -Author: Anthony -Date: Tue Apr 11 14:59:53 2017 -0500 - - Merge pull request #351 from lschaffer2/master - - only accepted experimental proteoforms used - -commit e143dbced204f46b37bb9dd4092ecb034fa06428 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Sun Apr 9 14:57:15 2017 -0500 - - AC's suggestions - -commit 9f814d745805da0272003ba53e665b231a15d25a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Sat Apr 8 13:31:35 2017 -0500 - - only accepted experimental proteoforms used - -commit 43f0a66521ecbba712985583372a7106b95a91be -Merge: 444f4b2 cc95026 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Apr 7 17:40:22 2017 -0500 - - merge upstream changes - -commit cc9502661f22f2966b4c49f1477f2afd89a2d37a -Merge: 78e5307 a06c0c8 -Author: Anthony -Date: Thu Apr 6 17:30:02 2017 -0500 - - Merge pull request #347 from lschaffer2/master - - small GUI changes, plot decoy histograms, fix EF - -commit a06c0c8c86d93058975142aa590ec83ae133dfac -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Apr 6 12:37:18 2017 -0500 - - small GUI changes, plot decoy histograms, fix EF - - unenable cb if no decoy relations - -commit 444f4b2a072a87876c0d0e173c9ffc4292b2427d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 5 10:07:31 2017 -0500 - - ef relations - -commit 97a204ab6437a6156b5ad77ef720dc799d84df4e -Merge: 85fb76c 78e5307 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Apr 5 10:02:45 2017 -0500 - - upstream - -commit 85fb76cdfe852e3f00e27b4def6ffd58eaa9b70c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Apr 4 17:15:35 2017 -0500 - - fixed EF issues - -commit 78e5307282006d21a02e3bdffe75df5da8692d7f -Merge: 73eccc7 a6b14bd -Author: Anthony -Date: Tue Apr 4 16:36:33 2017 -0500 - - Merge pull request #344 from lschaffer2/master - - speed up saving dgv to excel file - -commit a6b14bd4be558bc0ea83e40e20a11b2ca711d77c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Apr 4 13:52:16 2017 -0500 - - speed up saving dgv to excel file - -commit 60ada6def9c78634f9438fa2899587db9445620b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 3 19:49:27 2017 -0500 - - fix number format issue excel - -commit 0a49932413e9bb3aa774010a69313aaaa142aeac -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Apr 3 19:21:57 2017 -0500 - - moved ET/EE shared methods, sped up dgv saving - -commit 2e72946457385dc278252e43e65f163a10df1167 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Sun Apr 2 16:01:32 2017 -0500 - - sped up calibration excel writing - -commit bf6d9a1098663d440a00b91a198187ec580f3d27 -Merge: a34b35e 73eccc7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 31 18:11:49 2017 -0500 - - merge upstream conflicts - -commit a34b35ee6bc3a106c128696fc4510a8af0e31dbe -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 31 18:11:07 2017 -0500 - - upstream tests - -commit 73eccc7371cd9c57bd052063ebe39e408c51c695 -Merge: 87133b6 13713dd -Author: Anthony -Date: Fri Mar 31 11:33:15 2017 -0500 - - Merge pull request #342 from lschaffer2/master - - sort booleans - -commit 13713dda9d9f00376942cd0068f219dd369a04f1 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 31 11:20:54 2017 -0500 - - sort booleans - -commit 07d3b26dc7afe241756b73dbf4fb907dfa309c88 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 31 11:03:24 2017 -0500 - - auto peak acceptance - -commit 73163b7d0bc03685d41f0bc20efd4f1eb89843a7 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Mar 30 12:54:16 2017 -0500 - - merge RT and EF fixes - -commit 5282dc911b6f15487e6cacc52256d84006f5f7c7 -Merge: 1df9ebf 87133b6 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Mar 28 16:26:04 2017 -0500 - - merge upstream - -commit 1df9ebf80ad8e7058cafeb9a545fbabe45b1585c -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Mar 28 15:06:33 2017 -0500 - - bu psm readin mzidentml - -commit fb63585976071972ec2e0d17248be1d96662f20b -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 24 15:07:58 2017 -0500 - - temp - -commit 87133b6d8b406ad757e2e7718913e6fa02ff85eb (tag: 0.1.12) -Merge: a44f4d1 06ed114 -Author: Anthony -Date: Fri Mar 24 03:10:42 2017 -0500 - - Merge pull request #335 from acesnik/master - - Stability improvement to saving plots - -commit 06ed114c18089880288cee502c6c01fe25595653 -Author: Anthony -Date: Fri Mar 24 03:06:24 2017 -0500 - - stability improvement to saving plots - -commit a44f4d1d150f1a6db31b611a520be7f9b7d36ae7 -Merge: df682e1 cd962ef -Author: Anthony -Date: Fri Mar 24 02:40:26 2017 -0500 - - Merge pull request #334 from acesnik/master - - Automatic identification of experimental nodes; final datatable of identified experimentals - -commit cd962ef3b0a2ff477fac6aac44182f7574ddf8eb -Author: Anthony -Date: Fri Mar 24 02:38:26 2017 -0500 - - Updated results summary. Fix quant cytoscape build - -commit 121441ce2dc4eab45226ea00843c6eb3b173764a -Author: Anthony -Date: Fri Mar 24 01:54:23 2017 -0500 - - Testing results summary addition - -commit d4196f720602b9d28f059c4885d7c03af0c63824 -Author: Anthony -Date: Thu Mar 23 17:12:52 2017 -0500 - - Automatic identification of experimental nodes. Datatable report with all identified experimental proteoforms. Fixed minor bug in ET/EE. - -commit df682e195652e9cac5cfac9b664382709980f56a -Merge: 67b4c88 4ac69cb -Author: Anthony -Date: Wed Mar 22 15:39:07 2017 -0500 - - Merge pull request #332 from acesnik/master - - Added theoretical proteins and expanded theoretical proteins to results - -commit 4ac69cbae5d43a311e746391e36889e15e6fca7d -Author: Anthony -Date: Wed Mar 22 15:31:39 2017 -0500 - - Added theoretical proteins and expanded theoretical proteins to results - -commit 23c06c4f9c32432c5287d32f4d132d4bae1eaf58 -Author: Anthony -Date: Tue Mar 21 20:11:07 2017 -0500 - - Basic correction reading test - -commit 67b4c88523192a8a461b10482fe35fe3da941d64 -Merge: f4d5e39 338082d -Author: Anthony -Date: Tue Mar 21 20:04:23 2017 -0500 - - Merge pull request #330 from acesnik/master - - Bugfix for one that was introduced in testing just now - -commit 338082db021c6a3900c6e70a37b15dd3bcdc4cc2 -Merge: 5358b3c f4d5e39 -Author: Anthony -Date: Tue Mar 21 20:02:55 2017 -0500 - - Merge branch 'master' into master - -commit 5358b3cf89c6965cd2d4d123004459d70fce1bae -Author: Anthony -Date: Tue Mar 21 19:51:48 2017 -0500 - - whoops, bugfix in loading components - -commit f4d5e396b698934d567af538cd30cbb7cefa7377 (tag: 0.1.11) -Merge: a40bfcc c836800 -Author: Anthony -Date: Tue Mar 21 18:35:28 2017 -0500 - - Merge pull request #327 from acesnik/master - - Gene-centric proteoform families - -commit c836800f909ee4b264828ff6025710a36aaed08a -Author: Anthony -Date: Tue Mar 21 18:33:28 2017 -0500 - - More tests; simplified raw_component processing slightly - -commit 0312b34dd5e1d4bf806179b82c9c6f258ccb4203 -Author: Anthony -Date: Tue Mar 21 17:45:13 2017 -0500 - - Test gene-centric family construction - -commit f249bf2dfd3d3a7a7f7d9d42f939ca5d7bff9021 -Author: Anthony -Date: Tue Mar 21 16:17:56 2017 -0500 - - Few more small tests for bigrational and proteoformcommunity - -commit 79c3e1853fb9f681443ea0b6ed6c579e34af3bc3 -Author: Anthony -Date: Tue Mar 21 15:55:26 2017 -0500 - - Proteoform family genelist test. Cleaning up input file. - -commit 64bf1ac01f4e56e18c295df65b5193f73a2a89a7 -Author: Anthony -Date: Tue Mar 21 15:39:20 2017 -0500 - - better GeneName test - -commit a9e53231d20f90da0be0bdf29b90f886d7d0efba -Author: Anthony -Date: Tue Mar 21 15:18:50 2017 -0500 - - Simplified checking for contaminants in making sequence and theoretical groups; fixed accessions for contaminants; moved testing constructors to test project - -commit ba436ddfa4fea7ef16546cd68dc4039aeb3cdf7c -Author: Anthony -Date: Tue Mar 21 00:51:23 2017 -0500 - - Fixed ET discrepancies. - -commit 7f0880c9f8d0f5082a198fbe55782b7e1409d24b -Author: Anthony -Date: Mon Mar 20 21:31:42 2017 -0500 - - Gene-centric proteoform families; no more redundant theoretical accessions - -commit a40bfcc35888cca1b06d4ceddcd71451d2267e55 -Merge: 1e0496e e89ac94 -Author: Anthony -Date: Mon Mar 20 21:29:55 2017 -0500 - - Merge pull request #326 from lschaffer2/master - - relations acceptance wasnt changed if nUD peak threshold changed - -commit e89ac940e52c131624dfebe66987b4ae5505235b -Merge: 0214cf9 1e0496e -Author: Anthony -Date: Mon Mar 20 21:28:03 2017 -0500 - - Merge branch 'master' into master - -commit 22ea46f44cdf2a403d9dda890bd3c0ab49030cf9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Mar 20 15:46:33 2017 -0500 - - fixes - -commit 0214cf98dcb2c6f38287b4ceb1ba4afd59e9097f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Mar 20 13:37:33 2017 -0500 - - relations acceptance wasnt changed if nUD peak threshold changed - -commit f535d1c5c0425ef95f3fa8b7372fc68b12ce601f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Mon Mar 20 13:34:00 2017 -0500 - - small bug fixes - -commit bb2302389d10674aaa5222a79efb5fbd21e59e6a -Merge: 66517e2 1e0496e -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 17 17:48:06 2017 -0500 - - upstream merges - -commit 1e0496e88fe04c8f6aff90e829527be0238db97c -Merge: 252f019 2aac433 -Author: Anthony -Date: Fri Mar 17 17:29:03 2017 -0500 - - Merge pull request #322 from acesnik/master - - Allow mzLibProteinDatabases with mod references to be used - -commit 2aac4336318db6e349738eb56dc57ad35485242c -Author: Anthony -Date: Fri Mar 17 16:56:23 2017 -0500 - - Allow mzLibProteinDatabases with modifications to be used; allow exclusion of certain modification types (Metal;PeptideTermMod by default) - -commit 252f019015a6681f53e0d4e3228e97e44c1c646d -Merge: e87ee7a 85b249b -Author: Anthony -Date: Fri Mar 17 17:12:52 2017 -0500 - - Merge pull request #320 from lschaffer2/master - - inclusion list and GUI fixes - -commit 85b249b2339ce2c3bcf67a8b4838366e71c1c6dc -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 17 17:00:38 2017 -0500 - - GUI bug fixes - -commit 8fe58528aa068cc88eaa9872121c63f1d9dee7b4 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 17 13:48:43 2017 -0500 - - refresh changes - -commit 72604a873bd14d07b0a3ee199fb693c82168373d -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 17 12:06:38 2017 -0500 - - inclusion list - -commit 66517e2eb891374a96f903e544e570e7fe70a846 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 17 11:25:22 2017 -0500 - - GUI mods - -commit ebdd858446b09fbbf2be8a761a86e785bf3f101a -Merge: 20ef386 e87ee7a -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Mar 17 11:01:52 2017 -0500 - - merged from upstream - -commit e87ee7a02e6f2a167571324d68aa7f000cbc9406 -Merge: c351ca2 b36990c -Author: Anthony -Date: Thu Mar 16 23:05:39 2017 -0500 - - Merge pull request #312 from acesnik/master - - Contaminant decoy fix - -commit b36990cda9ca221776742c27bc8f939c57bd9bde -Author: Anthony -Date: Thu Mar 16 23:02:51 2017 -0500 - - Set contaminant for decoys to not run into problems when making TheoreticalProteoformGroups of decoys - -commit c351ca26d9348a59fb13ebc287ca6dcdfaa1869a (tag: 0.1.10) -Merge: 394a38a 986b6da -Author: Anthony -Date: Thu Mar 16 21:18:50 2017 -0500 - - Merge pull request #309 from acesnik/master - - Allow moving unquantified experimentals in cytoscape - -commit 986b6dad1ef35176d67c4f679940a3533bf8bd84 -Author: Anthony -Date: Thu Mar 16 21:16:35 2017 -0500 - - Allow moving unquantified experimentals in cytoscape - -commit 394a38afd127c5655819f6ac860e318113f77ecc -Merge: 881e2b1 a52893f -Author: Anthony -Date: Thu Mar 16 20:41:18 2017 -0500 - - Merge pull request #306 from acesnik/master - - GUI improvements - -commit a52893fc864f3a10b88947811a35f2f3ee771d2c -Author: Anthony -Date: Thu Mar 16 20:39:29 2017 -0500 - - again - -commit 521ad7157bdf85a450a9abc2a5d8f60b43a17eb5 -Author: Anthony -Date: Thu Mar 16 20:34:56 2017 -0500 - - expanding current tests for resultssummary - -commit ab7337112491173d4d14b088c2e499b6f0b5e593 -Author: Anthony -Date: Thu Mar 16 20:23:19 2017 -0500 - - Reworked ResultsSummary - -commit b6d86047753e86b8bc7deafe6fbf7e5d3c26146e -Author: Anthony -Date: Thu Mar 16 15:06:29 2017 -0500 - - Trying a new SortableBindingList ... nicer code, but still doesn't sort boolean, since those headers don't trigger the ApplySortCore event - -commit 9c61c6ff4034e42daf48e56c458d082b05b2693f -Author: Anthony -Date: Wed Mar 15 18:57:25 2017 -0500 - - Update proteoform families upon EE refresh; don't load automatically upon form load; fixed calibration add-file button OpenFileDialog - -commit 881e2b1fd3a96f8f74be6544ee1f442b7cc3979d -Merge: 661abae ab91ef0 -Author: Anthony -Date: Wed Mar 15 18:48:58 2017 -0500 - - Merge pull request #305 from acesnik/master - - Small speedup to making EE relations - -commit ab91ef046b9f9d6f4245ea0f323a4aaf0bdac024 -Author: Anthony -Date: Wed Mar 15 18:44:40 2017 -0500 - - Small speedup to making EE relations - -commit 20ef386e4506dcdc91cf247232014e6a12df5970 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Mar 15 11:04:09 2017 -0500 - - temp changes - -commit 661abaee396b8d20f2dabccd5084dc3bdaccaae4 -Merge: bbe947a c08ee37 -Author: Anthony -Date: Wed Mar 15 06:32:27 2017 -0500 - - Merge pull request #304 from acesnik/master - - >10x speedup for unlabeled - -commit c08ee3792d1196f1141aa0da4dd5386bc6306835 -Author: Anthony -Date: Wed Mar 15 04:24:02 2017 -0500 - - Threaded family construction by choosing seed proteoforms arbitrarily. Improved IndexOf call speed for ordered-list speedup. - -commit f3f21bb17e32ea35870ad8707445da1b110aec1a -Author: Anthony -Date: Wed Mar 15 02:26:05 2017 -0500 - - Speedup with ordered lists to find nearby relations - -commit ffa2adec56d08f745dc111a19dd2f90f73ce1446 -Author: Anthony -Date: Wed Mar 15 02:06:21 2017 -0500 - - 10x speedup in unlabeled via parallel count_nearby_relations and threaded accept_deltaM_peak - -commit bbe947a9d89cc724fd1ef74317e519dd29e6c81c -Merge: dc2c1ee 0d1ee64 -Author: Anthony -Date: Tue Mar 14 21:45:32 2017 -0500 - - Merge pull request #303 from acesnik/master - - Housekeeping - -commit 0d1ee647ec6f9fffa0e3247cc0ddebf6fca6fad8 -Author: Anthony -Date: Tue Mar 14 21:43:26 2017 -0500 - - Housekeeping - -commit dc2c1eeb6e81cc9e1dfcaad2e0288885a281a633 -Author: Anthony -Date: Tue Mar 14 21:38:49 2017 -0500 - - comment out some more top-down code for now - -commit 0bf72b88d24a305cf50515330be1ffa35b3c44a4 -Author: Anthony -Date: Tue Mar 14 21:36:56 2017 -0500 - - null check - -commit 1e9e3ed2cf4e860a5d4a99124a2d7a35b060c94e -Author: Anthony -Date: Tue Mar 14 21:30:08 2017 -0500 - - More simplification of BigRational for tests - -commit 16ef29475bba656203a8fd5fb7e760ea7a136080 -Author: Anthony -Date: Tue Mar 14 21:13:50 2017 -0500 - - compliance error fixes - -commit fd6aec434318f6b78f0862d41bcf715abf605c82 -Author: Anthony -Date: Tue Mar 14 21:10:49 2017 -0500 - - Testing bigrational - -commit 4d9220d9fb9d3682d4812846bc68480c1f777a25 -Author: Anthony -Date: Tue Mar 14 19:42:20 2017 -0500 - - cleanup; fix contaminant handling in proteinseqgroups - -commit 1f3dc9aa19fea0a36dce23ffa18cc94b64d36e42 -Author: Anthony -Date: Tue Mar 14 19:10:19 2017 -0500 - - Fixed GO-Term permutation analysis overflow issues; Allow user-specified GO-Term background - -commit c94508a22962a6fd9848a2ede36a1980a60becb2 -Author: Anthony -Date: Thu Mar 9 16:35:00 2017 -0600 - - Updated mzLib. Beginning testing TheoreticalCreation. Beginning protein list for GO term analysis. - -commit 96ef20ac36e5eb828e860822e9a78f5ff616b65f -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Wed Mar 8 16:56:43 2017 -0600 - - topdown fixes and GUI enhancements - -commit aeb254292da5eb626e541218325bdbc136a12801 (tag: 0.1.9) -Author: Anthony -Date: Mon Mar 6 16:48:42 2017 -0600 - - Reaggregation now runs through the rest of the pipeline. - -commit e78ebe7215547e7a964b3d946334b73161811588 -Author: Anthony -Date: Mon Mar 6 15:21:24 2017 -0600 - - Count distinct go terms in each protein. Because GO Terms are aggregated in protein sequence groups, there are reduncancies. - -commit 820854afdd155d4535e990262e38ea61e34e2943 -Author: Anthony -Date: Sat Mar 4 20:39:00 2017 -0600 - - Fixed GO Term analysis, in that the background set is not ~700 proteins from the expanded set for the full yeast quantitative dataset. Reorganized some of the classes. More testing for GO Terms. - -commit 4b8238992d186319201c959cb3d7b6c91e2691d7 -Author: Anthony -Date: Sat Mar 4 16:17:11 2017 -0600 - - updated mzLib and aggregated GO terms in protein sequence grouping - -commit 7b4fc89cb86c9aaf44ad3c69eb3defc3701b65a8 -Author: Anthony -Date: Fri Mar 3 19:14:04 2017 -0600 - - Added table filter to AggregatedProteoform - -commit 852e5a00de16b62674c4d0ff9ba4da4063dd1598 -Author: Anthony -Date: Thu Mar 2 18:22:29 2017 -0600 - - Fixed error in theoretical database test that stemmed from whitespace included in one of the sequences ... are the rest of the values correct? - -commit a4d14fcdcbdbdfb1f51acf6dcb55e373e6e1e85b -Author: Anthony -Date: Thu Mar 2 18:02:20 2017 -0600 - - Updated mzLib and aggregated GoTerms upon construction of TheoreticalProteoformGroups. - -commit e4e5e560a9ffee7e4f21b9e3f1816ee51d437922 (tag: 0.1.8) -Author: Anthony -Date: Wed Mar 1 17:15:33 2017 -0600 - - Compute background standard deviation with selected proteoform intensity distribution. - -commit 7f3c89d6c92a9eec971cda14a778f9d7f6b8ea59 -Author: Anthony -Date: Wed Mar 1 12:55:17 2017 -0600 - - Double checking CytoscapeScript and ProteoformFamily with more tests. - -commit 1e21f1e6871e3d946372e50c805142cc5970025a -Author: Anthony -Date: Tue Feb 28 18:12:27 2017 -0600 - - Fixed bug where not all theoreticals were contained in each family, due to an error in comparing proteoforms by accession, since not all accessions are unique currently. Now doing that by simple hash-code comparison of Proteoform objects. Also, sped up full run of yeast quant dataset by ~30 sec of 10 min by running raw_experimental_components and theoretical_database at the same time. - -commit cb8a78973a84c629134e230086aa65aac797d52e -Author: Anthony -Date: Mon Feb 27 18:28:58 2017 -0600 - - Cytoscape theoretical naming fix and testing, but now cytoscape flakes out on the node table for no clear reason... - -commit 2e233b9a0bfac148b4fcb6b6df4d48526740999d -Merge: ab03ec2 fc3fcf6 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Feb 27 10:21:14 2017 -0600 - - merge from upstream - -commit fc3fcf671814086865188f69f10cc2f81d7e5fa9 -Author: Anthony -Date: Fri Feb 24 14:22:53 2017 -0600 - - New tests and two bug fixes. Added checkbox for whether to validate - aggregated proteoforms. - -commit ab03ec231274870b40ca051089e199bb87015791 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Fri Feb 24 17:05:27 2017 -0600 - - temporary changes - -commit bc61280070e52f0ef5e02ded73238977f8d3942e -Author: Michael Shortreed -Date: Fri Feb 24 11:04:39 2017 -0600 - - fixed broken lollipoop - -commit abc074af35fd35f24a3730a32bb25f613190c65d -Author: Michael Shortreed -Date: Fri Feb 24 09:13:03 2017 -0600 - - some new tests - -commit e6ca9d75afb5efea6af093369215f6ef199601ad -Author: Anthony -Date: Fri Feb 24 00:16:16 2017 -0600 - - houskeeping - -commit 4ef09947c90d37a69cf2b306f7f6bb494075ceb6 -Author: Anthony -Date: Thu Feb 23 23:43:10 2017 -0600 - - Added table filter for TheoreticalDatabase - -commit 510250bbb30842e466262fd0878678698c7c01f3 -Author: Anthony -Date: Thu Feb 23 23:42:31 2017 -0600 - - Fixed bugs in aggregation; added aggregation tests - -commit 50c3d24763831113df793fc8831cc45cfc8a92d0 -Author: Anthony -Date: Thu Feb 23 01:53:34 2017 -0600 - - TheoreticalDatabase speedup by parallelizing, simplifying finding unique positional PTM combinations, and using dictionaries to group by identical sequence and mass - -commit cea47ce82743380184ceddf783e5550888a8add9 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Thu Feb 23 17:53:37 2017 -0600 - - td fixes - -commit cdc03c4c76f726347b205197d5913f2930b57c3a -Author: Anthony -Date: Thu Feb 23 01:25:26 2017 -0600 - - More quant testing - -commit e80f65fc64ecec8b43f4922301f0c94dedb93077 -Author: Anthony -Date: Wed Feb 22 02:21:26 2017 -0600 - - Testing gaussian histogram creation and area calculation - -commit f861800b6f0d134fec7db8dcfd2e3cd366bc6386 -Author: Anthony -Date: Tue Feb 21 17:58:00 2017 -0600 - - Testing addition of directory of files - -commit 4bc79c8b98f57b867456c1e9a1a9612ddc26f658 -Author: Anthony -Date: Tue Feb 21 17:30:28 2017 -0600 - - Testing methods for threaded aggregation - -commit 4371abd079b793b4c1ba705a706648d416daf02c -Author: Anthony -Date: Tue Feb 21 15:28:22 2017 -0600 - - Allow drag and drop of gzipped XMLs. - -commit 808d413a866aedde6913704746e2f23947a3610a -Author: Michael Shortreed -Date: Tue Feb 21 07:12:43 2017 -0600 - - imputation bug fix plus unit testing quantification - -commit a79f5e96b55101c7036b67f06277b536c43ae436 -Merge: 97316fd 86b33f9 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Feb 21 11:37:28 2017 -0600 - - moved raw file reader - -commit 86b33f98f8783069e931971bdcd7b9ccf80caee2 -Author: U-DESKTOP-PP8NT74\lschaffer2 -Date: Tue Feb 21 11:32:35 2017 -0600 - - mzlib update - -commit 461a927470935a2bad0cf768d25e42d57843e0a0 -Author: Anthony -Date: Tue Feb 21 00:41:55 2017 -0600 - - Testing ExperimentalProteoform copy. - -commit 31d29e825b26e2fef54317b78e0e9ba17ee41302 -Author: Anthony -Date: Mon Feb 20 23:22:33 2017 -0600 - - InputFile cleanup - -commit a2033506fe4971c2d3f5b985b94b8f978b744f61 -Author: Anthony -Date: Mon Feb 20 22:23:19 2017 -0600 - - Mark contaminants if a contaminant database is used. Added testing. - -commit dbf8d6abc75f2e0776ed36f92ec9f695171dca20 (tag: 0.1.7) -Author: acesnik -Date: Fri Feb 17 13:21:53 2017 -0600 - - Using mzLib & allow multiple databases including GPTMD - - * Implemented mzLib methods for reading databases - * Restructured LoadDeconvolution to allow three load DGVs - * Allows multiple databases - * Can read GPTMD databases created in MetaMorpheus - -commit 7e0c390b5359f98be2fdd038718b69c635cd2526 -Author: trishorts -Date: Mon Feb 20 12:49:05 2017 -0600 - - update readme - -commit fe759baf40c974ee47b5249e49d2889c1ae4f28f -Author: Michael Shortreed -Date: Mon Feb 20 11:53:37 2017 -0600 - - corrected permutation and go analysis - -commit 97316fd08d1612c7a6c5fd296c33d1a82676b5e9 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Feb 20 10:11:55 2017 -0600 - - see if intact E was fragmented - -commit dfe110a7bc80b76dfaf971bc8a8e842c8ad0d5a5 -Merge: fdc99da ec079fe -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Feb 16 10:31:03 2017 -0600 - - fixed merge conflicts - -commit fdc99dabe2dd4a590e33f08ce146ba4b85e939b2 -Merge: 64fecc1 d2e9af1 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Feb 16 10:28:41 2017 -0600 - - upstream master update - -commit ec079fe0c3fd66d652999bf5d928b9713fbcd83f -Author: Leah Schaffer -Date: Tue Feb 14 16:50:46 2017 -0600 - - cytoscape fix - -commit 797d9cd16e5f9cd6f07448ba255060f7760be530 -Author: Leah Schaffer -Date: Tue Feb 14 15:04:15 2017 -0600 - - ef fix and can export identified relaitons to cytoscape - -commit 64fecc10c4cf5991e6850c8e91f52488ecf081d1 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Feb 14 09:24:16 2017 -0600 - - EF fixes - -commit bda6baf0c2869618f687edbcd530da25de18f81f -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Feb 9 19:05:11 2017 -0600 - - close files after use - -commit 2e68b130448a0dda49eb6b4b505c77ebe0d93cbb -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Feb 9 16:37:43 2017 -0600 - - calibration fixes in PS - -commit 75eae00d9c0c5523ea8551a38fe99b2de33c2007 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Feb 8 21:18:58 2017 -0600 - - calibration module - -commit d2e9af1d46846c23753dbb46028bdb20a27cb623 -Author: Leah Schaffer -Date: Wed Feb 8 11:46:00 2017 -0600 - - update packages - -commit bcd0596a3a0727400a68cd470e3a4065f9fa0fa6 -Author: Leah Schaffer -Date: Wed Feb 8 11:32:27 2017 -0600 - - ed relation bug fix - -commit b6c166aed14b1b8d17969a05872d98f26de2c82b -Author: Leah Schaffer -Date: Wed Feb 8 10:27:16 2017 -0600 - - make peak accepted fdr bug fix - -commit 653859b3f353dfee48e4d978a8687f81d93a7a91 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Feb 6 11:43:22 2017 -0600 - - notch mass ET and EE - -commit 2ed91833aff7859b50e0385252ab5603b6b0e769 -Author: Leah Schaffer -Date: Sun Feb 5 16:10:22 2017 -0600 - - check targeted td results - -commit 52a7775dd1be3cf07553be1c5d672ef347a5e3fd -Merge: 0b8e34d b3af494 -Author: Leah Schaffer -Date: Sun Feb 5 14:20:51 2017 -0600 - - merge conflicts - -commit 0b8e34d7e0a62eb5991f9664239a5f9cd269c9cb -Author: Leah Schaffer -Date: Sun Feb 5 14:15:33 2017 -0600 - - targeted td - -commit b3af494f6f2382514f319005f28ef6247fb651ca -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sun Feb 5 14:14:06 2017 -0600 - - changed how td proteoforms organized - -commit 59f375f7c2b171bcf8a3cd49f8a2e3c16b9ec63e -Author: Michael Shortreed -Date: Thu Feb 2 09:10:56 2017 -0600 - - GoTerm testing - -commit 28092a6e77c5344e1cc7e65dc6b706476a8c9f52 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Jan 31 14:43:13 2017 -0600 - - td groups - -commit 4e6aa74ef705b83e8dfe72819151dd8c6f656048 (tag: 0.1.6) -Author: Anthony -Date: Mon Jan 30 18:33:49 2017 -0600 - - Small fixes to LDR GUI page - -commit de1fc0b2e4c9c403bf3c31a2c491c619a5ff8379 -Author: Anthony -Date: Mon Jan 30 16:38:37 2017 -0600 - - Fixed inconsistencies due to concurrent LINQ queries on lists using - locks on the objects that contain them. - -commit 8b96070efd10dc73b94885bf2c41e4c5e2a7498a -Merge: 365ec74 830f4a1 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Jan 30 15:21:01 2017 -0600 - - merge conflicts - -commit 365ec74d8d44d597ae1028b1d0b3fb231cd35ce6 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Jan 30 15:09:48 2017 -0600 - - bug fixes, SN exp parameter - -commit 830f4a1edc6113594d3a6b40bdf5b8f840caa190 -Author: Anthony -Date: Mon Jan 30 13:51:10 2017 -0600 - - cleanup - -commit 54ea605ab1045dd1a552cad904e619616764770b -Author: Anthony -Date: Mon Jan 30 13:42:11 2017 -0600 - - Disabled editing XML, ptmlist textboxes, since we haven't implemented text-changed event. - -commit 8c94c8b710e0977392cb2b7ccea91102cc04d381 -Author: Anthony -Date: Wed Jan 25 01:36:14 2017 -0600 - - Quantitative visualization fix. NeuCodePair speedup. - - * Quantification now creates qvals for each ExpProt, not just the - interesting ones. - * Parallelized NeuCode pair creation; evaluating whether to keep them - after all NeuCodePairs are created. - -commit e2c0f73d297c2061a3de6bb4db9c55c6397f9bdf -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sat Jan 28 12:42:16 2017 -0600 - - invisible advanced dgvs, cleared out out-dated td code - -commit cb6d5a06026b2c9f8af52f3f1ade439d0e17dfea -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Fri Jan 27 10:23:12 2017 -0600 - - FDR display & change visibility of dgvs on load page - -commit a7c081c09810bc153afea6a55879b38c464d0d5a -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sat Jan 28 15:19:36 2017 -0600 - - changed how top down proteoforms organized in groups - -commit 95081dd311e99003db9456c9e836cbb6a96946f4 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Fri Jan 27 09:48:19 2017 -0600 - - bug - -commit 43e3ec54d49655c6205fb33f743010174dc76c2f -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jan 26 18:33:48 2017 -0600 - - fixed test issues - -commit 65b1125fcb0d3ea3e993156e7a363028a62733dc -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Jan 26 17:30:55 2017 -0600 - - s/n bug - -commit aa8d4790df6f707467eb91b074ae13e5f3377107 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Jan 25 21:35:43 2017 -0600 - - calibration bug - -commit f2efb24b874234184b549287366e951dc6253e45 -Merge: 102730d 8101076 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Jan 25 20:56:45 2017 -0600 - - merge - -commit 102730dc30be601c5488f064871e2610ec99eb0d -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Jan 25 20:56:32 2017 -0600 - - dont see td correction - -commit 8101076e69e529040ca9815f39ff04dc955b114a -Merge: 4b0b92f 7c0b1de -Author: Leah Schaffer -Date: Wed Jan 25 20:55:29 2017 -0600 - - merge conflicts - -commit 4b0b92fba9f44c3f62c374fb7de9ac2ca1fd7e82 -Author: Leah Schaffer -Date: Wed Jan 25 20:36:21 2017 -0600 - - inclusion list - -commit 7c0b1deb0030d3cc246a8fcbb69225a1fcabf35d -Merge: 2c2ad48 98711ed -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Jan 25 20:18:17 2017 -0600 - - merge conflicts from upstream master - -commit 2c2ad48c2849267148835a569bf00b82ddca8cfa -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Jan 25 19:23:04 2017 -0600 - - signal to noise values - -commit 98711ed8a8403908507fcd3a33a0a14a8064aacb -Author: Anthony -Date: Tue Jan 24 22:43:10 2017 -0600 - - Finishing touches; small speed improvement in quantitation via PValue - LINQ simplification; fix to visualizing quantified families with members - having no quantitative components - -commit e3d99d0940163159b6dfe7f737f9dab469f5b66f -Author: Anthony -Date: Mon Jan 23 18:31:37 2017 -0600 - - Aggregation speedup by ~50x - - * In parallel, selects several masses as roots for aggregation in order of intensity, each > 20 Da from others that have been selected - - * Eliminated costly get-method for weighted_monoisotopic_mass in Component - - * Manually checked validity. Before and after both: 744 aggregated proteoforms, 20139 raw components, and 4768 neucode pairs. - -commit ea29e84a92e98be00777fb668703f7aae4abd633 -Author: Anthony -Date: Wed Jan 18 17:16:26 2017 -0600 - - Quantitative visualization; updated ProteoformFamily DGV; viz options - - * Quantitative visualization, including pie charts and highlighting significant differences. - - * Proteoform families main DataGridView now displays GO terms and theoreticals, which can be selected for visualization. - - * Added row text filters to look for interesting families, theoreticals, or GO terms for selective visualization. - - * Added several Cytoscape visualization options, including label location and color schemes. - -commit 43c6c1a246b4d8f8a7d2a5134f5e972be3cf5d65 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Jan 24 14:17:11 2017 -0600 - - calibration, s/n test - -commit fa29f8e3e39060ec53b5638adbcf290a3598de0a -Author: Michael Shortreed -Date: Fri Jan 20 13:26:57 2017 -0600 - - component and charge state testing with bug fix - -commit 638505c7627b226b8d52ebcaf1f509b2101ee3f1 -Author: Anthony -Date: Thu Jan 19 14:19:42 2017 -0600 - - Quant click fix - -commit df9e119e3dd489bdbca425811df31f6b043db828 -Author: Anthony -Date: Wed Jan 18 17:41:09 2017 -0600 - - Fixed Quant refresh (#251) - -commit bf09dfc812b24e3f5564b18c35477052e304fd72 -Author: Anthony -Date: Mon Jan 16 19:06:27 2017 -0600 - - Quantification -- 1) fixed crash on accidental load, 2) added it into full_run workflow. - -commit 86ac0c1e934d29be98c1482b8cabbe9e31bd0946 -Author: Michael Shortreed -Date: Tue Jan 17 13:21:59 2017 -0600 - - GO term background select experimental or theoretical - -commit 7e96063775e546561c4d9a050a03f331fbb6503a -Author: Michael Shortreed -Date: Mon Jan 16 12:01:24 2017 -0600 - - quant - -commit b4841eb817b1deb3b3eac0689ec5a1b448d14bf0 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Jan 16 11:12:50 2017 -0600 - - mass cali - -commit 7dece4745baea70ddc5b8cbbf8aa0bc71f27ace0 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Jan 9 19:16:00 2017 -0600 - - started adding mzcal - -commit 1d60d7e43096c081aa385aed834dd92fba95c540 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Jan 3 12:12:15 2017 -0600 - - td - -commit 5ae4431af7d9de9cce73416bd547e3b77721226c -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Dec 13 17:23:12 2016 -0600 - - td mass calibration - -commit 134c4eaaec264d5cdd3c696c46f0440d3fba63ee -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sun Dec 11 16:25:44 2016 -0600 - - theoretical td relations - -commit 611400fdbb4e2a60d21f1e8703f0c186002df410 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Fri Dec 9 10:54:26 2016 -0600 - - topdown - -commit a733cc72aaab99516c1fdbde0f310b2acde1d45f -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Dec 6 14:42:26 2016 -0600 - - monoisotopics to TD relations - -commit 6cd12c4075d4c1cc743e79adf40ed7ceffc0a6e6 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Dec 5 08:43:10 2016 -0600 - - use td hits - -commit 77e8d17184b034ef06fa7fbf21c447b2c8ec3882 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Nov 29 18:19:02 2016 -0600 - - gene id and able to export family list - -commit d302d6badbc03847874740ff52dbadfd874a4c03 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Nov 28 17:44:03 2016 -0600 - - moved one line - -commit 353cd1ffd268d92a92a51103f63e963ff2cc94fe -Merge: 316e520 d21baac -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Nov 28 17:21:40 2016 -0600 - - fixed merge conflicts - -commit 316e5200d45be7baa6a2a859edd5b1b711dd1492 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Mon Nov 28 16:52:26 2016 -0600 - - TD in families - -commit d21baac0be2cef959c23799a4f574820a2c4a5c1 (tag: 0.1.5) -Author: Michael Shortreed -Date: Mon Nov 21 11:56:46 2016 -0600 - - component reader cleanup - -commit e98d64c75936862b4631caafc1b28e293730cdf2 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Nov 17 10:51:49 2016 -0600 - - import/export neucode relation results, use as fiter for labelfree - -commit 8cafc31ce8cced0d2763b953fed60bb690d681f6 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sun Nov 13 12:31:53 2016 -0600 - - small ED change for min agg count - -commit 11c6f7640d3270ea0e814af5219281124d68a761 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Fri Nov 11 12:46:02 2016 -0600 - - fix - -commit 314beccd500953648bbbd10f35df8ccb1ce962fe -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Nov 8 18:12:47 2016 -0600 - - option to wait for form to run when loaded - - updated rawlockmass shifs - one column - option to not automatically process page when it loads - -commit 8fbcdca58120b66a410d7e14f8a8cc1ead9edcd0 -Merge: 78e191a 31e92df -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Fri Nov 11 12:29:50 2016 -0600 - - Merge branch 'master' of https://github.com/lschaffer2/proteoform-suite-1 into TD_BU_integration - -commit 78e191afd12839db3a148a8caec8e300b2ba9f30 -Merge: ba80599 55350e5 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Fri Nov 11 12:21:52 2016 -0600 - - merged upstream master - -commit 31e92df80d673ae5d02a0294d358a8083e25f48a -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Nov 8 18:12:47 2016 -0600 - - option to wait for form to run when loaded - - updated rawlockmass shifs - one column - option to not automatically process page when it loads - -commit 55350e5f6e192cf4665c14fb33b0d3d245faf8b4 -Author: Michael Shortreed -Date: Fri Oct 28 14:05:56 2016 -0500 - - removed missed monoisotopics and harmonics - -commit ba805991e291037df02b7873af193b05a48ebc31 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Nov 8 09:33:02 2016 -0600 - - can limit ET search to T with BU or TD PSMs - -commit 8abf54eb5bb0ac232bb6f883c69c5953cdf08062 -Author: Anthony -Date: Thu Nov 3 20:43:07 2016 -0500 - - Removed drafting of save-all open-all - -commit f9d44bcd31f41129c0989251262c3ebb8c72b8db -Author: Anthony -Date: Thu Nov 3 20:13:44 2016 -0500 - - Restored processing upon page clicks. Sort peak lists by relation count before displaying. - -commit cb331da22d0f56eac2e4aaa07093be050c373fdc -Author: Anthony -Date: Thu Nov 3 20:02:18 2016 -0500 - - Added clear results button to LoadDeconvoluitionResults page. - -commit 842fdc5e1443b8b9b25601afed7b48b7e3905e02 -Author: Anthony -Date: Wed Nov 2 22:51:48 2016 -0500 - - Save method XML; Load method XML. Tested and implemented. - - Includes draft of Save All and Open All with XML. However, this is incomplete and thus not implemented. - -commit 95db4eecbb0d11c648ed9e2175527688850571d3 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Thu Nov 3 15:48:30 2016 -0500 - - export DGVs to excel - -commit 142b9013fbd58272ca8453552edc7421bc84bbcf -Author: Anthony -Date: Wed Nov 2 18:30:05 2016 -0500 - - Added orphan count to ProteoformFamilies page. - -commit 3bd9aa96cfe5f3b2262259c50600c531bb699562 -Author: Anthony -Date: Tue Nov 1 20:45:47 2016 -0500 - - Refactored and tested mass shifting - -commit da93660f6d9742c224d73bb7fec848fc265b404e -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Nov 1 17:33:00 2016 -0500 - - fixed up MS1 scan issues for td files - -commit f21631e720bfac674962420dbb5d3363ffe7c73d -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Sun Oct 30 12:56:16 2016 -0500 - - added back in ED option - -commit f9d96a7d51d798bbe6b78ef367404f06d1ca58f5 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Oct 26 21:24:45 2016 -0500 - - open form and set params, click to start each; cleaned up code - - load and run test + fixed EE/ET GUI bug w/ parameters) - - test issues - - test issues - -commit 7910d5f9ca144a5e4214531af2da98668cc4e3f0 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Oct 26 17:30:53 2016 -0500 - - can set arbitrary peak threshold; debugged peak/pair accepted - -commit 70e4de8671fd2f5c695c44a5c3f384e433b02305 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Oct 25 18:00:30 2016 -0500 - - added experimental agg cutoff options - -commit 3ce539460f18e1a5e6b12beea52a36d9819b9659 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Wed Oct 19 14:24:03 2016 -0500 - - made min/max neucode pair params less than or equal to - -commit 24de07317bcae338d668d53637bc58340be3a252 -Author: Michael Shortreed -Date: Fri Oct 28 14:05:56 2016 -0500 - - parallel file processing - -commit a822552928d236c96078b77f8a83166cf87878ba (tag: 0.1.4) -Author: Anthony -Date: Tue Oct 25 21:02:54 2016 -0500 - - Added information to the ProteoformFamilies display. There is still some weirdness with the theoretical accessions not being unique. - -commit 8153ae0ff3e9c7459e11dda547edb09f546ae31e -Author: Anthony -Date: Tue Oct 25 15:51:55 2016 -0500 - - Corrected modified theoretical display for Cytoscape. Decimal rounding available for labels for Cytoscape display. Improved timing for Cytoscape script. Improved stability for opening form pages in wrong order. - -commit 8bad9bed8e8b8ecf577ac94ca977f9ac995ca4e8 -Author: Michael Shortreed -Date: Tue Oct 25 13:22:29 2016 -0500 - - parallelize Go term analysis - -commit 6ddb57fd05f463fcf9763b4c65759dc7631be8ad -Author: Anthony -Date: Mon Oct 17 14:20:03 2016 -0500 - - Implemented cytoscape scripting to quickly load and stylize proteoform families in cytoscape. - -commit 6421159ce0f98c4b3e5441cf30b0cc62047af6a1 -Author: Anthony -Date: Fri Oct 21 17:27:15 2016 -0500 - - Corrected ET/EE clear to only clear relations of that type from ProteoformCommunity. Implemented ProteoformFamilies update button. Standardized load behavior of several forms, using ProteoformSweet instead of Load events. - -commit 0754612b42a14a0f8f5ad22e88c0880b9a7adc73 -Author: trishorts -Date: Wed Oct 19 15:37:29 2016 -0500 - - fixed lollipop.process_raw_components but that overwrote componets + parallel file processing (#224) - -commit bbe24c64a57e68fac5850c280e9475c0a18c5019 -Author: U-LAPTOP-8LS393FL\LeahSchaffer -Date: Tue Oct 18 11:17:16 2016 -0500 - - open theoretical database + changed how threshold set/no more ED - -commit f3d70c94727db2fc84ac9ce43685aefd6b496fc7 -Author: Anthony -Date: Fri Oct 14 11:15:09 2016 -0500 - - Combining theoretical proteoforms by mass (#222) - - * Combining theoretical proteoforms by mass, similar to protein grouping when making theoretical proteoform databases. - -commit 4231b66d6489919099560121e7a2dcf101e41b29 -Author: Michael Shortreed -Date: Mon Oct 10 14:33:31 2016 -0500 - - remove missed monoisotopics from within the same scan and merge components - -commit 5473f385b479e8e59317b66d85144f1b4173a017 -Author: trishorts -Date: Fri Oct 7 17:23:13 2016 -0500 - - infile ID added to component ID (#218) - - * infile ID added to component ID - - * fixed tests for changes in component class - - * fixed bugs in lollipop.find_neucode_pairs - - * remove missed monoisotopics that show up in the same scan - -commit 52152dbbf5274b757708b3cfa0249aadcd354e34 -Author: Leah Schaffer -Date: Mon Oct 3 13:28:55 2016 -0500 - - fixed up buttons, can open raw exp comps only, fixed calibration (#217) - - * added open button to open just a raw exp comps file - - * fixed small Td-files bug - - * changed open option to toolbar - - * added mass shifter to update button - - * made targeted button invisible for now - - * changed calibration back to way that worekd better - - * as usual had to fix a failed test - -commit 0d014e72f0a9d58ca4b15c0d4f2adde0e319fdf0 -Author: Anthony -Date: Wed Sep 21 15:26:45 2016 -0500 - - one line. (#216) - -commit f0d845eb763428db741ebea476f5857a61aaee5a (tag: 0.1.3) -Author: trishorts -Date: Fri Sep 16 12:24:32 2016 -0500 - - improvements to quantification; addition of GO analysis (#215) - -commit 103f8cc8c2fbdb035473870ab6cb2b0413fb953d -Author: Leah Schaffer -Date: Wed Sep 7 13:35:05 2016 -0500 - - load in TD, mark accession of interest, mark missed monoisotopics (#212) - - * fixed correction factors bug - first line doesn't matter now - - * updated open/save results - - * read in TD results - - * can add list of accession numbers of interest - - * can mark EE peaks as missed monos, then num ET relations in each ET peak w/ missed monos summed. Can help find problematic ET peaks quicker - - * tiny changes - - * removed unused using statement - - * small bug fixes - - * reading in TD PSMs - - * load in deconvoluted TD file - - * export targeted TD list - - * fixed merge conflic - - * fixed test issue - -commit 23eb9418b889f75e6feda5be21cd8c8228c99a0e -Author: trishorts -Date: Tue Sep 6 15:05:59 2016 -0500 - - quantification (#213) - - * load quantitative results and added quantification form - - * load quantitative results and added quantification form - - * added quantitative stuff to experimental proteoform - - * added quantification module - - * resolved merge conflicts - -commit 35c672e60ca7f4f8ede14a352f6a8654d6e1ddb2 -Author: trishorts -Date: Tue Aug 23 12:14:57 2016 -0500 - - quantitative added to experimental proteoform (#211) - - * load quantitative results and added quantification form - - * load quantitative results and added quantification form - - * added quantitative stuff to experimental proteoform - -commit 4b44933db693396f1fcf847c4d0b00806db881ad -Author: Leah Schaffer -Date: Tue Aug 23 10:25:58 2016 -0500 - - Fixed correction files/path issue (#210) - - * fixed correction factors bug - first line doesn't matter now - - * changed variable name to make more clear - -commit 658166413f9a50002b560adf3cbf78d1ec829ae3 -Author: trishorts -Date: Fri Aug 19 13:42:39 2016 -0500 - - load quantitative results and added quantification form (#209) - - * load quantitative results and added quantification form - - * load quantitative results and added quantification form - -commit a127346f7c2e76517bf6667c5f97202faed6a68a -Author: Leah Schaffer -Date: Fri Aug 19 12:34:31 2016 -0500 - - multiple mass shifts at once, and click for tool-tip in charts (#208) - - * change multiple mass shifts at once, edit in dgv column & click button - - * click ct to see tool tip - - * dont show mass_shifter in EE - -commit 5ae655308cca1899e8d099b54872372333aeee10 -Author: Leah Schaffer -Date: Wed Aug 17 17:56:05 2016 -0500 - - only read in target PSMs (#207) - -commit fa4bef11665f4e0f9e3815120ed07bd88b47bc9a -Author: Leah Schaffer -Date: Wed Aug 17 15:42:04 2016 -0500 - - Added option to load in morpheus results (#206) - - * updated examples folder files - - * added option to load in Morpheus results, match PSMs with genes - - * added parallel foreach loop to make PSMs addition a bit faster - -commit fa5ebdd6073050c3bcad52eb5dbfe777e3c6e268 -Author: Anthony -Date: Mon Aug 15 12:07:43 2016 -0500 - - Fixed functionality of Add Results buttons on LDR form (#205) - - * drag and drop - - * Starting to reshape the new LDR form - - * Changed LDR over to using datagridviews. Matching files updates the gridview immediately. I removed the separate lists of InputFile objects and used one instead, so we can iterate over all of them and use the Purpose property (formerly InputFileType) to pick out the ones we want to use. Added info buttons, although the default run doesn't work yet because we need a default ptmlist path. - - * Fixed functionality of Add Results buttons. - -commit fd8076d07d9df5d4d7b91c14bfdfa879a06c0562 -Author: Anthony -Date: Mon Aug 15 11:13:38 2016 -0500 - - LoadDeconvolutionResults with DataGridViews for each of the input file types (#204) - - * drag and drop - - * Starting to reshape the new LDR form - - * Changed LDR over to using datagridviews. Matching files updates the gridview immediately. I removed the separate lists of InputFile objects and used one instead, so we can iterate over all of them and use the Purpose property (formerly InputFileType) to pick out the ones we want to use. Added info buttons, although the default run doesn't work yet because we need a default ptmlist path. - -commit f6e49e75c627c855cb42b99afac652fadf659344 (tag: 0.1.2) -Author: Anthony -Date: Fri Aug 12 13:25:55 2016 -0500 - - Corrected small errors in aggregated mass calculation; added tests for ExperimentalProteoform (#203) - - * Fixed tests to reflect Parallel.For not returning items in the same order as before. - - * Minor test fixes... - - * Fixed mysterious proteoform aggregation bug to do with the lower bound of proteoforms, where it was slightly high. Shifting the mass before doing the other calculations somehow gave this lower bound the expected values. - - * Corrected error in calculation of aggregated mass, where the monoisotopic error was being added again instead of removing before aggregation. Introduced several tests for these calculations. - - * Refactored ExperimentalProteoform tests. - - * Added small test for unlabeled aggregation. Changed a -1000000 placeholder to NaN for display table. - - * Small updates to aggregated dgv headers. - - * Small note. - -commit 103dc9755a0264426e6d9361aaf467af7a46592b -Author: Anthony -Date: Wed Aug 10 12:16:00 2016 -0500 - - Fixed tests to reflect Parallel.For not returning items in the same order as before. (#201) - - * Fixed tests to reflect Parallel.For not returning items in the same order as before. - - * Minor test fixes... - -commit 15540e0e5183577ea37c39b5f633ccacbb98bc32 -Author: Anthony -Date: Tue Aug 9 23:30:51 2016 -0500 - - Revised organization of Results.cs class; added testing for results (#200) - - - - Each results test asks whether the output strings lead to the same objects once they're read in; I made it through theoretical/decoy databases. - - Results now saves all ED relations (and a number of other changes). Added tests for the checking the validity of Components, in addition to the number processed from an excel file. - - I revised the correction interpolation code, since it was giving me a consistent "No sequence elements" error. I also moved the code for reading corrections to Lollipop, since it's fairly short. - - - * Major refactoring and reorganization of results text strings, using the new Result.cs class to host that all. Made some changes to the File and Folder dialogs. - - * Better refactoring in results, by the object we're saving. Now for testing. - - * Now saves all ED relations. - - * Added tests for validity of components added from an excel file (some failed, and they're commented out, since Shortreed's working on them). - - * Tests for Component, NeuCodePair, and ExperimentalProteoform results in-out - - * Placeholder for family results - - * added a note - - * Added test for theoretical proteoform results in-out. Still one or two things to iron out. - - * Debugged theoretical_proteoform in/out - - * Testing for decoys in/out - - * Rename one variable - - * Added corrections to method file - - * Added test for charge state correction using correction factor text file. Fixed slight error in ProteoformSweet. Checking functionality - - * Debugging corrections. - - * another edit - - * Debugged correction. It didn't work for me for the longest time. - - * Changes to Results test for theoretical proteoforms -- the Parallel.For appears to give inconsistent ordering. - -commit 73ea1112cc76685308018827f1f4a273e8edd7ae -Author: trishorts -Date: Tue Aug 9 14:16:48 2016 -0500 - - added software lockmass and fixed scan-range/reten time load (#198) - - * ET peak list change propagates to ET pairs list grid view - - * added lockmass calibration and fixed scan-range - - * merge conflicts fixed - - * try again - - * removed conflict from ET - - * fixed ldr designer - - * remove unused variable - - * display EE retention times and limit RT difference - - * allow .tsv files for correction factors - - * fixed interpolation and zero filling - - * supports 3 column data choosing best value - - * added unit test for correction factor interpolation - -commit 2807a6cb9c343001d4fd3bc3da60608e458c252c -Author: Anthony -Date: Fri Aug 5 21:30:39 2016 -0500 - - Refactoring and reorganization of results text strings, using the new Result.cs class to host that all. Made some changes to the File and Folder dialogs. (#197) - - Refactoring and reorganization - -commit 918cf804747d033dee31107e58f184ab90527cba -Author: Leah Schaffer -Date: Fri Aug 5 18:07:26 2016 -0500 - - Added save/open options (#192) - - * load and run fixes - - * excel writer - - * added save/open options - - * minor fixes - - * changed back some unintentional changes - - * minor change so PFA can be run after open results - - * fixed open bug and updated results summary - - * fixed test issue - - * fixed some things with previous commits - - * fixed typo - - * fixed small test issues - -commit eae25f285ed2050d1c09d27c4e8d83c4f2eb8568 -Author: Anthony -Date: Thu Aug 4 17:41:46 2016 -0500 - - Removed outdated Clear() method; tested add(ExperimentalProteoform) (#195) - - More tests (EF relations; ED calculation of FDR with even # of decoy DBs) - -commit 0a151f332e148dab01b709a3b9bf82fc686c5f9d -Author: Anthony -Date: Thu Aug 4 15:46:20 2016 -0500 - - ProteoformCommunity testing (#194) - - - * Updated from upstream; created new test file. - - * Tested accept_deltaM_peak and constructing families. - -commit aabd8f0465973420f20457942303ea76b94a24bc -Author: trishorts -Date: Thu Aug 4 11:47:53 2016 -0500 - - ET peak list change propagates to ET pairs list grid view (#193) - -commit 437daa6fb61d591f27aa871c1f3f7bcb2b279d71 -Author: Anthony -Date: Sun Jul 31 21:08:24 2016 -0500 - - ProteoformRelation display in families module. Resolved several crash situations. (#191) - - * Resolved crash when clicking on zero count for theoretical or experimental proteoforms in proteoform families. Some refactoring of PDR. - - * Now displays ProteoformRelations in each family when that column is clicked. Fixed TheoreticalDatabase crash on method run in DisplayWichDB event. - - * Displays table names again in dropdown during normal runthrough. - - * Allow user to cancel method load. - - * Added packages for graphing displays - -commit 814acc02325b8cfd2858fa633779f32ad05ea837 -Author: Anthony -Date: Fri Jul 29 19:20:48 2016 -0500 - - ProteoformFamilies functional (untested, as of yet) (#190) - - * Implemented proteoform family construction, using only accepted peaks. Getting very few proteoforms right now. Get many more using all relations... The data grid views now display the proteoform families, and then the experimental/theoretical proteoforms if you click on those columns in the first DGV. - - * In process of changing ProteoformRelation to only have unadjusted count in effort to simplify those relationships and find the error of getting no theoreticals in proteoform families, when only taking accepted peaks. - - * Restructured ProteoformRelation and DeltaMassPeak to have only initial putative group of relations, and then for DeltaMassPeak make the double-averaged deltaMass group. - - * Display LoadDeconvolutionResults at load. More functional this way. We'll have to figure out how to display the logo on the back of the white file list, probably with some less opacity. Also, debugged DeltaMassPeak a little more -- was finding the relation group twice, which wasn't helpful. The ProteoformFamilies looks quite a bit better, now. - - * Resolved testing error. Thanks for writing that one, Stefan\! - -commit a239f4b01ad1a7bf819dd1464fa4da932dd286b1 (tag: 0.1.1, tag: 0.1.0) -Author: trishorts -Date: Fri Jul 29 15:03:21 2016 -0500 - - manual peak shift (#189) - -commit 63d2feb962af0e063397c186cba0538cb726a94e -Author: trishorts -Date: Thu Jul 28 16:03:06 2016 -0500 - - right click change monoisotopic error (#187) - - * autoscale ET peak chart - - * added textbox for total aggregated proteoforms that updates with boundary changes - - * autoscale ee peaks and enable ee histogram axes to be adjusted - - * allow only one connection between an experimental proteoform and a unique theoretical accession number - - * allow only one connection between an experimental proteoform and a unique theoretical accession number - - * repaired conflict - - * right click adjust monoiosotpic error - - * Resolved conflicts, again... - -commit 06aff328cc3fff72e972de4de208023f9ad96c46 -Author: Anthony -Date: Thu Jul 28 15:34:55 2016 -0500 - - Updated peak displays; house cleaning (#186) - - * Returned ET peak graph to peak & dot data. - - * Updated the chart displays to have the peak count and decoy count, along with a trace from the unadjusted relation count, which is now used to select peaks. - - * Renamed decoy count to be Median Decoy Count for ET comparisons. - - * Corrected headers for the peak count and peak delta mass. Removed the columns for adjusted relation count and delta mass, since we're not using those apart from establishing peaks. Min value is used for relations that arent assigned a peak. - - * Moved the ProteoformRelation and DeltaMassPeak dgv formatting over to the DisplayUtility. Implemented this for the EEComparison form. - - * Expanded range of values for ET and EE histograms. - - * Removed field I didn't implement - - * Updated method run to not output pairs and peaks tables. - - * Polished new code in ProteoformCommunity - - * Conditional formatting for ET/EE relation dgvs. - - * Expanded range of NeuCodePair charts to allow negative chart bounds. - - * some formatting in NeuCodePairs. - -commit 903658eda0bf7351a8c25a48e068a7605722153e -Author: trishorts -Date: Thu Jul 28 14:24:19 2016 -0500 - - one theoretical accession per aggregated proteoform (#185) - - * autoscale ET peak chart - - * added textbox for total aggregated proteoforms that updates with boundary changes - - * autoscale ee peaks and enable ee histogram axes to be adjusted - - * allow only one connection between an experimental proteoform and a unique theoretical accession number - - * allow only one connection between an experimental proteoform and a unique theoretical accession number - - * repaired conflict - -commit ac54dc23b86ad12b753aa583459cae3555609410 -Author: Leah Schaffer -Date: Thu Jul 28 14:05:40 2016 -0500 - - load and run (#184) - - * EE GUI - - * GUI improvements - - * fixed some relation peak issues - - * GUI improvements + moved acceptable field to component - - * load and run - - * test - - * fixed small EE ct issue - -commit 72c89d4579886eca45d7ac6c73aa684e7f6c0950 -Author: Leah Schaffer -Date: Thu Jul 28 11:34:12 2016 -0500 - - GUI edits + fixed some peak issues (#181) - - * EE GUI - - * GUI improvements - - * fixed some relation peak issues - -commit 629f42f772d9e9c685fbc4648a400d779331931f -Author: trishorts -Date: Wed Jul 27 21:16:37 2016 -0500 - - ee improvments (#180) - - * autoscale ET peak chart - - * added textbox for total aggregated proteoforms that updates with boundary changes - - * autoscale ee peaks and enable ee histogram axes to be adjusted - -commit a3a5ce350ed4820f20c2836c51220fe6820f85a4 -Author: trishorts -Date: Wed Jul 27 21:04:25 2016 -0500 - - textbox for aggregated proteoforms that updates with boudary changes (#179) - - * autoscale ET peak chart - - * added textbox for total aggregated proteoforms that updates with boundary changes - -commit d19eb040c3eb3c3a3e0444f51c0ea6eb646c6935 -Author: trishorts -Date: Wed Jul 27 19:21:15 2016 -0500 - - autoscale ET peak chart (#178) - -commit 184baf94587374a0eb38c249a44a7d4473cef058 -Author: stefanks -Date: Wed Jul 27 18:02:08 2016 -0500 - - Test relate_ed method (#177) - - * Move excelreader - - * coverage - -commit be8e955961ef6de1639fafd4b9ee63d6ace084a0 -Author: stefanks -Date: Wed Jul 27 16:57:59 2016 -0500 - - Move excelreader (#176) - -commit ad574e1ba1cbfc8720ec07b1db3718a14f7ee207 -Author: Anthony -Date: Wed Jul 27 16:24:14 2016 -0500 - - Peak charts now display peak count, decoy count, and unadjusted relation trace (#174) - - * Returned ET peak graph to peak & dot data. - - * Updated the chart displays to have the peak count and decoy count, along with a trace from the unadjusted relation count, which is now used to select peaks. - -commit af78cbceb1304ce3c57cac0aa8bef8c8dd587849 -Author: trishorts -Date: Wed Jul 27 16:11:51 2016 -0500 - - peak accepted (#173) - - * add ptm assignmenet to detalmass peak - - * corrected test of deltamasspeakcreate - - * format peak assignment column in peaks_dgv and autoscale et_peaks_chart - - * made grid editable - - * delta mass peak accepted - - * delta mass peak accepted - - * update ee figures of merit - - * formated EE peaks datagridview table - -commit ae067bdda54941837ff9dfdb7307f3f7cf2da3ee -Author: trishorts -Date: Wed Jul 27 11:29:13 2016 -0500 - - formating et peak assignment column in dgv and added autoscale of et peak in chart (#171) - - * add ptm assignmenet to detalmass peak - - * corrected test of deltamasspeakcreate - - * format peak assignment column in peaks_dgv and autoscale et_peaks_chart - - * made grid editable - -commit ad8f299065a1d063d4bba9bd1d3f8e95c73d69e7 -Author: trishorts -Date: Tue Jul 26 17:05:41 2016 -0500 - - add ptm assignmenet to detalmass peak (#170) - - * add ptm assignmenet to detalmass peak - - * corrected test of deltamasspeakcreate - -commit 2901ae769f110e913af8a3ab700feb43fe71815f -Merge: 92fcd63 70e1503 -Author: Anthony -Date: Tue Jul 26 13:52:35 2016 -0500 - - Merge pull request #169 from trishorts/master - - parallel fix System.AggregateException: One or more errors occurred. … - -commit 70e1503829b88f9d8bbae3309a86ddc283271ecf -Author: trishorts -Date: Tue Jul 26 13:03:30 2016 -0500 - - parallel fix System.AggregateException: One or more errors occurred. ---> System.IndexOutOfRangeException: Index was outside the bounds of the array. - -commit 92fcd634b33797922633cc2059314cf7ee4eb390 -Merge: 7e50c53 0ce658a -Author: Anthony -Date: Tue Jul 26 12:54:37 2016 -0500 - - Merge pull request #166 from lschaffer2/master - - ET GUI, and only allow in-range decimals to form peaks for EE/ET - -commit 0ce658a43fc5d3fb1a23d65ba05a8a963119865f -Merge: 8bc7e47 7e50c53 -Author: Leah Schaffer -Date: Tue Jul 26 12:43:05 2016 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit 8bc7e47fc0d5b2d2c4e42b52db43b40256f393d0 -Author: Leah Schaffer -Date: Tue Jul 26 12:42:53 2016 -0500 - - undadjusted group count/histogram - -commit 7e50c534e9a982efa6a6c8f3b825cf496bcb99f0 -Merge: 114bd42 42d112a -Author: Anthony -Date: Tue Jul 26 11:49:25 2016 -0500 - - Merge pull request #167 from trishorts/master - - test 0PTMs in theoreticaldatabasecreate - -commit 42d112a5651baa1cec46996314cbf41165ac5329 -Author: trishorts -Date: Tue Jul 26 11:03:44 2016 -0500 - - background thread processing of raw components and deleted null removal - -commit 8a321736e6843ec352d431a6e88635c6fcb1cc49 -Author: trishorts -Date: Tue Jul 26 09:24:48 2016 -0500 - - Fix error in parallel method - -commit bd28d0d78417555541763213b5ff5faded01fcda -Merge: d3228d8 0de5cfb -Author: trishorts -Date: Tue Jul 26 08:30:19 2016 -0500 - - Merge branch 'master' of https://github.com/trishorts/proteoform-suite - -commit d3228d8c5de91c61b7f9fd3ba3d608151a5bb5c4 -Author: trishorts -Date: Tue Jul 26 08:08:11 2016 -0500 - - test 0PTMs in theoreticaldatabasecreate - -commit 0de5cfb59da80bd202a51be85b28459e4008b9af -Merge: d1e98ae 114bd42 -Author: trishorts -Date: Tue Jul 26 08:09:02 2016 -0500 - - Merge branch 'master' into master - -commit d1e98ae7f525f8d2b56ff3a4c14ad1173c034fe2 -Author: trishorts -Date: Tue Jul 26 08:08:11 2016 -0500 - - test 0PTMs in theoreticaldatabasecreate - -commit 7d994e17efc7cda20a4b330b25953a141eb81a88 -Author: Leah Schaffer -Date: Mon Jul 25 19:08:41 2016 -0500 - - acutally fixed merge conflicts... - -commit c3f233d3366ac1fa73429b8963936949b481495d -Merge: bbeedd8 114bd42 -Author: Leah Schaffer -Date: Mon Jul 25 18:53:09 2016 -0500 - - fixed merge conflict - -commit bbeedd8c61d79b5fc71f903eeefdf6db162fe28b -Author: Leah Schaffer -Date: Mon Jul 25 18:51:08 2016 -0500 - - ET GUI, fixed some relation peak formation - -commit 114bd421ad10083b787e32f1b715230dd855839f -Merge: d5376c2 1d8d371 -Author: Anthony -Date: Mon Jul 25 11:21:12 2016 -0500 - - Merge pull request #165 from trishorts/master - - adjust the upper and lower bounds of ET depending on neucode_labelled - -commit 1d8d371e890bc89b2680f394f40919eab2fd6028 -Author: trishorts -Date: Mon Jul 25 10:45:45 2016 -0500 - - nothing. fixed my test architecture to x64 to run tests - -commit 2a311e74df6d31eebc6fcab76d45d56aa5129640 -Author: trishorts -Date: Mon Jul 25 10:25:54 2016 -0500 - - activate makedatabase button only after xml and ptmlist files are selected - -commit 4f47407af030a2cefd81c6161d9ca9dad890ecd4 -Author: Leah Schaffer -Date: Mon Jul 25 10:13:58 2016 -0500 - - added neucode pairs test - -commit a329fd5ca64999fba1f1d0a541dcd34fefba4cfa -Author: trishorts -Date: Mon Jul 25 09:38:06 2016 -0500 - - adjust the upper and lower bounds of ET depending on neucode_labelled - -commit d5376c244e49bf3a4d0a0ae3c4c74edda417adf6 -Merge: 490bfc1 731fa5d -Author: Anthony -Date: Thu Jul 21 21:01:58 2016 -0500 - - Merge pull request #162 from lschaffer2/master - - Added neucode pairs testing - -commit 731fa5d10a994c4edf9f44c38cd994c6ee3d7683 -Author: Leah Schaffer -Date: Thu Jul 21 19:12:20 2016 -0500 - - added tests for neucode pairs - -commit a5fb2bc63a8c43cccd556db9c049ce43ad90a8e6 -Author: Leah Schaffer -Date: Thu Jul 21 19:11:51 2016 -0500 - - more dgv formatting - -commit eeeec13b26baae2e28b73ebab418deb33cbc4a8a -Merge: 490bfc1 67320ca -Author: Leah Schaffer -Date: Thu Jul 21 18:12:01 2016 -0500 - - Merge branch 'master' of https://github.com/trishorts/proteoform-suite into trishorts_branch - -commit 490bfc185c5af27ecc988fd3422004c53bb6bb1e -Merge: 17cc45c b1d0219 -Author: Anthony -Date: Thu Jul 21 17:43:14 2016 -0500 - - Merge pull request #158 from lschaffer2/master - - DGV formatting, commenting out parallel loops w/ issues, no mans land bug - -commit 67320ca78da7d6ffe7fc7c9bfd856e040279ab28 -Author: trishorts -Date: Thu Jul 21 14:20:44 2016 -0500 - - TestProcessRawCompnoents with traveling excel file - -commit b1d0219bc06000d1041319603fc04271f78a9d8a -Author: Leah Schaffer -Date: Thu Jul 21 13:43:59 2016 -0500 - - fixed neucode pair bugs w/ I ratio and K count - -commit f0f5c3f8fa377d536d1832e96215c50855b4bd03 -Author: Leah Schaffer -Date: Thu Jul 21 13:42:10 2016 -0500 - - REC dgv formatting - -commit 2aec87d1b88faf706e5270d04078795dad9078e3 -Author: Leah Schaffer -Date: Wed Jul 20 09:53:59 2016 -0500 - - tiny change to values of max et and ee - -commit 40170669d24f31d131937029e7f3e287b0120f02 -Author: Leah Schaffer -Date: Wed Jul 20 09:51:06 2016 -0500 - - fixed issues with previous commits - -commit 1a4ce379f125b1630fac187a34358d22d0597ead -Author: Leah Schaffer -Date: Tue Jul 19 20:30:04 2016 -0500 - - format dgv for theoretical - -commit bc62883bec96f4b1492a4e41a00f580fbe26fa49 -Merge: 1d2c416 17cc45c -Author: Leah Schaffer -Date: Tue Jul 19 20:28:13 2016 -0500 - - fixed merge conflicts - -commit 1d2c41662bcd69bed3c2f68443d0d41a4c61be9c -Author: Leah Schaffer -Date: Tue Jul 19 20:16:42 2016 -0500 - - fixed noMansLand bug, commented out issue-causing parallel foreach loops - -commit 17cc45c581fb2c57cc7c6b6a1cc4988e379d63bb -Merge: cda41e0 86fa466 -Author: Anthony -Date: Tue Jul 19 14:17:36 2016 -0500 - - Merge pull request #157 from trishorts/master - - using the new DisplayUtility for Target and Decoy - -commit 86fa4660fbd7685a87acf5f9c38130a32636c0b3 -Author: trishorts -Date: Tue Jul 19 14:13:32 2016 -0500 - - displays fragment in theo database display. added uniq identifier - -commit 48be42bea36247b461fb44e761da79208cfa01d3 -Author: trishorts -Date: Tue Jul 19 12:53:30 2016 -0500 - - removed parllelization in database creation - -commit 459629c0470780f71b9575da83e1affab351843e -Author: trishorts -Date: Tue Jul 19 12:47:08 2016 -0500 - - fixed - -commit e0991f27506ca6f925ad1f090db04fa993ac08a6 -Author: trishorts -Date: Tue Jul 19 12:33:24 2016 -0500 - - using the new DisplayUtility for Target and Decoy - -commit e986990c3b5fd10c4c3e32a088e67899f5a4ce9b -Author: Leah Schaffer -Date: Tue Jul 19 09:24:18 2016 -0500 - - fixed ET Run the Gamut and small EE/ET relation issues - -commit 219ef20c0ad4bb09988b7512dee9b5d2659be788 -Author: Leah Schaffer -Date: Fri Jul 15 12:01:13 2016 -0500 - - fixed dgv for neucode, agg, and theoretical - -commit cda41e0c238e9861d20f99351c01f74c244a1b16 -Merge: 08d2890 0c20568 -Author: Anthony -Date: Mon Jul 18 12:03:37 2016 -0500 - - Merge pull request #156 from trishorts/master - - split relate into relate_et and relate_ee - -commit 0c205688365121e065a967e58ed5e134c96b09e6 -Author: trishorts -Date: Mon Jul 18 12:00:55 2016 -0500 - - dlete - -commit f87ff836a33e6ad91ddf67acab552f9f0fe27999 -Author: trishorts -Date: Mon Jul 18 11:42:57 2016 -0500 - - split relate into relate_et and relate_ee - -commit 08d28903acf2857c083b6726c475ea480cfdc6e0 -Merge: b7b9f86 8e314d2 -Author: Anthony -Date: Fri Jul 15 15:48:26 2016 -0500 - - Merge pull request #155 from trishorts/master - - allow unlabel in proteoform community relate and add multiple unit tests - -commit 8e314d2900c48200ca05a521b2e3705f8b2edb36 -Merge: cba3455 ac1fd9c -Author: trishorts -Date: Fri Jul 15 15:08:14 2016 -0500 - - Merge branch 'master' of https://github.com/trishorts/proteoform-suite - -commit cba3455bd5b9910817a55e7f36cb22d0845b55a6 -Author: trishorts -Date: Fri Jul 15 15:04:26 2016 -0500 - - add test class - -commit ac1fd9cdcc56fc63eeae5804461dfa1e98eb6595 -Merge: aec41a8 b7b9f86 -Author: trishorts -Date: Fri Jul 15 14:37:07 2016 -0500 - - Merge branch 'master' into master - -commit aec41a8783770f5d6db9ccc3bede27aad67f7db9 -Author: trishorts -Date: Fri Jul 15 14:34:15 2016 -0500 - - allow unlabel in proteoform community relate and add multiple unit tests - -commit b7b9f86ec9645dbddf8f387e8c2f7058c59ca8ca -Merge: 1b50e53 0ca8f16 -Author: Anthony -Date: Fri Jul 15 13:40:17 2016 -0500 - - Merge pull request #154 from stefanks/master - - Fix get_combinations and test it - -commit 0ca8f1654037b43a65e02b10f40fff50522ce5bd -Author: Stefan S -Date: Fri Jul 15 13:39:13 2016 -0500 - - TheoreticalProteoform.ToString() fix to account for empty ptm_list. Don't artificially add empty PTM list to proteoform_community - -commit 01ce4f6443dfedfc310926e3b620cde6e8b2c745 -Author: Stefan S -Date: Fri Jul 15 13:27:43 2016 -0500 - - Make sure mass of 0 combination is returned - -commit 7532716b71fb55b7f66d5ca8596b6ea5ec5e4f23 -Author: stefanks -Date: Fri Jul 15 13:11:46 2016 -0500 - - Add coverage badge - -commit 1fefe65369083c9e6bedc864b724387eaee27711 -Author: Stefan S -Date: Fri Jul 15 11:20:04 2016 -0500 - - Make get_combinations return an empty combination as well - -commit c34bfbf1416b5b925796caa86a4bfd3db55fa0c0 -Merge: 836d1e4 ab30361 -Author: Stefan S -Date: Fri Jul 15 11:06:24 2016 -0500 - - Merge branch 'master' of https://github.com/stefanks/proteoform-suite - -commit 836d1e4af8c68b717217238cbd8126f6c93f850b -Author: Stefan S -Date: Fri Jul 15 11:06:21 2016 -0500 - - Fix bugs with modification combination code - -commit ab303611cfe9eae3700ef5759fd76557aaecd080 -Merge: a967937 1b50e53 -Author: stefanks -Date: Fri Jul 15 08:45:30 2016 -0500 - - Merge pull request #2 from smith-chem-wisc/master - - merge - -commit 1b50e5388541f545696a337646d5576d63679283 -Merge: 0e8b311 042501a -Author: Anthony -Date: Thu Jul 14 23:40:54 2016 -0500 - - Merge pull request #152 from acesnik/master - - Finished implementing peak assignments, display in peak charts - -commit 042501ae0d96c03d7acd2bd26b8d77473da6ff41 -Author: Anthony -Date: Thu Jul 14 23:34:32 2016 -0500 - - Finished implementing peak assignments. Worked out the display of peaks in the charts, along with the decoy counts (or unequal lysine falses for EE) in the chart. Some minor edits to the split container positions. Deleted ED, since I'm displaying that information in the ET plot; we don't make ED peaks,so a whole separate form doesn't seem necessary. - -commit 0e8b311e0e86c43e52eef7dc1a42d94001c4fc30 -Merge: 83d1e91 eb5670b -Author: Anthony -Date: Thu Jul 14 17:59:57 2016 -0500 - - Merge pull request #151 from lschaffer2/master - - added results summary, formatted dgv, fixed if user updates parameter, changed filepath in load-and-run method - -commit eb5670b59306f724ea82fd56ce7e1b110f0287e3 -Author: Leah Schaffer -Date: Thu Jul 14 15:20:34 2016 -0500 - - made it so only acceptable neucode pairs are aggregated - -commit 2462eef9c8999b319b47ef3b5ad3105c486c5afa -Author: Leah Schaffer -Date: Thu Jul 14 15:09:35 2016 -0500 - - commented out unused variable that was causing error - -commit 42bf9e049189e97e48ceca6216298e978e896c46 -Author: Leah Schaffer -Date: Thu Jul 14 14:31:24 2016 -0500 - - made dgv look nicer, added code to account for certain parameter changes - -commit 9a38254861256d16d7146fcf9d7067e7f87f6f2e -Author: Leah Schaffer -Date: Thu Jul 14 14:27:56 2016 -0500 - - made file path from Debug folder for xml - -commit 54a2c35870409ce2819da3165b0175e60eca85bb -Author: Leah Schaffer -Date: Thu Jul 14 14:09:08 2016 -0500 - - added results summary page - -commit 83d1e91e91ae7288f61e3d4a2edaf6cf837c13e8 -Merge: 496ce62 77a793e -Author: Anthony -Date: Wed Jul 13 17:39:49 2016 -0500 - - Merge pull request #149 from acesnik/master - - Extended the sortable DataGridView display to the other Forms - -commit 77a793eb5bf13c123ddba3b97f11227604b014ab -Author: Anthony -Date: Wed Jul 13 17:35:25 2016 -0500 - - Extended the sortable DataGridView work to the other Forms. Also, NeuCodePairs works more consistently. There were null objects being entered into the list, which is concerning; I simply removed those null elements for the time being. - -commit 496ce623da6673305c5789fe4a58b87be65d4d5f -Merge: 17ca7e1 e9f36b7 -Author: Anthony -Date: Wed Jul 13 12:03:30 2016 -0500 - - Merge pull request #148 from trishorts/master - - utility for sortable lists of objects in datagridview - -commit e9f36b77339f9631861e33b93d3385356ed7f604 -Merge: 21ba530 17ca7e1 -Author: trishorts -Date: Wed Jul 13 12:01:20 2016 -0500 - - Merge branch 'master' into master - -commit 21ba53052078378f61ea1101f0f86bbccb1bf8a0 -Author: trishorts -Date: Wed Jul 13 11:58:49 2016 -0500 - - utility for sortable lists of objects in datagridview - -commit 17ca7e1bf47e65293539e409aef5048f46d7d988 -Merge: 6cc89c0 0d8836b -Author: stefanks -Date: Wed Jul 13 09:23:55 2016 -0500 - - Merge pull request #147 from trishorts/master - - space for test of pull - -commit 0d8836b9e44e2c423323c801408e7480fdbe9ebf -Author: trishorts -Date: Wed Jul 13 09:05:19 2016 -0500 - - space for test of pull - -commit 6cc89c0c6f24c146d010661a0a75bc2e1f264123 -Merge: ea84771 11aeb9b -Author: stefanks -Date: Tue Jul 12 17:22:43 2016 -0500 - - Merge pull request #146 from smith-chem-wisc/stefanks-patch-1 - - Update README.md - -commit 11aeb9badc3b08f05f858ee37647b4a06f4fdf3c -Author: stefanks -Date: Tue Jul 12 17:16:26 2016 -0500 - - Update README.md - -commit ea8477137e9654ca9809bc0ba96e0e7e91438a2f -Author: stefanks -Date: Tue Jul 12 17:13:34 2016 -0500 - - update readme - -commit e1e5df9c0d0a71444e589fb460748ff1f413086b -Author: stefanks -Date: Tue Jul 12 17:13:10 2016 -0500 - - update readme - -commit f21c48cf13a5cc21d031c53d1417ff1627218a27 -Merge: fce9ed3 a967937 -Author: stefanks -Date: Tue Jul 12 16:55:47 2016 -0500 - - Merge pull request #145 from stefanks/master - - change to x64 - -commit a9679370aa22eab78a39b0ac6995413f230677cc -Author: Stefan S -Date: Tue Jul 12 16:55:36 2016 -0500 - - change to x64 - -commit fce9ed31124d9d23528db4a9dd697d85c6ba59d1 -Merge: e6fe4db 8e7bec9 -Author: stefanks -Date: Tue Jul 12 16:47:54 2016 -0500 - - Merge pull request #144 from stefanks/master - - remove unused - -commit 8e7bec9a5fdf9f92242ab2d9d5aa4ffdee7e8935 -Author: Stefan S -Date: Tue Jul 12 16:47:39 2016 -0500 - - remove unused - -commit e6fe4db3ad6a4c8e4ad9593460134789e76acbb9 -Merge: b821771 329b786 -Author: stefanks -Date: Tue Jul 12 16:33:37 2016 -0500 - - Merge pull request #143 from stefanks/master - - remove unused - -commit 329b786f914cfc908304a59e028537f8ae88a381 -Author: Stefan S -Date: Tue Jul 12 16:33:25 2016 -0500 - - remove unused - -commit b8217710d2720661f6a01499fa2644e6e4117ca1 -Merge: 03f33c5 da6071e -Author: stefanks -Date: Tue Jul 12 16:27:34 2016 -0500 - - Merge pull request #142 from stefanks/master - - add new keyword - -commit da6071e8f6ef61a6cd91a2c9e18e330d13c6c7c1 -Author: Stefan S -Date: Tue Jul 12 16:27:07 2016 -0500 - - add new keyword - -commit 03f33c551e27c061ae0d3e586a1571dc003c2526 -Merge: 3663c92 37a669e -Author: stefanks -Date: Tue Jul 12 14:41:19 2016 -0500 - - Merge pull request #141 from stefanks/master - - renaming, organizing - -commit 37a669ec7300f2a66bde55c043e44f435d284f2c -Author: Stefan S -Date: Tue Jul 12 14:40:57 2016 -0500 - - renaming, organizing - -commit 3663c92c7dc8b66169e7c30e7d6039de27c50150 -Merge: 150777d aa9c58b -Author: stefanks -Date: Tue Jul 12 14:38:23 2016 -0500 - - Merge pull request #140 from stefanks/master - - renaming - -commit aa9c58b4464bfe5144ddabf85a56d3f9ba16008b -Author: Stefan S -Date: Tue Jul 12 14:38:03 2016 -0500 - - renaming - -commit 150777d14801beb131add9a0a042e53b4a8076ec -Merge: c2112c3 f11944c -Author: stefanks -Date: Tue Jul 12 14:35:12 2016 -0500 - - Merge pull request #139 from stefanks/master - - merge structural changes - -commit f11944cc272d2f21217fdfb0a2f3d8197a69332a -Author: Stefan S -Date: Tue Jul 12 14:34:37 2016 -0500 - - make compile - -commit b57c5aefefc34ffb444b5464b38ed21733b465c5 -Merge: 52f789e afcd5ac -Author: Stefan S -Date: Tue Jul 12 14:30:51 2016 -0500 - - Merge branch 'smith-chem-wisc-master' - -commit afcd5ac2916805ac32284fa91e9414f2a3cda224 -Merge: 52f789e c2112c3 -Author: Stefan S -Date: Tue Jul 12 14:29:45 2016 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite into smith-chem-wisc-master - -commit 52f789eba3745c8ce5b9f243d99401199e598295 -Author: Stefan S -Date: Tue Jul 12 14:25:56 2016 -0500 - - update to commit - -commit c2112c3181f15b40dab82fcd79eab9afce020501 -Merge: a02dbc6 614bb52 -Author: Anthony -Date: Tue Jul 12 14:02:54 2016 -0500 - - Merge pull request #138 from trishorts/master - - unmodified theoretical bug fixes - -commit 614bb528c76a6266c12300a7bac929e0fefca963 -Author: trishorts -Date: Tue Jul 12 13:57:13 2016 -0500 - - unmodified theoretical bug fixes - -commit 92c0331926e282bc2a53e7dc81dc459db07116ad -Author: Stefan S -Date: Tue Jul 12 13:09:04 2016 -0500 - - Add testing - -commit a02dbc6de61b14ed2075dc4ecaf129abdf70f090 -Merge: 2f0fd97 274a063 -Author: Anthony -Date: Tue Jul 12 12:05:19 2016 -0500 - - Merge pull request #137 from acesnik/master - - Implemented NeuCode toolstrip disable in DataTable-oriented code - -commit 274a063550a1fa30e356534323d97d757d86bc4d -Author: Anthony -Date: Tue Jul 12 11:57:16 2016 -0500 - - Implemented NeuCode toolstrip disable in DataTable-oriented code when neucode labeled checkbox unchecked. - -commit cfb22b5bda3e7d4c2484a35539b97deecc83fe82 -Author: Stefan S -Date: Tue Jul 12 11:50:04 2016 -0500 - - so many - -commit 2f0fd97276d26fceba4b142954d6746ecf818140 (tag: 0.0.2) -Merge: cc48307 f66e960 -Author: Anthony -Date: Mon Jul 11 22:11:26 2016 -0500 - - Merge pull request #136 from acesnik/master - - Modified data structure to allow for ExperimentalProteoforms to be constructed from Component - -commit f66e96042fb54b296faa24e930f37ab281a8ae2d -Author: Anthony -Date: Mon Jul 11 22:10:14 2016 -0500 - - Restored the dgv functionality through TheoreticalDatabase. NeuCodePair works inconsistently, for unkown reasons. - -commit b3d1995a380113d5ce880ce53827cc56da770989 -Author: Anthony -Date: Mon Jul 11 18:56:16 2016 -0500 - - Added NeuCode-labeled checkbox and implemented the change to ProteoformSweet's toolbar for the neucode step. Implemented this checkbox in the raw component aggregation. Also, changed the csv file generation to tsv. - -commit 2cf019b749286202fc6d4ea45ac6f7fb7bc1a385 -Author: Anthony -Date: Mon Jul 11 13:27:28 2016 -0500 - - another small change to NeuCodePair. - -commit 9d2064f4cee09c39ce06e904638cbd0a2cf2d29b -Author: Anthony -Date: Mon Jul 11 13:25:20 2016 -0500 - - typo correction - -commit af554226e278340e6c5aad5be77626e2c7909b77 -Author: Anthony -Date: Mon Jul 11 13:21:50 2016 -0500 - - Modified proteoform aggregation to allow for aggregation of raw experimental components when no neucode pairs are created. This includes making NeuCodePair a derivative class of RawExperimentalComponent, where the light neucode component is taken as the base component. Also, ExperimentalProteoform now takes in a list of Component objects, which may be NeuCodePair objects, and it aggregates them irrespective of lysine count if the component is not a NeuCodePair. Proteoforms now start with a lysine count of -1 to indicate there is no lysine count assigned. - -commit 3d91da94d81c9baa46bbc6a78d6a1491e65f0e19 -Author: Anthony -Date: Mon Jul 11 11:46:34 2016 -0500 - - annotation of tests - -commit cc483075570097e416dace07881fa8d2d951ed06 -Merge: d9d5d0e 9f98d7f -Author: Anthony -Date: Fri Jul 8 15:05:22 2016 -0500 - - Merge pull request #134 from acesnik/master - - Basic unit test example, using method from Lollipop - -commit 9f98d7f3a27c5db14f0230fec0a3223736c62d80 -Author: Anthony -Date: Fri Jul 8 14:57:58 2016 -0500 - - Basic unit test example using method in Lollipop. - -commit f66112f5797dbafe1960f836a1d97eacfbb4a41c -Author: Anthony -Date: Thu Jul 7 18:11:00 2016 -0500 - - Typographical changes to PDR - -commit d9d5d0e93d9c018a36c01292ae07383dc660cb61 -Merge: 634d55c 1bda020 -Author: Anthony -Date: Thu Jul 7 17:07:23 2016 -0500 - - Merge pull request #133 from acesnik/master - - Revised trishorts changes to accomodate compressed files. - -commit 1bda0206cd2476c9d561f32cce948219313bc7dc -Author: Anthony -Date: Thu Jul 7 17:04:51 2016 -0500 - - Revised trishorts changes to accomodate compressed files. - -commit 634d55cda8d9f6442be37ee4013f649a071644f2 -Merge: ee6e5ab c4666f6 -Author: Anthony -Date: Thu Jul 7 08:44:00 2016 -0500 - - Merge pull request #131 from trishorts/master - - Now streaming XML files for lower RAM usage - -commit c4666f64d58a916153f779882e7cccdc5af76498 -Author: trishorts -Date: Wed Jul 6 15:02:44 2016 -0500 - - eliminated .gz files from uniprot filetype til I can figure it out - -commit 865805dfb5631752d07cdb4b01e003c8e0b1cd80 -Author: trishorts -Date: Wed Jul 6 15:01:54 2016 -0500 - - Streams UniProt XML by entry to lower memory footprint - -commit ee6e5ab5ff5493a902f83b8aa8825987ef330370 -Merge: afe5073 b87276b -Author: Anthony -Date: Wed Jun 29 17:15:49 2016 -0500 - - Merge pull request #130 from acesnik/master - - Added object-oriented implementation - -commit b87276bb666f4c2df3f2e2e21ca9dc22b1f81fb7 -Author: Anthony -Date: Wed Jun 29 17:12:10 2016 -0500 - - Added object-oriented implementation as a folder in master. See branch in acesnik for commit history. - -commit 34af2936948873ffe472f157ad2efc5508f3fdb7 -Merge: afe5073 0e53ad3 -Author: Anthony -Date: Wed Jun 29 15:55:50 2016 -0500 - - Merge branch 'master' of https://github.com/acesnik/proteoform-suite - -commit afe507314ca2e4795f458f43009990ff89e8f122 (tag: 0.0.1) -Merge: d24a4ac 5540f26 -Author: Anthony -Date: Wed Jun 29 15:52:58 2016 -0500 - - Merge pull request #129 from lschaffer2/master - - fixed up load and run, added label free to L&R, updated results summary - -commit d24a4aceac22a73175657d0f8700e9753084f30c -Merge: c592157 db699e0 -Author: Anthony -Date: Wed Jun 29 12:14:00 2016 -0500 - - Merge pull request #128 from trishorts/master - - fix ET for label free comparison and add more feature types to proteoform database reader - -commit 5540f26fa7d2167102094bd72fff44836149389d -Author: Leah Schaffer -Date: Tue Jun 28 16:14:23 2016 -0500 - - updated results summary - -commit 8dc8896d0339ca55f67108dc74da6997a86443ad -Author: Leah Schaffer -Date: Tue Jun 28 16:14:00 2016 -0500 - - added load and run with default parameters to test data - -commit fb7fe808293dc320a3ccddade53ab31086a06446 -Author: Leah Schaffer -Date: Tue Jun 28 15:49:56 2016 -0500 - - changed back 2 accidental changes - -commit 90af6a191c0edfa28cc73c166e0264c18f969dfa -Merge: f57d1d7 c592157 -Author: Leah Schaffer -Date: Tue Jun 28 15:20:47 2016 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit db699e0cc2ec81288bc474565d8270bc219574aa -Author: trishorts -Date: Tue Jun 28 15:13:07 2016 -0500 - - add more switch case conditions to stop crash during read of feature in debug mode - -commit 7bab8498f855487de40f37c68a5af13228b8112c -Author: trishorts -Date: Tue Jun 28 15:12:05 2016 -0500 - - adjusted comparision for label free and eliminated greater than sign - -commit f57d1d70c8722b1ede1aca1cb4ef2d24dc6ae816 -Author: Leah Schaffer -Date: Tue Jun 28 15:05:49 2016 -0500 - - fixed some load and run issues - -commit 05cf3770c4a1d8f25afc92b997037b96a3f492c1 -Author: Leah Schaffer -Date: Thu Jun 23 18:14:39 2016 -0500 - - added unlabeled option for load and run - -commit 0e53ad393f2b9c4d6a254e9fa4ccfa87727ae6bd -Author: Anthony -Date: Mon Jun 20 19:09:33 2016 -0500 - - post-build - -commit c5921579bc540f1b52a09fdcd57338152427ba96 (tag: 0.0.0) -Merge: 3535138 0dd9939 -Author: Anthony -Date: Mon Jun 20 19:07:26 2016 -0500 - - Merge pull request #126 from acesnik/master - - Add license and readme - -commit 0dd99397a819dadb8ff5cd4d555be52d68743d44 -Author: Anthony -Date: Mon Jun 20 19:01:30 2016 -0500 - - Add license and readme - -commit 3535138f3f6ab5643b28d75930fb5e0b530f927c -Merge: cf3af35 77fe018 -Author: Anthony -Date: Mon Jun 20 18:43:13 2016 -0500 - - Merge pull request #124 from lschaffer2/master - - fixed decoy-decoy bugs, fixed EE updates, added label free option - -commit 77fe01809ce323de7d830ea5de052b886e80dde5 -Author: Leah Schaffer -Date: Mon Jun 20 11:02:24 2016 -0500 - - added label free option - -commit d28aef7bed68b56cdbbab5a57a19fb014ec51975 -Author: Leah Schaffer -Date: Fri Jun 17 10:37:53 2016 -0500 - - fixed EE for when user updates something - -commit 7415f2bce0977bcad09a0804b48ee83e67fbbd6e -Author: Leah Schaffer -Date: Mon Jun 6 15:06:12 2016 -0500 - - fixed decoy-decoy bugs - -commit cf3af353ad6ee5e6579e235d8dc90e3782c3b430 -Merge: 65ccff9 efa4798 -Author: Anthony -Date: Thu Jun 2 10:11:03 2016 -0500 - - Merge pull request #122 from lschaffer2/master - - fixed decoy-decoy, added this to results summary temporarily - -commit efa4798ddcd4effbde2813d68176a190da412ecf -Merge: ba1be57 65ccff9 -Author: Leah Schaffer -Date: Tue May 31 17:26:08 2016 -0500 - - fixed merge conflict - -commit ba1be57fdce952016de189f6f12a8165783744c1 -Author: Leah Schaffer -Date: Tue May 31 17:22:51 2016 -0500 - - fixed decoy-decoy, added this to results summary temporarily - -commit 65ccff9207179ef75c27ca9d4e1014a4d76cbd15 -Merge: e2f48ef d43fa48 -Author: Anthony -Date: Tue May 31 11:32:40 2016 -0500 - - Merge pull request #121 from acesnik/master - - Output all results of method-run to CSV. - -commit d43fa48cc42520a98427826b881169118b7ab205 -Author: Anthony -Date: Tue May 31 11:31:04 2016 -0500 - - Output all results of method-run to CSV. Also, runs theoretical database construction and raw component processing in parallel. - -commit e2f48ef3f341b4586a8a381b9b77a22dd6780382 -Merge: ef73b06 7d291de -Author: Anthony -Date: Tue May 31 09:43:18 2016 -0500 - - Merge pull request #120 from trishorts/master - - parallelization and csv output - -commit 7d291dee710fb88620341d4b3afb0ae88d58c9cf -Author: trishorts -Date: Tue May 31 09:40:41 2016 -0500 - - parallelization and csv output - -commit ef73b0662e1ca492edd4e46f0f0883d67e9cce6f (origin/object-oriented) -Merge: 91ac21a 95fce13 -Author: Anthony -Date: Fri May 20 19:23:58 2016 -0500 - - Merge pull request #115 from zrolfs/master - - Reworked PFA - -commit 91ac21ad6c8bf58faf561701ae0487b8282231fb -Merge: 5cc6652 10a9b77 -Author: Anthony -Date: Fri May 20 19:22:41 2016 -0500 - - Merge pull request #118 from lschaffer2/master - - added results summary page per Brian's request - -commit 10a9b77bac7e9736bd9674896b3cd0173b94e27c -Author: Leah Schaffer -Date: Fri May 20 15:31:09 2016 -0500 - - added results summary page per Brian's request - -commit 95fce135ec405c975d01ce0921040a77dcdde54d -Author: zrolfs -Date: Fri May 20 14:46:25 2016 -0500 - - changed EE back - -commit c010eb1f1f0b0f19d5979d352120a2865dc1723b -Author: zrolfs -Date: Fri May 20 14:44:13 2016 -0500 - - Completely changed approach for assigning families to accomodate ET pairs without EE pairs - -commit 13000021c22c160fd780d192b6f53c52726d3583 -Merge: f2406f1 5cc6652 -Author: zrolfs -Date: Fri May 20 14:42:22 2016 -0500 - - updating local copyMerge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit 5cc6652ee1e2d08ab7756502916b8b20f54788ab -Merge: 8857e92 dddd540 -Author: Anthony -Date: Fri May 20 14:25:31 2016 -0500 - - Merge pull request #114 from lschaffer2/master - - added decoy-decoy module, also short decon results file for tests - -commit dddd5400497f88b0fdafc7c51a69ef78c7c975b6 -Merge: d254871 8857e92 -Author: Leah Schaffer -Date: Fri May 20 13:34:48 2016 -0500 - - added decoy decoy module - -commit d254871df6f602d8cbc3edd203c399d73ffce0a9 -Author: Leah Schaffer -Date: Thu May 19 15:00:09 2016 -0500 - - small decoy database change - -commit 8857e92bfcacd8fb88d9f6e2382aab80462caa80 -Merge: 4f466e5 356ed92 -Author: Anthony -Date: Wed May 18 20:28:30 2016 -0500 - - Merge pull request #112 from trishorts/master - - added parallel processing to getExperimentalComponents also change to decoy databases - -commit 356ed9223d18ca6951094950517433ece05b2af2 -Author: trishorts -Date: Wed May 18 13:46:36 2016 -0500 - - added 1 line to make decoy databases have identical lysine count profile to theoretical - -commit 4a1a7fcd5bc2a0137dacc4a67869b5bd587f69fb -Author: trishorts -Date: Wed May 18 13:45:46 2016 -0500 - - added some parallel processing to make rawExpComp faster - -commit f2406f156ab69873afe76867ee9d66a871282fe4 -Author: zrolfs -Date: Tue May 17 13:05:08 2016 -0500 - - Added framework for PFA fix - -commit 4f466e5a0b957494a83949ffc5cc19e1b851101f -Merge: 8d1a5d0 1416cab -Author: Anthony -Date: Mon May 16 18:17:42 2016 -0500 - - Merge pull request #111 from zrolfs/master - - Remade export on a reset master and force pushed - -commit 1416cabfb404f208d2d429a3a5c5fb5dc2710796 -Author: zrolfs -Date: Mon May 16 16:46:34 2016 -0500 - - Remade export on a reset master after royaly confusing myself - -commit 8d1a5d0183b16ab3b99d1541ce18dc64e85e5032 -Merge: 202f90c 6fe9490 -Author: Anthony -Date: Fri May 13 19:04:13 2016 -0500 - - Merge pull request #109 from acesnik/master - - Selected, modified changes from Zach - -commit 6fe949036b5d44344999c5cb9898aced9b8258b4 -Author: acesnik -Date: Fri May 13 19:03:09 2016 -0500 - - Modified Zach's changes to work with method run. - -commit 4710f80f1e19933f9748883b4b2792b6d65422b5 -Author: acesnik -Date: Fri May 13 18:45:34 2016 -0500 - - Test selected changes from Zach - -commit 202f90c6871a630d5d05d0c372d5552799a9c2a8 -Merge: f46f558 dc6298f -Author: Anthony -Date: Wed May 11 21:41:01 2016 -0500 - - Merge pull request #106 from acesnik/master - - Added icon; NeuCodePairs settings panel made not so tiny by default - -commit dc6298f614b8cb7c10499e4a94a2f088769b5e8b -Author: Anthony -Date: Wed May 11 21:39:03 2016 -0500 - - Added icon; NeuCodePairs settings panel made not so tiny by default. - -commit f46f558b958a179313aa6eafdd49cf7d44e2d3fd -Merge: 47cd8e5 9b9631d -Author: Anthony -Date: Wed May 11 19:43:28 2016 -0500 - - Merge pull request #105 from acesnik/master - - Allow regeneration of databases. Simplified using ProteinGroups -> Protein casting. - -commit 9b9631dcf46988fad1932f19eaefc6dff1773373 -Author: Anthony -Date: Wed May 11 19:38:41 2016 -0500 - - Added new checkbox to method file - -commit 308dea3b240779ba7602f355482dcad2ec0d5caa -Author: Anthony -Date: Wed May 11 19:35:50 2016 -0500 - - Used ProteinSequenceGroup -> Protein type casting to reduce redundancy - -commit 47cd8e55be8ddb15acc66d917b9d889d0eb69c62 -Merge: 6bac3aa 2cf9f30 -Author: Anthony -Date: Wed May 11 17:03:48 2016 -0500 - - Merge pull request #104 from acesnik/master - - Allow user to read *.xml.gz to generate databases. - -commit 2cf9f3082e7f573fc260fe8475f67db0488a9393 -Author: Anthony -Date: Wed May 11 17:00:28 2016 -0500 - - Allow user to read *.xml.gz to generate databases. - -commit 6bac3aa4545340a4014d06953915ee7d25a03581 -Merge: ed4b8fb eb9ae74 -Author: Anthony -Date: Wed May 11 16:06:38 2016 -0500 - - Merge pull request #102 from zrolfs/master - - Resolved whatever was going on earlier. - -commit eb9ae74a6d04e43f56bf9f3193c7bb71abeef098 -Author: zrolfs -Date: Wed May 11 15:20:44 2016 -0500 - - 160511_320 - -commit 2930d95a5e2e161d615129efa3f5869b090d3981 -Merge: db3ac5a ed4b8fb -Author: zrolfs -Date: Wed May 11 15:06:32 2016 -0500 - - do not want this commit - -commit db3ac5a10d6e4e48e3a77b62b5d1f2b72272dc48 -Author: zrolfs -Date: Wed May 11 14:56:01 2016 -0500 - - 160511_255 - -commit ed4b8fb80da64298c91250b4ad79061813abb58c -Merge: 57652b1 2633bc6 -Author: Anthony -Date: Wed May 11 14:28:06 2016 -0500 - - Merge pull request #101 from acesnik/master - - Reverted pull 99, fixed EE bug, kept Shortreed's changes - -commit 2633bc64d1e95a4e097e1ddb727cf08788c8da7a -Merge: 477660b 4add0c6 -Author: Anthony -Date: Wed May 11 14:22:11 2016 -0500 - - Merge commit '4add0c6358fc643cec3e1c26fe0f80e80fe6a290' into reverted_99 - -commit 477660b62a5bf5a2a8b66155ca38737dd8ef4b08 -Merge: 3c87266 57652b1 -Author: Anthony -Date: Wed May 11 14:20:46 2016 -0500 - - Merge commit '57652b1a32eef55a2db4c2d260bc514cef010b7c' into reverted_99 - -commit 4add0c6358fc643cec3e1c26fe0f80e80fe6a290 -Author: Anthony -Date: Wed May 11 14:12:33 2016 -0500 - - Fixed bugs that prevented manual runthrough in EE. - -commit 5d04956410e2f806bb36ecc21cfaef7d66716830 -Merge: e54e801 57652b1 -Author: zrolfs -Date: Wed May 11 13:21:36 2016 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - - WhyAmIMerging160511_122 - WhyAmIMerging160511_122 - -commit e54e8011f8f4beb656bdce358e708dfb57d53ea8 -Merge: e4bff80 e204a3c -Author: zrolfs -Date: Wed May 11 13:21:21 2016 -0500 - - 160511_121commit - -commit 57652b1a32eef55a2db4c2d260bc514cef010b7c -Merge: e204a3c c966af4 -Author: Anthony -Date: Wed May 11 13:20:30 2016 -0500 - - Merge pull request #100 from trishorts/master - - use aggregated database for theo and decoy and ET - -commit 3c8726633e90b483300da226b8840ef238a00f8a -Author: Anthony -Date: Wed May 11 13:19:12 2016 -0500 - - Revert "Export Proteoform Families" - -commit e204a3c65b6dc00341527077dfc0074bc8764f39 -Merge: 7b68d12 acf3262 -Author: Anthony -Date: Wed May 11 13:19:03 2016 -0500 - - Merge pull request #99 from zrolfs/master - - Export Proteoform Families - -commit c966af410144b0e3641b385ad7eea2c4fe6f1ffd -Author: trishorts -Date: Wed May 11 13:16:02 2016 -0500 - - uses aggregated DB for theo/decoy when checked - -commit e4bff80d8b95804a71eb926c405a4c0a9ebc8820 -Author: zrolfs -Date: Wed May 11 12:52:11 2016 -0500 - - tiny edits preventing a rebase - -commit c383d9dd906033b0e0124c6ff1916763083e6fd8 -Author: zrolfs -Date: Wed May 11 09:40:44 2016 -0500 - - Export Data Upload Attempt 3 - -commit 9fe9be8e79a8e6c0ddfde06f0237b770b7c1be3d -Author: zrolfs -Date: Tue May 10 15:10:34 2016 -0500 - - Export Proteoform Families to CSV - -commit 0afd40932787d30479c27712edab579c8528557b -Author: trishorts -Date: Wed May 11 12:52:19 2016 -0500 - - added aggregated proteoforms checkbox - -commit acf3262b1cacb5859d053477e893d0b359b3c30b -Author: zrolfs -Date: Wed May 11 09:40:44 2016 -0500 - - Export Data Upload Attempt 3 - -commit 7b68d12c6fc354009599c60637822a2df5995fde -Merge: d0e1130 f872a5e -Author: Anthony -Date: Tue May 10 20:06:58 2016 -0500 - - Merge pull request #98 from acesnik/master - - Looked through that commit; replaced 2 lines missing from EE - -commit f872a5e5d8c5350243baf02fcb8f07a7c8822c86 -Merge: 3c27e96 d0e1130 -Author: Anthony -Date: Tue May 10 19:58:47 2016 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit 3c27e9674f07ad912ea0d49345e3ff13228d3299 -Author: Anthony -Date: Tue May 10 19:58:10 2016 -0500 - - Manual validation of bad commit; found missing MouseMove events in EE - -commit d0e1130c7f35543738cd894dac46ef78cdef35a6 -Merge: 7ff635a d33681a -Author: Anthony -Date: Tue May 10 16:42:49 2016 -0500 - - Merge pull request #96 from acesnik/master - - Allow user to select files in LoadDeconvolution form for method run - -commit d33681a479a7e76edb14af910d5a3d2e1b707561 -Author: Anthony -Date: Tue May 10 16:41:57 2016 -0500 - - Allow user to select files in LoadDeconvolution form for method run. - -commit 7ff635ac307c4892f6602b3fd40e6e0051646489 -Merge: b024afb 5ee53af -Author: Anthony -Date: Tue May 10 16:22:29 2016 -0500 - - Merge pull request #95 from lschaffer2/master - - Decoy databases now different from one another - -commit df72acab5a2c43cde13aa5947caae98c3754fd5c -Merge: dd5a576 b024afb -Author: zrolfs -Date: Tue May 10 16:16:23 2016 -0500 - - Export Proteoform Families for CytoScape - -commit 5ee53af2620000304e779f51ae178e43f4c159b0 -Author: Leah Schaffer -Date: Tue May 10 16:08:32 2016 -0500 - - Decoy databases now different from one another - -commit b024afbeac89e970cb6fe35ff29e158dccd7b117 -Merge: ff253b0 5d5ec75 -Author: Anthony -Date: Tue May 10 16:03:05 2016 -0500 - - Merge pull request #93 from trishorts/master - - added proteinSequenceGroups class and aggregator code - -commit 9bda18bfd83c417621907097a50c9f3bf41a92d8 -Author: Anthony -Date: Tue May 10 15:32:37 2016 -0500 - - created packages.config - -commit dd5a576e9061c25daf068b48cba02b4423081f85 -Author: zrolfs -Date: Tue May 10 15:10:34 2016 -0500 - - Export Proteoform Families to CSV - -commit 5d5ec75ea92b8f8e91df02b0e39c165a28063887 -Author: trishorts -Date: Tue May 10 15:03:55 2016 -0500 - - small bit of code to aggregate protein[] proteins into proteinSequenceGroups[] - -commit 69147bf8991db512355e8b71e800599bce8663b5 -Author: trishorts -Date: Tue May 10 15:02:57 2016 -0500 - - added the proteinSequenceGroups class that aggregates proteins that share sequences - -commit ff253b050749c836cea3b0aa7c46da7fc7f26b75 -Merge: 98bcc82 aa5c7fd -Author: Anthony -Date: Tue May 10 14:44:35 2016 -0500 - - Merge pull request #91 from trishorts/master - - deleted some comments - -commit 98bcc82eaa38c3385845f28a51b305508c0197f3 -Merge: 260a7f7 ec533a8 -Author: Anthony -Date: Tue May 10 14:43:17 2016 -0500 - - Merge pull request #92 from acesnik/master - - Fixed/refined if-statements in load events - -commit ec533a8e34359ee04578988de308c6a2be73e82b -Author: Anthony -Date: Tue May 10 14:40:54 2016 -0500 - - Modified checks for whether the form has been loaded. This fixes the one that was throwing an exception in ED, and the others are now more general. - -commit aa5c7fd1dbfeadde181927ea282aae07144f567c -Merge: d09c876 260a7f7 -Author: trishorts -Date: Tue May 10 14:33:47 2016 -0500 - - updated neucode pairs to current and deleted comments - -commit 260a7f7d443cc08d146a98304947c6bd524f1b88 -Merge: 087d92b 5f9d17c -Author: Anthony -Date: Tue May 10 14:25:51 2016 -0500 - - Merge pull request #90 from lschaffer2/master - - Fixed ED - -commit 5f9d17cba8a4b3c1d8d699b6ae27252e169da1b1 -Author: Leah Schaffer -Date: Tue May 10 13:55:00 2016 -0500 - - Fixed ED - -commit 087d92bb2663757b4fc644ad21d2d376ee41b05d -Merge: 36a62c6 462d41c -Author: Anthony -Date: Mon May 9 22:03:52 2016 -0500 - - Merge pull request #89 from acesnik/master - - Implemented Save, Load-&-Run method file - -commit 462d41cbbc3e04890729d6dbc14ab5803c2aa46b -Author: Anthony -Date: Mon May 9 21:59:26 2016 -0500 - - Implemented Load-&-Run method. After saving a method file from a test run, the method can be modified with the files to run in a tab-delimited format. The program will then run through the working logic of each module. When finished, it loads the data into the DataGridViews and graphs, but does not run through the working logic again upon load. - -commit c425a42f71b6fea2eab9db8c1f31f4c3f4a1faaf -Author: Anthony -Date: Mon May 9 19:49:33 2016 -0500 - - Reorganized Form1 to allow the display of each form in succession. Added methods to print and read settings from a method file. Next: move working logic out of GUI actions to allow full run. - -commit 36a62c67a457e6009239bc07267edb0f4e1af571 -Merge: 8ad802f d99f4eb -Author: Anthony -Date: Fri May 6 17:44:58 2016 -0500 - - Merge pull request #88 from acesnik/master - - Recovered Shortreed and Leah's changes - -commit d99f4eb114ea9663e73fd341841919e4030bcff6 -Author: Anthony -Date: Fri May 6 17:34:49 2016 -0500 - - Small edit to neuCodePairs dgv display. - -commit d955a108fea46e0ef022cfdc7b14856e29914b28 -Author: Anthony -Date: Fri May 6 17:21:51 2016 -0500 - - Reloaded ProteoformFamilyAssignment from most recent commit to fix errors. Code from commit b4259de524fd23a3d4133af52253e9ffdc0b730b, which I based this fix on, specifically the Excel work, was the issue. - -commit c94877117083d026d278281e1365948c81d85ce7 -Merge: eb2ce6e 8ad802f -Author: Anthony -Date: Fri May 6 16:50:25 2016 -0500 - - Finished purging bad commit - -commit eb2ce6ee34a68793804132a546d610f5dd1b76c6 -Merge: 62be224 2afe078 -Author: Anthony -Date: Fri May 6 16:34:51 2016 -0500 - - Merge branch 'shortreed_latest_commit' into after_shortreed_commit - -commit 62be224c5dd332b65b5e0cb5b00870e22f6d5121 -Merge: 08c6f02 e52c23d -Author: Anthony -Date: Fri May 6 16:32:25 2016 -0500 - - Merge branch 'fix_build_errors' into after_shortreed_commit - -commit 08c6f026d447c9f21e262d13f60269544840d979 -Merge: 7ff4675 51219e0 -Author: Anthony -Date: Fri May 6 16:28:54 2016 -0500 - - Merge branch 'shortreed_changes' into after_leahs_commit - -commit 7ff4675db2c96feea30c56ccd027ea1d0feea275 -Merge: fd7e69c 593d025 -Author: Anthony -Date: Fri May 6 16:27:23 2016 -0500 - - Added Leah's changes from 'can't load ED w/out decoy database' - -commit fd7e69ce3ecea81854b831c67a72b1e8fb1c398c -Merge: b4259de aecafd8 -Author: Anthony -Date: Fri May 6 14:51:01 2016 -0500 - - Purged bad commit f9af7a1f488dd5c85e3844266ad6bf10aec6e74b - -commit d09c8763c18b1c45a08618fb99e8158f83cc2c50 -Author: trishorts -Date: Fri May 6 12:48:48 2016 -0500 - - eliminates dictionary lookup in favor or dt.select to fix bug related to duplicate entries - -commit 4a9b93c9ca21b1e217c1c9024bc9024ed1ccdc4f -Author: trishorts -Date: Fri May 6 12:46:10 2016 -0500 - - uses proteoform family columns from ee and et to construct families - -commit 8ad802fd3d629ca945182309b12bb2af76a5cddb -Merge: 2afe078 cb8f9dd -Author: Anthony -Date: Fri May 6 11:31:45 2016 -0500 - - Merge pull request #85 from acesnik/master - - Updated rounding to column formatting. Removed DataTableHandler class. - -commit 2afe078c6b76eb4c57c90aa251b3a1e6fc5d476b -Merge: 7782507 1df158f -Author: Anthony -Date: Fri May 6 11:30:38 2016 -0500 - - Merge pull request #84 from trishorts/master - - added proteoform family column to eePairs List. Also added event hand… - -commit 1df158f117b763e70aa81b5474bdd5eaa24b38d6 -Author: trishorts -Date: Fri May 6 10:21:48 2016 -0500 - - RunTheGamut back in action in EE-form - -commit bc241cd3c9234bf12330e3183f40c84dd1160650 -Author: trishorts -Date: Fri May 6 09:57:03 2016 -0500 - - changes to eePeakList causes changes to eePairsList proteoform family - -commit f046bec5c3b691fe82782fb499e066fc19c5ba92 -Author: trishorts -Date: Fri May 6 09:22:02 2016 -0500 - - added proteoform family column to eePairs List. Also added event handlers for changes to eePeaksAcceptable - -commit cb8f9dd787025196eaa41b9a079e58d5888ffa41 -Author: Anthony -Date: Fri May 6 00:31:02 2016 -0500 - - Updated rounding to column formatting. Removed DataTableHandler class. - -commit 778250707b8fee590328726112c0d1b2aeabc346 -Merge: c073cd8 e52c23d -Author: Anthony -Date: Thu May 5 23:13:57 2016 -0500 - - Merge pull request #83 from acesnik/master - - Fixed build errors in EDComparison and ETComparison.Designer - -commit e52c23d0609de6c965037c16f20e4be6db361fbd -Author: Anthony -Date: Thu May 5 23:13:20 2016 -0500 - - Fixed build errors in EDComparison and ETComparison.Designer - -commit c073cd82d747ed07b09f51f27eae5ebb0a6557de -Merge: 591d7fb 51219e0 -Author: Anthony -Date: Thu May 5 22:52:48 2016 -0500 - - Merge pull request #82 from acesnik/master - - Accepted Shortreed & Leah's changes - -commit 51219e0dd29398f080ed0165e364848c47cbbd9a -Merge: 593d025 980b4c0 -Author: Anthony -Date: Thu May 5 22:48:52 2016 -0500 - - Merge branch 'master' of https://github.com/trishorts/proteoform-suite - -commit 593d025ca96333be7cabb8890148b7a5f1d2ae49 -Merge: 591d7fb aecafd8 -Author: Anthony -Date: Thu May 5 22:44:35 2016 -0500 - - Merge branch 'master' of https://github.com/lschaffer2/proteoform-suite - -commit 980b4c0e3d76f4c538d5f0bcc4b9fc8f11f78833 -Author: trishorts -Date: Thu May 5 15:54:18 2016 -0500 - - ddd - -commit eab5e4a1fa43379b50988e4ea38ca89d6c25c286 -Author: trishorts -Date: Thu May 5 15:17:57 2016 -0500 - - minor naming changes - -commit 4f85cdc9ad7212d21f3661b7e1c59b2dcbce0a9d -Author: trishorts -Date: Thu May 5 15:17:08 2016 -0500 - - local form control of datagridview plus local eePairs and eePeaks datatables - -commit e8e1aced322195d338d22d68474eb0ebd9be65e1 -Author: trishorts -Date: Thu May 5 12:12:32 2016 -0500 - - proteoform family assignment now uses different column from ETPairs that limits with pairs can be used in families - -commit 5dac8ebcec99ffe117c6b60bfd1ce8d0430a0db7 -Author: trishorts -Date: Thu May 5 11:41:53 2016 -0500 - - re-activated run the gammut. added comments. added boolean flag to prevent several events from automatically firing on form load - -commit d0dd8f73e368a45efb2d2e937890f05a4bf8b29a -Author: trishorts -Date: Thu May 5 09:45:07 2016 -0500 - - propagate changes to etPeakList acceptable to etPairsList Proteoform Family which will modulate which pairs are used in the family construction - -commit 57a136237246ed0588e135d3b407c538fed5c330 -Author: trishorts -Date: Wed May 4 13:32:55 2016 -0500 - - change edit permission on dgv_ET_peaks to prevent change to delta mass and count but allow changes to acceptable - -commit d70550001420f6850e8f6234da8059d588a0adde -Author: trishorts -Date: Wed May 4 12:28:19 2016 -0500 - - readline in etpairs histogram moves with threshold changes - -commit e28003b77f87e364928ca9de99c63a45ebdfb278 -Author: trishorts -Date: Wed May 4 12:05:24 2016 -0500 - - Figures of merit updated with changes in peakCtMinThreshold - -commit 30009e8cb495cf901a72fde13cd723527b977581 -Author: trishorts -Date: Wed May 4 11:53:56 2016 -0500 - - boolean Acceptable in etPeakList and Proteoform Family in etPairsList are adjusted automatically with changes to nUD_minthreshold - -commit 755ae9e3c23b3bfff2fca907f1e322a3c6626373 -Author: trishorts -Date: Wed May 4 10:15:19 2016 -0500 - - added column to etpairs table boolean for inclusion in proteoform families - -commit 372a4958212223be29d2b2265a04e836ad2c3602 -Author: trishorts -Date: Wed May 4 10:00:14 2016 -0500 - - further trimming. use local etpeaks and etpairs table in place of global.etpairs - -commit 1c171f5058689da53dc912474c4feb8c444adc85 -Author: trishorts -Date: Wed May 4 09:43:27 2016 -0500 - - eliminated BindingSource in ET Form - -commit aecafd88545250a9865ac36e2c89ab1c2d2d861b -Author: Leah Schaffer -Date: Tue May 3 14:26:07 2016 -0500 - - can't load ED w/out decoy database - -commit 591d7fbdacac4b208da6658078f097b86022d99d -Merge: 72b7b30 e2d14e4 -Author: Anthony -Date: Tue May 3 11:37:25 2016 -0500 - - Merge pull request #77 from zrolfs/master - - Issue 75 - -commit e2d14e4d407c64b0688a0c915b394eb0d0189c3e -Author: zrolfs -Date: Tue May 3 11:09:11 2016 -0500 - - added zipped test data file - -commit 98b98a985b908ca3277e39ef4d9e7201189cd36c -Author: zrolfs -Date: Tue May 3 10:44:00 2016 -0500 - - Issue 75, upload attempt3 - -commit 8aa9f4c9dd1b45d4daa0f3b77ba298df4b9cab30 -Author: zrolfs -Date: Tue May 3 10:31:28 2016 -0500 - - Closed issue #75 upload issues part 2 - -commit 5a6c4a85d995bc93a8d6d4c9b4903d8502ffc477 -Author: zrolfs -Date: Tue May 3 10:13:40 2016 -0500 - - Closed issue #75 - -commit f9af7a1f488dd5c85e3844266ad6bf10aec6e74b -Merge: b4259de 72b7b30 -Author: zrolfs -Date: Tue May 3 09:36:29 2016 -0500 - - Merge remote-tracking branch 'refs/remotes/smith-chem-wisc/master' - -commit b4259de524fd23a3d4133af52253e9ffdc0b730b -Author: zrolfs -Date: Tue May 3 09:27:59 2016 -0500 - - not sure how dated this is, but closed issue #75 - -commit 72b7b3043fec18ea537f2069c591df7543e8fe7c -Merge: b972ff3 5ccca72 -Author: Anthony -Date: Fri Apr 29 16:16:51 2016 -0500 - - Merge pull request #76 from trishorts/master - - ET Form Tables displayed/controled/rounded in form - -commit 5ccca72446e16c70789d46313ebc7c58023b5e36 -Author: trishorts -Date: Fri Apr 29 15:48:22 2016 -0500 - - ET Form datgridview tables controlled locally with rounding. Eliminated datatablehandler here - -commit b972ff3108a54696481343bae77e55919a3fedf2 -Merge: 630972d 57d2c40 -Author: Anthony -Date: Tue Apr 26 17:26:15 2016 -0500 - - Merge pull request #73 from lschaffer2/master - - added peak intellisense to everything - -commit 630972db1c5814929a8635ce9455f91c5193ff61 -Merge: 3e4b4b2 b6c2856 -Author: Anthony -Date: Tue Apr 26 17:26:04 2016 -0500 - - Merge pull request #74 from zrolfs/master - - PFA is fast, Node datagrid added, peak bug fixed - -commit b6c2856022572d0d42037d4d39ea31c4e7fa2410 -Author: zrolfs -Date: Tue Apr 26 16:36:48 2016 -0500 - - Fixed the most obnoxious little bug in PFA like you would not believe - -commit 57d2c40ee568d13253d5145c928c439fa621c3d4 -Author: Leah Schaffer -Date: Tue Apr 26 16:00:14 2016 -0500 - - added peak intellisense to everything - -commit 89e083648c197bb420627a6d168667e96578825c -Author: zrolfs -Date: Tue Apr 26 10:03:43 2016 -0500 - - Made ProteoformFamilyAssignment peak sensitive (do what it was meant to do) - -commit 3e4b4b26263eb787d5a4f842499d2f8bc3780ea3 -Merge: 0bcc8ed 11877ed -Author: Anthony -Date: Mon Apr 25 18:38:49 2016 -0500 - - Merge pull request #71 from lschaffer2/master - - fixed up ED - -commit 11877ed7dbb787f683e3ceb18398b4d67f02bdc0 -Author: Leah Schaffer -Date: Mon Apr 25 17:16:14 2016 -0500 - - added run the gamut to ET - -commit 04344cda0ff123cf9a36bce1a1f46ff362dc429b -Author: Leah Schaffer -Date: Mon Apr 25 16:39:54 2016 -0500 - - update - -commit 36085a036d49e37e4e964da2bd9bfa5097aed715 -Author: Leah Schaffer -Date: Mon Apr 25 15:52:57 2016 -0500 - - fixed up ED - -commit 0bcc8ed484eee3338e503477ba808d4c118bef98 -Merge: 4f50089 20414d2 -Author: Anthony -Date: Mon Apr 25 10:01:52 2016 -0500 - - Merge pull request #70 from trishorts/master - - added decimal display column to table of ED - -commit 20414d282ccd11fa43c242763ce692fa8acb7d35 -Author: trishorts -Date: Mon Apr 25 09:18:08 2016 -0500 - - added decimal display column to table of ED - -commit 4f500891ff94ba206422b140ffdc709be2a7c818 -Merge: d00fdbd 4411811 -Author: Anthony -Date: Fri Apr 22 16:00:32 2016 -0500 - - Merge pull request #68 from trishorts/master - - resolve problems with identical monoisotopic mass in raw proteoform list - -commit 44118117f77d9dbd1fcc9ef59aaf9cd33c1c4526 -Author: trishorts -Date: Fri Apr 22 14:04:41 2016 -0500 - - resolve problems with identical monoisotopic mass in raw proteoform list - -commit d00fdbd9df18d6b1a35714bf19bfe4af519de67c -Merge: cc78535 a0b4333 -Author: Anthony -Date: Thu Apr 14 20:58:02 2016 -0500 - - Merge pull request #67 from lschaffer2/master - - ED - only works for one decoy database - -commit cc7853506b7271ae019d376689c4a9a541e01f21 -Merge: 557aca3 9331a35 -Author: Anthony -Date: Thu Apr 14 20:56:53 2016 -0500 - - Merge pull request #66 from zrolfs/master - - Added axis and shaded PFA. Oddly says all modules have been changed, … - -commit a0b43338135e3f9b9d2e2caf38e91d7978461e0f -Author: Leah Schaffer -Date: Thu Apr 14 19:42:38 2016 -0500 - - ED - only works for one decoy database - -commit 9331a355d29ca58e0c9a232b75fc172289b39229 -Author: zrolfs -Date: Thu Apr 14 18:15:16 2016 -0500 - - Added axis and shaded PFA. Oddly says all modules have been changed, so have to look into that... - -commit 557aca302ffd911b4118566142037f64b84fca8e -Merge: 2660be7 a40530f -Author: Anthony -Date: Tue Apr 12 14:30:13 2016 -0500 - - Merge pull request #63 from zrolfs/master - - Made ProteoformFamilyAssignment supa speedy. Like, 0.5 s speedy - -commit a40530f5b5e0928defdb414da0c15e569d16cc1d -Author: zrolfs -Date: Tue Apr 12 13:46:17 2016 -0500 - - Made ProteoformFamilyAssignment supa speedy. Like, 0.5 s speedy - -commit 2660be797306ee8c9e070427c1969a485cf23530 -Merge: 11e8ee4 0bd990b -Author: Anthony -Date: Sat Apr 2 20:28:09 2016 -0500 - - Merge pull request #47 from acesnik/master - - Table rounding extravaganza - -commit 0bd990bb50068760af6fd3e363c5a2689ad8e3ff -Author: Anthony -Date: Sat Apr 2 20:26:03 2016 -0500 - - Table rounding extravaganza. I added a new class DataTableHandler, which simplifies the creation of BindingSources for DataGridView objects. This class also features a method for rounding tables before displaying them. We need to be should keep the full number of sig figs stored for calculations and recalculations. This class allows that, while enabling rounding for displays. Finally, I also changed the name of RawExperimentalProteoforms to RawExperimentalComponents, per Brian's notes. - -commit 11e8ee44489901ffb86deb95a29a368c54d277e7 -Merge: 915e143 41d62c6 -Author: Anthony -Date: Fri Apr 1 13:43:59 2016 -0500 - - Merge pull request #46 from acesnik/master - - Merged bug fixes for PFA, ET, and TD - -commit 41d62c6e4683645e13e19dd21eef2c2cbcae54dd -Author: Anthony -Date: Fri Apr 1 13:42:58 2016 -0500 - - Merged bug fixes for ET, PFA and TD - -commit 717568cc4adf65d937132ac5465127d0d9d5a7a0 -Merge: 915e143 6be4951 -Author: Anthony -Date: Fri Apr 1 13:40:05 2016 -0500 - - Merge branch 'master' of https://github.com/acesnik/proteoform-suite - -commit 915e143747d568999a47f5c5893e6a732223dbbc -Merge: 55900bf bbf9836 -Author: Anthony -Date: Fri Apr 1 13:19:55 2016 -0500 - - Merge pull request #44 from lschaffer2/master - - fixed ET bug that messed up peak list - -commit 6be4951f744007b2f4b51b6df3c4e69441afd366 -Author: Anthony -Date: Fri Apr 1 13:02:16 2016 -0500 - - Updated TheoreticalDatabase GUI to show miniumum peptide length; Updated fragment name to fill empty lines; removed messageBoxes in proteoformFamilyAssignment - -commit bbf98368c55e81a72e05f58a22bea5626cde244c -Author: Leah Schaffer -Date: Fri Apr 1 12:26:43 2016 -0500 - - fixed ET bug that messed up peak list - -commit 55900bf44b3f7c6b4458a7e45134d2d4b7dec6a5 -Merge: 7617548 5612aa9 -Author: Anthony -Date: Fri Apr 1 10:19:09 2016 -0500 - - Merge pull request #43 from lschaffer2/master - - add mini histogram to ET - -commit 5612aa9dc4ab3424530b0cb6a982911267e063c0 -Author: Leah Schaffer -Date: Fri Apr 1 10:10:20 2016 -0500 - - add mini histogram to ET - -commit 761754867a8acbef4c4913a46417d3dea193cad7 -Merge: c789292 1d3ad56 -Author: Anthony -Date: Thu Mar 31 16:53:09 2016 -0500 - - Merge pull request #29 from zrolfs/master - - prettier ProteoformFamilyAssignment code - -commit c789292eb5dc05693c0fd6a9dd7362ae7646dbdb -Merge: d0cf8b0 4c4a03b -Author: Anthony -Date: Thu Mar 31 16:50:47 2016 -0500 - - Merge pull request #28 from lschaffer2/master - - EE xmin and xmax for graph were switched around - -commit 1d3ad56aac3a7452aa52bf9941c5b7da2f5f4a80 -Author: zrolfs -Date: Thu Mar 31 16:41:44 2016 -0500 - - prettier code - -commit 4c4a03bdfb452a78057aa722c934718a664b61d4 -Author: lschaffer2 -Date: Thu Mar 31 15:06:42 2016 -0500 - - EE xmin and xmax for graph were switched around - -commit d0cf8b02e3bf93905af035aae7127d04e28903bb -Merge: fd88d2b 775f7d5 -Author: Anthony -Date: Thu Mar 31 10:19:57 2016 -0500 - - Merge pull request #23 from zrolfs/master - - Functional Proteoform Family Assignment code - -commit 775f7d5f4a4cf5f3040079cc45d599405f03474d -Author: zrolfs -Date: Thu Mar 31 09:43:01 2016 -0500 - - Removed messageboxes used for troubleshooting - -commit 4a77379a5f8d24ba41032683a194ea74fdfe23fc -Author: zrolfs -Date: Thu Mar 31 09:38:21 2016 -0500 - - Works on my machine with the rest of the suite now! - -commit fd88d2b499fb7a8500fb0d5480a5d3327af0c0f4 -Merge: f617078 a4c63fa -Author: Anthony -Date: Wed Mar 30 19:13:56 2016 -0500 - - Merge pull request #22 from acesnik/master - - Leah's fixes to the EE design - -commit a4c63faf86edc4386df3735b63ed51571e4cdcec -Merge: f617078 8101f1d -Author: Anthony -Date: Wed Mar 30 19:09:42 2016 -0500 - - Pulled Leah's changes to try merger - -commit 8101f1dfd51e326c55f8a350142faf2b1dd297d5 -Author: lschaffer2 -Date: Wed Mar 30 18:34:52 2016 -0500 - - fixed EE design - -commit f617078861e4c3dd6eb79e1a934bb9ece4cbdc7e -Merge: bb2bad8 3389cdb -Author: Anthony -Date: Wed Mar 30 18:12:38 2016 -0500 - - Merge pull request #20 from acesnik/master - - Rewrite of TheoreticalDatabase to take custom XML proteome DBs - -commit 3389cdb48e8849e3d34774917c89beaa2e057edd -Merge: c319c7b 2b318c4 -Author: Anthony -Date: Wed Mar 30 18:07:37 2016 -0500 - - Successful, tested merge of rewritten TheoreticalDatabase implementation with the current version of the code from upstream. Also, successful test of reading a custom geneprotxml database. - -commit 2b318c401375f75eb0a578f3c6f5ad80e1cd85a5 -Author: Anthony -Date: Wed Mar 30 17:34:41 2016 -0500 - - Implemented XDocument instead of XmlReader in rewrite of TheoreticalDatabase. - Also, I fixed two issues regarding fragments: 1) previously, single amino acid fragments were being included in the databases. These are now excluded with a minimum peptide length cutoff that the user can select; 2) previously, chain peptides redundant of methionine cleavage products or the full length protein were not considered. Now, these are filtered out. - These changes were tested with the manual testing we have been doing so far. - -commit c319c7b6e92d12cb875d5c70bf9dcea1b3c898ab -Merge: c6617c6 bb2bad8 -Author: Anthony -Date: Wed Mar 30 00:57:43 2016 -0500 - - Merge branch 'master' of https://github.com/smith-chem-wisc/proteoform-suite - -commit aab487a52dd5b659ebd94486265bc4cd09ab02b5 -Author: Anthony -Date: Wed Mar 30 00:54:42 2016 -0500 - - Removed XML Serializer as the means of reading xml databases. Implemented XML Reader in its place. Performed large amount of code simplification in the process. - -commit bb2bad8e0e05f72b1ac12b1069b9c125bb83e0e1 -Merge: 83e3340 0f89374 -Author: Anthony -Date: Tue Mar 29 19:47:33 2016 -0500 - - Merge pull request #19 from zrolfs/master - - Integration of ProteoformFamilyAssignment code & form - -commit 0f89374a0b526f6b44735ccd460d71d1e4f8a75e -Author: zrolfs -Date: Tue Mar 29 14:19:41 2016 -0500 - - Oh Lawd please let this work/goodluck/thanks Anthony/you the best/is there a character limit? - -commit 20e438cc450edeffdc8c54a5caa56e575a8ca1bc -Author: zrolfs -Date: Tue Mar 29 13:00:25 2016 -0500 - - Hellllo Anthony? - -commit 456045e5726c98f5a13cd413e04dca7e14504644 -Author: zrolfs -Date: Tue Mar 29 10:26:49 2016 -0500 - - Hi Anthony! - -commit c6617c699f2a0549687788824b34a4c681c57911 -Author: Anthony -Date: Fri Mar 25 15:10:04 2016 -0500 - - Small change to ptmlist.txt refresh - -commit 85789591d9e09bc4fbd3e2ae02b7bb070d34d2b6 -Author: Anthony -Date: Fri Mar 25 15:01:12 2016 -0500 - - Refactored Modifications.cs (from ModData.cs) and ProteomeDatabaseReader (from ReadPTMList.cs) - -commit 83e33402f770eb150c0d1d214333c26751f604f2 -Merge: 8e9f0f1 043f21f -Author: Anthony -Date: Thu Mar 24 19:16:53 2016 -0500 - - Merge pull request #18 from acesnik/master - - Refactored TheoreticalDatabase - -commit 043f21fff13af5facca74fa159039e7af7636baf -Author: Anthony -Date: Thu Mar 24 19:14:31 2016 -0500 - - Refactored TheoreticalDatabase -- 1) Removed redundancies, 2) singularized the problem of entering theoretical proteoform families with the new method EnterTheoreticalProteoformFamily. - -commit 8e9f0f1662f912fffb7b4ae970c4944fa0fde512 -Merge: 1c7a3fa a9717b7 -Author: Anthony -Date: Thu Mar 24 11:36:39 2016 -0500 - - Merge pull request #17 from acesnik/master - - Removed commandline codebase; added test data - -commit a9717b70d2c78026dfff8ffe925daa50a606ace4 -Author: Anthony -Date: Thu Mar 24 11:34:29 2016 -0500 - - Added test data - -commit a3810977e6b70819bbc13c91930e632050dac3b3 -Author: Anthony -Date: Thu Mar 24 11:19:08 2016 -0500 - - Removed older commandline codebase - -commit fa8fa9b50c86784d981d98d67375afdfe52ce174 -Merge: 6d4301b 1c7a3fa -Author: Anthony -Date: Thu Mar 24 11:15:02 2016 -0500 - - Accepted changes from upstream - -commit 6d4301bbd0f255b361ce2251c481107598524ada -Author: Anthony -Date: Thu Mar 24 11:13:30 2016 -0500 - - Deleted more test-run files from cache - -commit 1c7a3fa5dfee739bcd806e323edd04734f32e4d4 -Merge: 5df2b3d 9b7c177 -Author: Anthony -Date: Thu Mar 24 10:58:52 2016 -0500 - - Merge pull request #16 from lschaffer2/master - - fixed ee peak list bug - -commit 5df2b3d5367491bd0e2beb18c549ab595389c803 -Merge: a6f3c47 1349b82 -Author: Anthony -Date: Thu Mar 24 10:58:34 2016 -0500 - - Merge pull request #15 from trishorts/master - - me and ac deleted lines - -commit 9b7c1777ea843ee73e9dbbfd61d6082bb33aeab6 -Merge: 204cf1d a6f3c47 -Author: lschaffer2 -Date: Thu Mar 24 10:41:51 2016 -0500 - - deleted test file - -commit 204cf1d9121040d16978b5aa3088badee9d36760 -Author: lschaffer2 -Date: Thu Mar 24 10:32:52 2016 -0500 - - fixed ee peak list bug - -commit 1ceb1d1e4d95bb830be06d4a3358d8d29b386bf0 -Author: lschaffer2 -Date: Thu Mar 24 10:20:33 2016 -0500 - - fixed ee peak list bug - -commit 1349b8209b8d022db3f891be247ae65ecb068ef4 -Author: trishorts -Date: Wed Mar 23 15:12:10 2016 -0500 - - me and ac deleted lines - -commit a6f3c47e8172c3d0b332e1a5057acf7ff64dbcd6 -Merge: a5d6605 a56b56e -Author: Anthony -Date: Wed Mar 23 15:06:31 2016 -0500 - - Merge pull request #14 from acesnik/master - - Made a change from upstream for testing - -commit a56b56ed0d0d3c80e128514bc287eb6397497d79 -Merge: 5a5c6a1 a5d6605 -Author: acesnik -Date: Wed Mar 23 15:05:25 2016 -0500 - - Updated from upstream - -commit 5a5c6a13dd0359827d4c440210de114376cf3908 -Author: acesnik -Date: Wed Mar 23 15:00:49 2016 -0500 - - Trivial test change - -commit a5d66057f40b974a70e2c11a6c72a004a6db3cd4 -Merge: c8c233d 97629e0 -Author: Anthony -Date: Wed Mar 23 14:41:05 2016 -0500 - - Merge pull request #13 from trishorts/master - - test trivl commit - -commit 97629e027a9d879e464eeae220d086c9a9f08cfd -Author: trishorts -Date: Wed Mar 23 14:37:50 2016 -0500 - - 2nd trivial change - -commit 98b82707aab6f6b48cf1dcb23eabb0f2e4379805 -Author: trishorts -Date: Wed Mar 23 14:16:02 2016 -0500 - - test trivl commit - -commit b335baf57649da70383620d7a0327904af05ecf1 -Merge: 6e390d6 c8c233d -Author: acesnik -Date: Tue Mar 22 20:32:15 2016 -0500 - - Updated from upstream - -commit 6e390d6d3c301886bc0cd16e875619d8c210c082 -Author: acesnik -Date: Tue Mar 22 17:51:11 2016 -0500 - - Deleted VS testing files - -commit c8c233dd33b044c9f829b30dcf0a45f4a4daf94b -Merge: b9b7082 01762be -Author: Anthony -Date: Tue Mar 22 17:26:05 2016 -0500 - - Merge pull request #12 from lschaffer2/master - - Add eeComparison to suite - -commit 01762bed075b17c7756a2416335b01f6068e6f82 -Merge: b9b7082 4ccf9ae -Author: Leah Schaffer -Date: Tue Mar 22 16:46:44 2016 -0500 - - Merge pull request #1 from lschaffer2/eeComparison - - Ee comparison - -commit 4ccf9aef791eacd283587652eac2ba33dcf62b1c -Merge: eaa4905 c0b760f -Author: lschaffer2 -Date: Tue Mar 22 16:25:33 2016 -0500 - - Merge branch 'master' into eeComparison - -commit eaa4905d448247ac2415a5e424582e3ad7db8164 -Author: lschaffer2 -Date: Tue Mar 22 16:15:10 2016 -0500 - - deleted files that conflict w/ merge - -commit c0b760f6270e5ca2a6e03606f006c36a5794f6c6 -Merge: e1cd6db b9b7082 -Author: lschaffer2 -Date: Tue Mar 22 16:12:03 2016 -0500 - - merging upstream to master - -commit e1cd6db7fdc6967083602f7168d4d5d29d1173a9 -Author: lschaffer2 -Date: Tue Mar 22 15:24:19 2016 -0500 - - added ee comparison to ps0.00 - -commit b9b7082b6a7cae0ecc3f707abc4bbe68e4b24f98 -Merge: 9af94cd e926854 -Author: Anthony -Date: Tue Mar 22 11:57:02 2016 -0500 - - Merge pull request #11 from acesnik/master - - Refactored class names - -commit e9268541d2aa16869ded68e146efb9eea1d4daa1 -Author: acesnik -Date: Mon Mar 21 19:51:42 2016 -0500 - - Refactored class names - -commit 9af94cd16705db4f74fc9429a9ab6d3deacbc245 -Merge: 147b961 b1416bf -Author: Anthony -Date: Mon Mar 21 16:52:45 2016 -0500 - - Merge pull request #10 from acesnik/master - - Enable testing runs - added missing files - -commit b1416bf7ef573bef8d510c634db7b4d43b70eec7 -Author: acesnik -Date: Mon Mar 21 16:49:30 2016 -0500 - - Removed exe files due to permission issues - -commit 705e4b0a838a2ba6490e7da55ee2dbff37dfae3d -Author: acesnik -Date: Mon Mar 21 16:43:18 2016 -0500 - - Forced addition of all files in PS_0.00 - -commit 147b9613471ea60d87d6c9dfba0bd022b8cefc1e -Merge: 9e76a36 7302ead -Author: Anthony -Date: Mon Mar 21 16:38:56 2016 -0500 - - Merge pull request #9 from acesnik/master - - Forced addition of Release folders in PS_0.00/bin and PS_0.00/obj - -commit 7302ead60c43ccb9dd9df34b3302925ad049959a -Author: acesnik -Date: Mon Mar 21 16:37:56 2016 -0500 - - Forced addition of Release folders in PS_0.00/bin and PS_0.00/obj - -commit 9e76a3668880293d5b5008bc986d84845eaedd3e -Merge: e2096e0 fa75e0d -Author: Anthony -Date: Mon Mar 21 13:15:39 2016 -0500 - - Merge pull request #8 from acesnik/master - - Add working PS version - -commit fa75e0d9fa0034ca025fddb7596a90c56181f03f -Author: acesnik -Date: Mon Mar 21 12:55:26 2016 -0500 - - Add working PS version - -commit e2096e05ce0c2222b4df3b5989356b01c3523e65 -Merge: 5c9082b 4d05395 -Author: Anthony -Date: Thu Jan 28 12:35:46 2016 -0600 - - Merge pull request #7 from acesnik/ED_Decoy_Determination - - ED_Decoy_Determination - -commit 4d0539546978983e201f6a45d38423ef7b064a4b -Author: trishorts -Date: Thu Jan 28 08:31:53 2016 -0600 - - ED_Decoy_Determination - - This is a repair of the file submitted previously - -commit 5c9082b2650d4cddb3f463e3caef04fdb3ca817b -Merge: adfd4a7 f21eff6 -Author: Anthony -Date: Mon Jan 25 15:16:31 2016 -0600 - - Merge pull request #6 from acesnik/add_insulin_xml - - small xml file for db creation - -commit f21eff677b3fc5a618ea33c2556b6eb8b85a2ebd -Author: trishorts -Date: Mon Jan 25 15:06:07 2016 -0600 - - small xml file for db creation - -commit adfd4a754f3c0ecec0f1f17e81a7d53473199dca -Merge: 3f6ac57 3dcb272 -Author: Anthony -Date: Mon Jan 25 14:43:38 2016 -0600 - - Merge pull request #5 from acesnik/add_test_data - - files_for_debugging - -commit 3dcb272b671a2ff3c1d3227fe8bc2dfe67be55e4 -Author: trishorts -Date: Mon Jan 25 14:42:58 2016 -0600 - - files_for_debugging - - mass_lysineCt - promex_output - pmtlist from uniprot for database creation - -commit 3f6ac576664617f2a000762bc28c3cae6a117bce -Merge: 8141886 201e613 -Author: Anthony -Date: Mon Jan 25 13:49:24 2016 -0600 - - Merge pull request #4 from acesnik/Decoy_EE_Pairs - - Decoy Mass Differences for EE Pairs - -commit 201e6138c805a73afdc69af76b16c426d8c2a4d5 -Author: trishorts -Date: Mon Jan 25 13:39:20 2016 -0600 - - Decoy Mass Differences for EE Pairs - - Program that takes EE pairs as input and produces output file with mass - difference for mass/lysCt pair where lysCt differs by 2 and mass - difference < 500 - -commit 81418869dad2daaf790f769de2ee8eab9deacf21 -Merge: 6eaca9e aee64a3 -Author: Anthony -Date: Fri Jan 22 13:48:28 2016 -0600 - - Merge pull request #3 from acesnik/add_proteoform_suite - - Add proteoform suite - -commit aee64a317aa856f8a68764bb59153b86f3eb1064 -Author: Anthony -Date: Fri Jan 22 13:46:30 2016 -0600 - - Revert "Revert "Initial commit of proteoform suite framework"" - - This reverts commit a9bf358646659b7e34a04b31bcc587af7480c3ba. - -commit a9bf358646659b7e34a04b31bcc587af7480c3ba -Author: Anthony -Date: Fri Jan 22 13:46:04 2016 -0600 - - Revert "Initial commit of proteoform suite framework" - - This reverts commit 61988d2c443a226f05ae149ac7c1f4ad854a36f6. - -commit 61988d2c443a226f05ae149ac7c1f4ad854a36f6 -Author: Anthony -Date: Fri Jan 22 13:42:03 2016 -0600 - - Initial commit of proteoform suite framework - - see summary - -commit 6eaca9e8aee5214b5d5d286247dbccadc8681109 -Merge: 71169f8 d123234 -Author: Anthony -Date: Fri Jan 22 13:31:29 2016 -0600 - - Merge pull request #2 from acesnik/160122_proteoform_DB_with_Decoys - - enable_creation_of_N_Decoy_Databases - -commit d12323491122b27d6c74068a83a1e4fb9b5b8760 -Author: trishorts -Date: Fri Jan 22 13:28:56 2016 -0600 - - enable_creation_of_N_Decoy_Databases - - see summary - -commit 71169f85ba6807bcfd5a3e5db6ac4b3aadd76415 -Author: Anthony -Date: Thu Dec 17 17:25:43 2015 -0600 - - Created README - -commit 7fc8e0bae35a267b875a9c4854be1748e9783b2f -Merge: cdf784a b023655 -Author: Anthony -Date: Thu Dec 17 17:21:03 2015 -0600 - - Merge pull request #1 from acesnik/test-second-branc - - Testing merger - -commit b0236553e0c660922d02b7132871bbae89df8d70 -Merge: cdf784a 97dfb72 -Author: acesnik -Date: Thu Dec 17 16:57:47 2015 -0600 - - Merge branch 'master' into test-second-branc - -commit 97dfb72d4bd08809d700b70b14aeef4674954327 -Merge: 4006e4a cdf784a -Author: acesnik -Date: Tue Dec 15 16:28:43 2015 -0600 - - Initial commit - -commit 4006e4a7d532149b71d2697bf8bda37859d7735a -Author: acesnik -Date: Tue Dec 15 16:27:13 2015 -0600 - - Initial commit - -commit cdf784a0b499082c37c278eec104ea689cc5f9bd -Author: acesnik -Date: Tue Dec 15 12:49:32 2015 -0600 - - Initial commit