Added config files for Encode browser (mm9 and hg18)

resources/ucscEncodeDirectories.hg18.txt

@@ -0,0 +1,80 @@
+http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/
+wgEncodeAffyRnaChip
+wgEncodeBroadChipSeq
+wgEncodeBroadHmm
+wgEncodeBuOrchid
+wgEncodeCaltechRnaSeq
+wgEncodeChromatinMap
+wgEncodeCshlLongRnaSeq
+wgEncodeCshlShortRnaSeq
+wgEncodeDukeAffyExonArray
+wgEncodeGisDnaPet
+wgEncodeGisPet
+wgEncodeGisRnaSeq
+wgEncodeHelicosRnaSeq
+wgEncodeHudsonalphaChipSeq
+wgEncodeHudsonalphaCnv
+wgEncodeHudsonalphaMethyl27
+wgEncodeHudsonalphaMethylSeq
+wgEncodeHudsonalphaRnaSeq
+wgEncodeMapability
+wgEncodeNhgriBip
+wgEncodeNhgriNre
+wgEncodeReg
+wgEncodeRegDnaseClustered
+wgEncodeRegMarkEnhH3k4me1
+wgEncodeRegMarkEnhH3k4me1Gm12878
+wgEncodeRegMarkEnhH3k4me1H1hesc
+wgEncodeRegMarkEnhH3k4me1Hepg2
+wgEncodeRegMarkEnhH3k4me1Hmec
+wgEncodeRegMarkEnhH3k4me1Hsmm
+wgEncodeRegMarkEnhH3k4me1Huvec
+wgEncodeRegMarkEnhH3k4me1K562
+wgEncodeRegMarkEnhH3k4me1Nhek
+wgEncodeRegMarkEnhH3k4me1Nhlf
+wgEncodeRegMarkEnhH3k4me3Hepg2
+wgEncodeRegMarkEnhH3k27ac
+wgEncodeRegMarkEnhH3k27acGm12878
+wgEncodeRegMarkEnhH3k27acH1hesc
+wgEncodeRegMarkEnhH3k27acHepg2
+wgEncodeRegMarkEnhH3k27acHmec
+wgEncodeRegMarkEnhH3k27acHsmm
+wgEncodeRegMarkEnhH3k27acHuvec
+wgEncodeRegMarkEnhH3k27acK562
+wgEncodeRegMarkEnhH3k27acNhek
+wgEncodeRegMarkEnhH3k27acNhlf
+wgEncodeRegMarkPromoter
+wgEncodeRegMarkPromoterGm12878
+wgEncodeRegMarkPromoterH1hesc
+wgEncodeRegMarkPromoterHmec
+wgEncodeRegMarkPromoterHsmm
+wgEncodeRegMarkPromoterHuvec
+wgEncodeRegMarkPromoterK562
+wgEncodeRegMarkPromoterNhek
+wgEncodeRegMarkPromoterNhlf
+wgEncodeRegMarkRepressH3k27me3Gm12878
+wgEncodeRegMarkRepressH3k27me3H1hesc
+wgEncodeRegMarkRepressH3k27me3Hepg2
+wgEncodeRegMarkRepressH3k27me3Hmec
+wgEncodeRegMarkRepressH3k27me3Hsmm
+wgEncodeRegMarkRepressH3k27me3Huvec
+wgEncodeRegMarkRepressH3k27me3K562
+wgEncodeRegMarkRepressH3k27me3Nhek
+wgEncodeRegMarkRepressH3k27me3Nhlf
+wgEncodeRegTfbsClustered
+wgEncodeRegTxn
+wgEncodeRegTxnGm12878
+wgEncodeRegTxnH1hesc
+wgEncodeRegTxnHepg2
+wgEncodeRegTxnHuvec
+wgEncodeRegTxnK562
+wgEncodeRegTxnNhek
+wgEncodeRikenCage
+wgEncodeSangerGencode
+wgEncodeSunyalbanyRnaGeneChip
+wgEncodeUwAffyExonArray
+wgEncodeUwChIPSeq
+wgEncodeUwDGF
+wgEncodeUwDnaseSeq
+wgEncodeYaleChIPseq
+wgEncodeYaleRNAseq

src/org/broad/igv/ui/action/BrowseEncodeAction.java

@@ -1,7 +1,9 @@
 package org.broad.igv.ui.action;
 
 import org.apache.log4j.Logger;
+import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.ui.IGV;
+import org.broad.igv.ui.util.MessageUtils;
 import org.broad.igv.util.ResourceLocator;
 import org.broad.igv.util.encode.EncodeFileBrowser;
 import org.broad.igv.util.encode.EncodeFileRecord;
@@ -32,7 +34,13 @@ public BrowseEncodeAction(String label, int mnemonic, IGV igv) {
     public void actionPerformed(ActionEvent event) {
 
         try {
-            EncodeFileBrowser browser = EncodeFileBrowser.getInstance();
+            Genome genome = igv.getGenomeManager().getCurrentGenome();
+            EncodeFileBrowser browser = EncodeFileBrowser.getInstance(genome.getId());
+
+            if(browser == null) {
+                MessageUtils.showMessage("Encode data is not available for " + genome.getDisplayName() + " through IGV.");
+            }
+
             browser.setVisible(true);
             if(browser.isCanceled()) return;
 

src/org/broad/igv/util/encode/EncodeFileBrowser.java

@@ -34,7 +34,7 @@ public class EncodeFileBrowser extends JDialog {
 
     private static Logger log = Logger.getLogger(EncodeFileBrowser.class);
 
-    private static EncodeFileBrowser theInstance;
+    private static Map<String, EncodeFileBrowser> instanceMap = Collections.synchronizedMap(new HashMap<String, EncodeFileBrowser>());
     private static NumberFormatter numberFormatter = new NumberFormatter();
 
     private JButton cancelButton;
@@ -53,24 +53,39 @@ public class EncodeFileBrowser extends JDialog {
     private boolean canceled;
 
 
-    public synchronized static EncodeFileBrowser getInstance() throws IOException {
+    public synchronized static EncodeFileBrowser getInstance(String genomeId) throws IOException {
 
-        if (theInstance == null) {
-            List<EncodeFileRecord> records = getEncodeFileRecords();
+        String encodeGenomeId = getEncodeGenomeId(genomeId);
+        EncodeFileBrowser instance = instanceMap.get(encodeGenomeId);
+        if (instance == null) {
+            List<EncodeFileRecord> records = getEncodeFileRecords(encodeGenomeId);
+            if (records == null) {
+                return null;
+            }
             Frame parent = IGV.hasInstance() ? IGV.getMainFrame() : null;
-            theInstance = new EncodeFileBrowser(parent, new EncodeTableModel(records));
+            instance = new EncodeFileBrowser(parent, new EncodeTableModel(records));
+            instanceMap.put(encodeGenomeId, instance);
         }
 
-        return theInstance;
+        return instance;
+    }
+
+    private static String getEncodeGenomeId(String genomeId) {
+        if (genomeId.equals("b37") || genomeId.equals("1kg_v37")) return "hg19";
+        else if (genomeId.equals("1kg_ref")) return "hg19";
+        else return genomeId;
     }
 
-    private static List<EncodeFileRecord> getEncodeFileRecords() throws IOException {
+    private static List<EncodeFileRecord> getEncodeFileRecords(String genomeId) throws IOException {
 
         InputStream is = null;
 
         try {
 
-            is = EncodeFileBrowser.class.getResourceAsStream("encode.txt");
+            is = EncodeFileBrowser.class.getResourceAsStream("encode." + genomeId + ".txt");
+            if (is == null) {
+                return null;
+            }
             BufferedReader reader = new BufferedReader(new InputStreamReader(is));
             String[] headers = Globals.tabPattern.split(reader.readLine());
             List<EncodeFileRecord> records = new ArrayList<EncodeFileRecord>(20000);
@@ -232,8 +247,7 @@ private class RegexFilter extends RowFilter {
                     if (kv.length > 1) {
                         column = kv[0].trim();
                         value = kv[1].trim();
-                    }
-                    else {
+                    } else {
                         value = kv[0];  // Value is column name until more input is entered
                     }
                 }
@@ -382,7 +396,7 @@ public void actionPerformed(ActionEvent e) {
 
 
     public static void main(String[] args) throws IOException {
-        getInstance().setVisible(true);
+        getInstance("hg18").setVisible(true);
     }
 
 }

src/org/broad/igv/util/encode/UCSCEncodeUtils.java

@@ -29,7 +29,7 @@ public static void main(String[] args) throws IOException {
 
         //List<EncodeFileRecord> records =  new ArrayList();
         //parseFilesDotTxt("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/files.txt", records);
-       // updateEncodeTableFile();
+        updateEncodeTableFile(args[0], args[1]);
 
     }
 
@@ -63,10 +63,11 @@ private static List<EncodeFileRecord> parseTableFile(String url) throws IOExcept
     }
 
 
-    private static void updateEncodeTableFile() throws IOException {
-        List<EncodeFileRecord> records = parseUCSCMasterFile("resources/ucscEncodeDirectories");
+    private static void updateEncodeTableFile(String inputFile, String outputFile) throws IOException {
 
-        PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter("encode.txt")));
+        List<EncodeFileRecord> records = parseUCSCMasterFile(inputFile);
+
+        PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
 
         pw.print("path");
         for (String h : EncodeTableModel.columnHeadings) {