From 1913e7b6d60da8ab0bdb576a7f8f287e80a6d8db Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Tue, 18 Oct 2022 14:49:04 +0200
Subject: [PATCH 1/5] Update typings

---
 .../processors/functional/FunctionalSummaryProcessor.d.ts       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/types/business/processors/functional/FunctionalSummaryProcessor.d.ts b/types/business/processors/functional/FunctionalSummaryProcessor.d.ts
index 5162905f..8394fe25 100644
--- a/types/business/processors/functional/FunctionalSummaryProcessor.d.ts
+++ b/types/business/processors/functional/FunctionalSummaryProcessor.d.ts
@@ -14,5 +14,5 @@ export default class FunctionalSummaryProcessor {
      * @param ncbiOntology An Ontology that maps taxon id's onto the corresponding taxon objects. All of the taxa id's
      * that are present in the pept2data table should be available in this ontology.
      */
-    summarizeFunctionalAnnotation(element: FunctionalDefinition, peptideTable: CountTable<Peptide>, pept2data: ShareableMap<Peptide, PeptideData>, ncbiOntology: Ontology<NcbiId, NcbiTaxon>): Promise<string[][]>;
+    summarizeFunctionalAnnotation(element: FunctionalDefinition, peptideTable: CountTable<Peptide>, pept2data: ShareableMap<Peptide, PeptideData>, ncbiOntology: Ontology<NcbiId, NcbiTaxon>, definitionExtractor: (peptideData: PeptideData) => FunctionalDefinition[]): Promise<string[][]>;
 }

From 86e677d97b0f4fc5b1d3c1a29ff161a96b365481 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Tue, 26 Sep 2023 10:45:04 +0200
Subject: [PATCH 2/5] Bump to v2.1.1

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index de02d1aa..65fcd284 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "unipept-web-components",
-    "version": "2.1.0",
+    "version": "2.1.1",
     "scripts": {
         "dev": "vite",
         "build": "vue-tsc --emitDeclarationOnly && vite build && tsc --emitDeclarationOnly && tsc-alias && rm -rf types/test types/plugins types/main.d.ts",

From 5a37f67b66d698116c624ad5bb356055a6819ce0 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Tue, 31 Oct 2023 14:24:50 +0100
Subject: [PATCH 3/5] Fixed multi sample heatmap

---
 package.json                                    |  2 +-
 .../heatmap/multi/DataSourceMulti.vue           |  3 ++-
 .../heatmap/multi/HeatmapWizardMulti.vue        | 17 ++++++++++++-----
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/package.json b/package.json
index 65fcd284..065e6d1b 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "unipept-web-components",
-    "version": "2.1.1",
+    "version": "2.1.2",
     "scripts": {
         "dev": "vite",
         "build": "vue-tsc --emitDeclarationOnly && vite build && tsc --emitDeclarationOnly && tsc-alias && rm -rf types/test types/plugins types/main.d.ts",
diff --git a/src/components/visualizations/heatmap/multi/DataSourceMulti.vue b/src/components/visualizations/heatmap/multi/DataSourceMulti.vue
index f9974488..b8412efe 100644
--- a/src/components/visualizations/heatmap/multi/DataSourceMulti.vue
+++ b/src/components/visualizations/heatmap/multi/DataSourceMulti.vue
@@ -7,7 +7,7 @@
             class="flex-grow-0"
         />
 
-        <DataSourceMultiTable
+        <data-source-table
             :items="selectedDataSourceItems"
             :categories="categories"
             :loading="loading"
@@ -24,6 +24,7 @@ import { Ontology, NcbiTaxon, NcbiRank, EcNamespace, GoNamespace, InterproNamesp
 import DataSourceMultiTable from './DataSourceMultiTable.vue';
 import MultiProteomicsAnalysisStatus from '@/interface/MultiProteomicsAnalysisStatus';
 import DataSourceMultiItem from './DataSourceMultiItem';
+import DataSourceTable from "@/components/tables/DataSourceTable.vue";
 
 export interface Props {
     loading: boolean
diff --git a/src/components/visualizations/heatmap/multi/HeatmapWizardMulti.vue b/src/components/visualizations/heatmap/multi/HeatmapWizardMulti.vue
index 8ec1492a..c4763938 100644
--- a/src/components/visualizations/heatmap/multi/HeatmapWizardMulti.vue
+++ b/src/components/visualizations/heatmap/multi/HeatmapWizardMulti.vue
@@ -6,39 +6,45 @@
         >
             <v-stepper-header>
                 <v-stepper-item
+                    color="primary"
                     editable
                     title="Horizontal axis"
+                    :value="1"
                     :complete="currentStep > 1"
                     step="1"
                 />
                 <v-divider />
                 <v-stepper-item
+                    color="primary"
                     editable
                     title="Normalization"
+                    :value="2"
                     :complete="currentStep > 2"
                     step="2"
                 />
                 <v-divider />
                 <v-stepper-item
+                    color="primary"
                     editable
                     title="Heatmap"
+                    :value="3"
                     :complete="currentStep > 3"
                     step="3"
                 />
             </v-stepper-header>
             <v-stepper-window>
                 <v-stepper-window-item :value="1">
-                    <DataSourceMulti
+                    <data-source-multi
                         :loading="loading"
                         :assays="assays"
                         @select="verticalItems = $event"
                     />
                 </v-stepper-window-item>
                 <v-stepper-window-item :value="2">
-                    <NormalizationSelector @update="normalizer = $event" />
+                    <normalization-selector @update="normalizer = $event" />
                 </v-stepper-window-item>
                 <v-stepper-window-item :value="3">
-                    <VisualizationControls
+                    <visualization-controls
                         ref="heatmap"
                         caption="Scroll to zoom, drag to pan"
                         :loading="heatMapLoading"
@@ -50,7 +56,7 @@
                         overlap
                     >
                         <template #visualization>
-                            <HeatMap
+                            <heat-map
                                 :data="heatmapData"
                                 :row-labels="heatmapRows"
                                 :column-labels="heatmapColumns"
@@ -64,7 +70,7 @@
                                 @download="downloadModalOpen = $event"
                             />
                         </template>
-                    </VisualizationControls>
+                    </visualization-controls>
                 </v-stepper-window-item>
             </v-stepper-window>
             <v-stepper-actions
@@ -85,6 +91,7 @@ import NormalizationSelector from '../NormalizationSelector.vue';
 import DataSourceMulti from './DataSourceMulti.vue';
 import DataSourceMultiItem from './DataSourceMultiItem';
 import MultiProteomicsAnalysisStatus from "@/interface/MultiProteomicsAnalysisStatus";
+import { VStepper, VStepperActions, VStepperHeader, VStepperItem, VStepperWindow, VStepperWindowItem } from 'vuetify/labs/VStepper';
 
 export interface Props {
     loading: boolean

From 74e272e712a027c8a7472eca1cf2a118dcbaa192 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Tue, 31 Oct 2023 15:40:02 +0100
Subject: [PATCH 4/5] Fixed styling of cog icon for ec and interpro

---
 src/components/cards/EcSummaryCard.vue       | 5 +++--
 src/components/cards/InterproSummaryCard.vue | 3 ++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/components/cards/EcSummaryCard.vue b/src/components/cards/EcSummaryCard.vue
index 59ff51bc..ccec5ace 100644
--- a/src/components/cards/EcSummaryCard.vue
+++ b/src/components/cards/EcSummaryCard.vue
@@ -3,7 +3,7 @@
         <v-card-text>
             <v-row v-if="!analysisInProgress">
                 <v-col>
-                    <TrustLine
+                    <trust-line
                         class="mb-5"
                         :trust="ecProcessor.getTrust()"
                         :fa-kind="{
@@ -23,7 +23,8 @@
                 >
                     <v-btn
                         icon="mdi-cog-outline"
-                        color="grey-darken-1"
+                        size="small"
+                        variant="text"
                         @click="editFilterPercentageModalOpen = true"
                     />
                 </v-col>
diff --git a/src/components/cards/InterproSummaryCard.vue b/src/components/cards/InterproSummaryCard.vue
index 323996ab..cc5b2b91 100644
--- a/src/components/cards/InterproSummaryCard.vue
+++ b/src/components/cards/InterproSummaryCard.vue
@@ -24,7 +24,8 @@
                 >
                     <v-btn
                         icon="mdi-cog-outline"
-                        color="grey-darken-1"
+                        size="small"
+                        variant="text"
                         @click="editFilterPercentageModalOpen = true"
                     />
                 </v-col>

From ecc28feddb34c587d466d65aa796e5980b60e946 Mon Sep 17 00:00:00 2001
From: Pieter Verschaffelt <pieter.verschaffelt@ugent.be>
Date: Mon, 6 Nov 2023 10:52:21 +0100
Subject: [PATCH 5/5] Minor changes to single peptide summary

---
 src/components/analysis/SinglePeptideSummary.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/components/analysis/SinglePeptideSummary.vue b/src/components/analysis/SinglePeptideSummary.vue
index 42cf6a3d..06a53640 100644
--- a/src/components/analysis/SinglePeptideSummary.vue
+++ b/src/components/analysis/SinglePeptideSummary.vue
@@ -27,6 +27,7 @@
                     <a
                         :href="taxonomyUrl(lca(assay))"
                         target="_blank"
+                        class="link primary--text"
                     >
                         {{ lca(assay)?.name }}
                     </a> ({{ lca(assay)?.rank }}).
@@ -42,6 +43,7 @@
                                 v-if="node"
                                 :href="`https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${node.id}`"
                                 target="_blank"
+                                class="link primary--text"
                             >
                                 {{ node.name }}
                             </a>