Genomes

src/main/java/org/broad/igv/DirectoryManager.java

@@ -387,8 +387,7 @@ public static void moveDirectoryContents(File oldDirectory, File newDirectory) {
         }
     }
 
-    public static boolean isChildOf(File base, File child)
-            throws IOException {
+    public static boolean isChildOf(File base, File child) {
 
         File parent = child.getParentFile();
         while (parent != null) {

src/main/java/org/broad/igv/batch/CommandExecutor.java

@@ -123,7 +123,7 @@ public String execute(String commandLine) {
             } else if (cmd.equalsIgnoreCase("scrolltotrack") || cmd.equalsIgnoreCase("gototrack")) {
                 boolean res = this.igv.scrollToTrack(StringUtils.stripQuotes(param1));
                 result = res ? "OK" : String.format("Error: Track %s not found", param1);
-            } else if (cmd.equalsIgnoreCase("scrolltotop") ) {
+            } else if (cmd.equalsIgnoreCase("scrolltotop")) {
                 this.igv.scrollToTop();
                 result = "OK";
             } else if (cmd.equalsIgnoreCase("snapshotdirectory")) {
@@ -143,8 +143,7 @@ public String execute(String commandLine) {
                     return result;
                 }
                 String id = GenomeManager.getInstance().getCurrentGenome().getId();
-                if (id != null)
-                {
+                if (id != null) {
                     GenomeListItem item = GenomeListManager.getInstance().getGenomeListItem(id);
                     if (item != null) {
                         result = item.getPath();
@@ -633,25 +632,21 @@ private String genome(String param1) {
         if (param1 == null) {
             return "ERROR missing genome parameter";
         }
-        String result = "OK";
-        String genomeID = param1;
-
-        igv.selectGenomeFromList(genomeID);
-        if (GenomeManager.getInstance().getCurrentGenome().getId().equals(genomeID)) {
-            return result;
-        }
+        String result;
+        String genomeIDorPath = param1;
 
-        String genomePath = resolveFileReference(genomeID);
         try {
-            GenomeManager.getInstance().loadGenome(genomePath);
+            GenomeManager.getInstance().loadGenomeById(genomeIDorPath);
+            result = "OK";
         } catch (IOException e) {
-            result = "ERROR: Could not load genome: " + genomeID;
+            result = "ERROR: Could not load genome: " + genomeIDorPath;
             MessageUtils.showMessage(result);
         }
 
         return result;
     }
 
+
     /**
      * Load function for port and batch script
      *
@@ -1263,9 +1258,9 @@ private static AlignmentTrack.GroupOption getAlignmentGroupOption(String str) {
             return AlignmentTrack.GroupOption.READ_GROUP;
         } else if (str.equalsIgnoreCase("base")) {
             return AlignmentTrack.GroupOption.BASE_AT_POS;
-        }else if (str.equalsIgnoreCase("insertion")) {
+        } else if (str.equalsIgnoreCase("insertion")) {
             return AlignmentTrack.GroupOption.INSERTION_AT_POS;
-        }else {
+        } else {
             try {
                 return AlignmentTrack.GroupOption.valueOf(str.toUpperCase());
             } catch (IllegalArgumentException e) {

src/main/java/org/broad/igv/feature/genome/GenomeUtils.java → src/main/java/org/broad/igv/feature/genome/ChromSizesUtils.java

@@ -25,12 +25,11 @@
 
 package org.broad.igv.feature.genome;
 
-import org.broad.igv.Globals;
 import org.broad.igv.feature.Chromosome;
 import org.broad.igv.util.ParsingUtils;
 
 import java.io.*;
-import java.util.*;
+
 
 /**
  * Static utility functions for genome data-wrangling.
@@ -39,24 +38,14 @@
  *         Date: 4/22/13
  *         Time: 1:27 PM
  */
-public class GenomeUtils {
+public class ChromSizesUtils {
 
 
     public static void main(String[] args) throws IOException {
 
         String genomeListFile =  "genomes/genomes.tab";
         String outputDirectory = "genomes/sizes";
-        String outputFile = "nonFastas.txt";
-
         updateChromSizes(genomeListFile, new File(outputDirectory));
-
-        //findNonFastas(genomeListFile, new File(outputFile));
-
-//        mergeINCDCNames(
-//                new File("genomes/alias/hg38_alias.tab"),
-//                new File("/Users/jrobinso/projects/INSDC/GCF_000001405.26.assembly.txt"),
-//                new File("/Users/jrobinso/projects/INSDC"));
-
     }
 
 
@@ -136,92 +125,5 @@ public static void exportChromSizes(File directory, Genome genome) throws FileNo
 
     }
 
-    /**
-     * Merge chromosome names from an NCBI assembly.txt file with an existing IGV alias file
-     *
-     * @param aliasFile
-     * @param assemblyFile
-     */
-    public static void mergeINCDCNames(File aliasFile, File assemblyFile, File outputDirectory) throws IOException {
-
-        Map<String, Set<String>> aliasRows = new LinkedHashMap<String, Set<String>>();
-
-        BufferedReader br = null;
-        PrintWriter pw = null;
-
-        // Build alias dictionary
-        br = new BufferedReader(new FileReader(aliasFile));
-        String nextLine;
-        while ((nextLine = br.readLine()) != null) {
-            String[] tokens = Globals.whitespacePattern.split(nextLine);
-            HashSet<String> row = new LinkedHashSet<String>(Arrays.asList(tokens));
-            for (String nm : tokens) {
-                aliasRows.put(nm, row);
-            }
-        }
-        br.close();
-
-        // Loop through assembly file
-        int[] chrIndeces = {0, 4, 6, 9};
-        br = new BufferedReader(new FileReader(assemblyFile));
-        boolean start = false;
-        List<String> newRows = new ArrayList<String>();
-        while ((nextLine = br.readLine()) != null) {
-            if (start) {
-
-                String[] tokens = Globals.tabPattern.split(nextLine);
-                boolean foundRow = false;
-                for (int i : chrIndeces) {
-                    Set<String> row = aliasRows.get(tokens[i]);
-                    if (row != null) {
-                        for (int j : chrIndeces) {
-                            if (!"na".equals(tokens[j])) {
-                                row.add(tokens[j]);
-                            }
-                        }
-                        foundRow = true;
-                        break;
-                    }
-                }
-                if (!foundRow) {
-                    String newRow = tokens[chrIndeces[0]];
-                    for (int i = 1; i < chrIndeces.length; i++) {
-                        String chrNm = tokens[chrIndeces[i]];
-                        if (!"na".equals(chrNm)) {
-                            newRow += ("\t" + chrNm);
-                        }
-                    }
-                    newRows.add(newRow);
-                    System.out.println("New alias row: " + newRow);
-                }
-
-            } else if (nextLine.startsWith("# Sequence-Name")) {
-                start = true;
-            }
-
-        }
-        br.close();
-
-        pw = new PrintWriter(new BufferedWriter(new FileWriter(new File(outputDirectory, aliasFile.getName()))));
-        Set<Set<String>> output = new HashSet<Set<String>>();
-        for (Set<String> row : aliasRows.values()) {
-            if (row.size() == 0) continue;
-            if (!output.contains(row)) {
-                output.add(row);
-                List<String> chrNames = new ArrayList<String>(row);
-                pw.print(chrNames.get(0));
-                for (int i = 1; i < chrNames.size(); i++) {
-                    pw.print("\t" + chrNames.get(i));
-                }
-                pw.println();
-            }
-        }
-        for (String row : newRows) {
-            pw.println(row);
-        }
-        pw.close();
-
-    }
-
 
 }

src/main/java/org/broad/igv/feature/genome/DotGenomeUtils.java

@@ -0,0 +1,89 @@
+package org.broad.igv.feature.genome;
+
+import org.broad.igv.DirectoryManager;
+import org.broad.igv.feature.genome.load.GenomeDescriptor;
+import org.broad.igv.feature.genome.load.GenomeLoader;
+import org.broad.igv.logging.LogManager;
+import org.broad.igv.logging.Logger;
+import org.broad.igv.ui.IGV;
+import org.broad.igv.ui.util.download.Downloader;
+import org.broad.igv.util.HttpUtils;
+import org.broad.igv.util.Utilities;
+
+import java.awt.*;
+import java.io.*;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLDecoder;
+import java.util.Map;
+
+/**
+ * Utilities for the ".genome" format.  These files are not created anymore, having been replaced by the genome json
+ * format, but we need to maintain support for reading and managing them.
+ */
+public class DotGenomeUtils {
+
+    private static Logger log = LogManager.getLogger(DotGenomeUtils.class);
+
+
+    /**
+     * Returns a File of the provided genomePath. If the genomePath is a URL, it will be downloaded
+     * and saved in the genome cache directory.
+     *
+     * @param genomePath
+     * @return
+     * @throws MalformedURLException
+     * @throws UnsupportedEncodingException
+     */
+    public static File getDotGenomeFile(String genomePath) throws MalformedURLException, UnsupportedEncodingException {
+
+        File archiveFile;
+
+        if (HttpUtils.isRemoteURL(genomePath.toLowerCase())) {
+            // We need a local copy, as there is no http zip file reader
+            URL genomeArchiveURL = HttpUtils.createURL(genomePath);
+            final String tmp = URLDecoder.decode(genomeArchiveURL.getFile(), "UTF-8");
+            String cachedFilename = Utilities.getFileNameFromURL(tmp);
+            if (!DirectoryManager.getGenomeCacheDirectory().exists()) {
+                DirectoryManager.getGenomeCacheDirectory().mkdir();
+            }
+            archiveFile = new File(DirectoryManager.getGenomeCacheDirectory(), cachedFilename);
+            Frame parent = IGV.hasInstance() ? IGV.getInstance().getMainFrame() : null;
+            Downloader.download(genomeArchiveURL, archiveFile, parent);
+        } else {
+            archiveFile = new File(genomePath);
+        }
+        return archiveFile;
+    }
+
+
+
+    public static File getLocalFasta(String id) {
+        return GenomeLoader.localSequenceMap.get(id);
+    }
+
+    public static void removeLocalFasta(String id) {
+        GenomeLoader.localSequenceMap.remove(id);
+        updateSequenceMapFile();
+    }
+
+
+    private static void updateSequenceMapFile() {
+
+        PrintWriter pw = null;
+
+        try {
+            File sequenceFile = new File(DirectoryManager.getGenomeCacheDirectory(), GenomeDescriptor.SEQUENCE_MAP_FILE);
+            pw = new PrintWriter(new BufferedWriter(new FileWriter(sequenceFile)));
+
+            for (Map.Entry<String, File> entry : GenomeLoader.localSequenceMap.entrySet()) {
+                pw.println(entry.getKey() + "\t" + entry.getValue());
+            }
+        } catch (IOException e) {
+            log.error("Error writing sequence map", e);
+        } finally {
+            if (pw != null) pw.close();
+        }
+    }
+
+}