Additional track hub support: (#1651)

* Additional track hub support:
* Fix bugs preventing loading of CHM13 / hs1 hub.  Fixes #1643
* Enable addition of hubs as a track source to any IGV genome
* UI improvements to track selection dialog

Author: jrobinso

src/main/java/module-info.java

@@ -12,6 +12,7 @@
     opens org.broad.igv.feature.genome.load to com.google.gson;
     opens org.broad.igv.feature to com.google.gson;
     exports org.broad.igv.ucsc;
+    exports org.broad.igv.ucsc.hub;
 
     requires com.google.common;
     requires commons.math3;

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

@@ -53,7 +53,8 @@
 import org.broad.igv.logging.Logger;
 import org.broad.igv.track.FeatureTrack;
 import org.broad.igv.track.TribbleFeatureSource;
-import org.broad.igv.ucsc.Hub;
+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;
@@ -96,14 +97,16 @@ public class Genome {
     private String homeChromosome;
     private String defaultPos;
     private String nameSet;
-    private Hub hub;
+    private Hub genomeHub;
+    private List<Hub> trackHubs;
 
     public Genome(GenomeConfig config) throws IOException {
 
         id = config.getId();
         displayName = config.getName();
         nameSet = config.getNameSet();
         blatDB = config.getBlatDB();
+        trackHubs = new ArrayList<>();
         if (config.getUcsdID() == null) {
             ucscID = ucsdIDMap.containsKey(id) ? ucsdIDMap.get(id) : id;
         } else {
@@ -226,6 +229,16 @@ public Genome(GenomeConfig config) throws IOException {
             // TODO -- no place to go
         }
 
+        if(config.getHubs() != null) {
+            for(String hubUrl : config.getHubs()) {
+                try {
+                    trackHubs.add(HubParser.loadHub(hubUrl, getId()));
+                } catch (IOException e) {
+                    log.error("Error loading hub", e);
+                }
+            }
+        }
+
 
         addTracks(config);
 
@@ -254,6 +267,8 @@ public Genome(String id, List<Chromosome> chromosomes) {
         this.longChromosomeNames = computeLongChromosomeNames();
         this.homeChromosome = this.longChromosomeNames.size() > 1 ? Globals.CHR_ALL : chromosomeNames.get(0);
         this.chromAliasSource = (new ChromAliasDefaults(id, chromosomeNames));
+
+        this.trackHubs = new ArrayList<>();
     }
 
     private void addTracks(GenomeConfig config) {
@@ -794,12 +809,18 @@ public List<String> computeLongChromosomeNames() {
 
     }
 
-    public Hub getHub() {
-        return hub;
+    public Hub getGenomeHub() {
+        return genomeHub;
+    }
+
+    public void setGenomeHub(Hub genomeHub) {
+        this.genomeHub = genomeHub;
+        // A genome hub is by definition also a track hub
+        this.trackHubs.add(genomeHub);
     }
 
-    public void setHub(Hub hub) {
-        this.hub = hub;
+    public List<Hub> getTrackHubs() {
+        return trackHubs;
     }
 
     public synchronized static Genome nullGenome() {

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/GenomeConfig.java

@@ -54,7 +54,7 @@ public class GenomeConfig implements Cloneable {
 
     private List<TrackConfig> tracks;
 
-    private List<TrackConfig> annotations;  // Backward compatibility, synonym for tracks
+    private List<String> hubs;
 
     // The properties below support the legacy ".genome" file, which directly loads resources from a zip archive.
 
@@ -72,6 +72,14 @@ public static GenomeConfig fromJson(String json) {
     public GenomeConfig() {
     }
 
+    public List<String> getHubs() {
+        return hubs;
+    }
+
+    public void setHubs(List<String> hubs) {
+        this.hubs = hubs;
+    }
+
     public String getId() {
         return id;
     }
@@ -257,7 +265,7 @@ public void setChromSizesURL(String chromSizesURL) {
     }
 
     public List<TrackConfig> getTrackConfigs() {
-        return tracks != null ? tracks : annotations;
+        return tracks;
     }
 
     public void setTracks(List<TrackConfig> tracks) {

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

@@ -3,10 +3,11 @@
 import org.broad.igv.Globals;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.prefs.PreferencesManager;
-import org.broad.igv.ucsc.Hub;
-import org.broad.igv.ucsc.TrackConfigGroup;
+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.HubTrackSelectionDialog;
+import org.broad.igv.ucsc.hub.TrackHubSelectionDialog;
 
 import java.io.IOException;
 import java.util.*;
@@ -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
 
@@ -60,7 +61,6 @@ public Genome loadGenome() throws IOException {
             List<TrackConfig> selectedTracks = groupedTrackConfigurations.stream()
                     .flatMap(group -> group.tracks.stream())
                     .filter(trackConfig -> selectedTrackNames.contains(trackConfig.getName()))
-                    .sorted(Comparator.comparingInt(TrackConfig::getOrder))
                     .collect(Collectors.toList());
             config.setTracks(selectedTracks);
         }
@@ -69,7 +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();
             }
 
@@ -79,7 +79,7 @@ else if (IGV.hasInstance() && !Globals.isBatch() && !Globals.isHeadless() && !Gl
                     groupedTrackConfigurations.stream().filter(g -> g.label.startsWith("Gene")).collect(Collectors.toList());
 
 
-            HubTrackSelectionDialog dlg = new HubTrackSelectionDialog(filteredGroups, IGV.getInstance().getMainFrame());
+            TrackHubSelectionDialog dlg = new TrackHubSelectionDialog(hub, filteredGroups, IGV.getInstance().getMainFrame());
             dlg.setVisible(true);
 
             List<TrackConfig> selectedTracks = dlg.getSelectedConfigs();
@@ -91,7 +91,7 @@ else if (IGV.hasInstance() && !Globals.isBatch() && !Globals.isHeadless() && !Gl
         }
 
         Genome genome = new Genome(config);
-        genome.setHub(hub);
+        genome.setGenomeHub(hub);
 
         return genome;
 

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

@@ -2,13 +2,13 @@
 
 /**
  * A static json-like object, emulates javascript equivalent.   Created to ease port of session code from javascript.
- *
  */
 
 public class TrackConfig implements Cloneable {
 
     private String id;
     private String name;
+    private String longLabel;
     private String url;
     private String indexURL;
     private String trixURL;
@@ -26,20 +26,21 @@ public class TrackConfig implements Cloneable {
     private Boolean visible;
     private String infoURL;
     private String searchIndex;
-
     private String group;
-    private Integer order;
     private Integer visibilityWindow;
     private Boolean indexed;
     private Boolean hidden;
     private String html;
     private String panelName;
 
+    private String stanzaParent;   // For supporting track hubs
+
     public TrackConfig() {
     }
 
     /**
      * The only required property of a track configuration is a URL (which can be an actual URL or a static file path)
+     *
      * @param url
      */
     public TrackConfig(String url) {
@@ -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;
     }
@@ -206,14 +215,6 @@ public void setGroup(String group) {
         this.group = group;
     }
 
-    public Integer getOrder() {
-        return order;
-    }
-
-    public void setOrder(Integer order) {
-        this.order = order;
-    }
-
     public Integer getVisibilityWindow() {
         return visibilityWindow;
     }
@@ -254,6 +255,14 @@ public void setPanelName(String panelName) {
         this.panelName = panelName;
     }
 
+    public String getStanzaParent() {
+        return stanzaParent;
+    }
+
+    public void setStanzaParent(String stanzaParent) {
+        this.stanzaParent = stanzaParent;
+    }
+
     @Override
     protected TrackConfig clone() throws CloneNotSupportedException {
         return (TrackConfig) super.clone();

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;
                     }
                 }