Merge branch 'track_hubs'

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

@@ -54,6 +54,7 @@
 import org.broad.igv.track.FeatureTrack;
 import org.broad.igv.track.TribbleFeatureSource;
 import org.broad.igv.ucsc.hub.Hub;
+import org.broad.igv.ucsc.hub.HubParser;
 import org.broad.igv.ucsc.twobit.TwoBitSequence;
 import org.broad.igv.util.ResourceLocator;
 import org.broad.igv.util.liftover.Liftover;
@@ -231,7 +232,7 @@ public Genome(GenomeConfig config) throws IOException {
         if(config.getHubs() != null) {
             for(String hubUrl : config.getHubs()) {
                 try {
-                    trackHubs.add(Hub.loadHub(hubUrl));
+                    trackHubs.add(HubParser.loadHub(hubUrl, getId()));
                 } catch (IOException e) {
                     log.error("Error loading hub", e);
                 }

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

@@ -142,7 +142,6 @@ public boolean loadGenomeById(String genomeId) throws IOException {
         return loadGenome(genomePath) != null; // monitor[0]);
     }
 
-
     /**
      * The main load method -- loads a genome from a file or url path.  Note this is a long running operation and
      * should not be done on the Swing event thread as it will block the UI.

src/main/java/org/broad/igv/feature/genome/load/HubGenomeLoader.java

@@ -4,6 +4,7 @@
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.prefs.PreferencesManager;
 import org.broad.igv.ucsc.hub.Hub;
+import org.broad.igv.ucsc.hub.HubParser;
 import org.broad.igv.ucsc.hub.TrackConfigGroup;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ucsc.hub.TrackHubSelectionDialog;
@@ -44,9 +45,9 @@ public static String convertToHubURL(String accension) {
     @Override
     public Genome loadGenome() throws IOException {
 
-        Hub hub = Hub.loadHub(this.hubURL);
+        Hub hub = HubParser.loadAssemblyHub(this.hubURL);
 
-        GenomeConfig config = hub.getGenomeConfig(false);
+        GenomeConfig config = hub.getGenomeConfig();
 
         // Potentially override default tracks from hub with user selections
 
@@ -68,7 +69,7 @@ public Genome loadGenome() throws IOException {
         else if (IGV.hasInstance() && !Globals.isBatch() && !Globals.isHeadless() && !Globals.isTesting()) {
 
             int count = 0;
-            for(TrackConfigGroup g : groupedTrackConfigurations) {
+            for (TrackConfigGroup g : groupedTrackConfigurations) {
                 count += g.tracks.size();
             }
 

src/main/java/org/broad/igv/feature/genome/load/TrackConfig.java

@@ -8,6 +8,7 @@ public class TrackConfig implements Cloneable {
 
     private String id;
     private String name;
+    private String longLabel;
     private String url;
     private String indexURL;
     private String trixURL;
@@ -62,6 +63,14 @@ public void setName(String name) {
         this.name = name;
     }
 
+    public String getLongLabel() {
+        return longLabel;
+    }
+
+    public void setLongLabel(String longLabel) {
+        this.longLabel = longLabel;
+    }
+
     public String getUrl() {
         return url;
     }

src/main/java/org/broad/igv/track/FeatureTrack.java

@@ -389,7 +389,7 @@ public String getValueStringAt(String chr, double position, int mouseX, int mous
 
             StringBuffer buf = new StringBuffer();
             boolean firstFeature = true;
-            int maxNumber = IGV.getInstance().isShowDetailsOnClick() ? 100 : 10;
+            int maxNumber =  10;
             int n = 1;
             for (Feature feature : allFeatures) {
                 if (feature != null && feature instanceof IGVFeature) {
@@ -409,7 +409,7 @@ public String getValueStringAt(String chr, double position, int mouseX, int mous
                     }
                     firstFeature = false;
                     if (n > maxNumber) {
-                        buf.append("<hr><br<b>>+ " + (allFeatures.size() - maxNumber) +  " more ...</b>");
+                        buf.append("<hr><br<b>+ " + (allFeatures.size() - maxNumber) +  " more</b>");
                         break;
                     }
                 }

src/main/java/org/broad/igv/ui/panel/CollapsiblePanel.java → src/main/java/org/broad/igv/ucsc/hub/CollapsiblePanel.java

@@ -1,4 +1,4 @@
-package org.broad.igv.ui.panel;
+package org.broad.igv.ucsc.hub;
 
 import org.broad.igv.ui.FontManager;
 import org.broad.igv.ui.util.IconFactory;
@@ -26,9 +26,6 @@ public CollapsiblePanel(String label, JComponent content, boolean isOpen) {
 
         setLayout(new BorderLayout());
         this.content = content;
-
-        //setBorder(BorderFactory.createLineBorder(Color.BLACK));
-
         this.openIcon = IconFactory.getInstance().getIcon(IconFactory.IconID.MINUS);
         this.closeIcon = IconFactory.getInstance().getIcon(IconFactory.IconID.PLUS);
 
@@ -70,23 +67,22 @@ public void expand() {
         content.setVisible(true);
     }
 
-    @Override
-    public Dimension getPreferredSize() {
-        Dimension d = super.getPreferredSize();
-        if(!content.isVisible()) {
-            return new Dimension(d.width, header.getHeight());
-        } else {
-            return d;
-        }
-    }
+
+    /**
+     * Constrain the maximum height to prevent BoxLayout from needlessly resizing the panel to fill space.  This is
+     * rather hardcoded for the TrackHubSelectionDialog.
+     *
+     * @return
+     */
 
     @Override
     public Dimension getMaximumSize() {
-        Dimension d = super.getMaximumSize();
+        Dimension d4 = header.getMinimumSize();
         if(!content.isVisible()) {
-            return new Dimension(d.width, header.getHeight());
+            return new Dimension(Integer.MAX_VALUE, d4.height);
         } else {
-            return d;
+            Dimension d5 = content.getMinimumSize();
+            return new Dimension(Integer.MAX_VALUE, d4.height + (int) (1.2 * d5.height));
         }
     }
 
@@ -101,3 +97,5 @@ public static void main(String[] args) {
         f.setVisible(true);
     }
 }
+
+