Track hub selection

src/main/java/module-info.java

@@ -11,6 +11,7 @@
     exports org.broad.igv.feature.genome.load to com.google.gson;
     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;
 
     requires com.google.common;
     requires commons.math3;

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

@@ -1,9 +1,15 @@
 package org.broad.igv.feature.genome.load;
 
+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.ui.IGV;
+import org.broad.igv.ucsc.TrackSelectionDialog;
 
 import java.io.IOException;
+import java.util.*;
 
 public class HubGenomeLoader extends GenomeLoader {
 
@@ -20,15 +26,15 @@ public static boolean isHubURL(String obj) {
     public static String convertToHubURL(String accension) {
         //https://hgdownload.soe.ucsc.edu/hubs/GCF/016/808/095/GCF_016808095.1/
         //https://hgdownload.soe.ucsc.edu/hubs/GCA/028/534/965/GCA_028534965.1/
-       if(accension.startsWith("GCF") || accension.startsWith("GCA") && accension.length() >= 13) {
-           String prefix = accension.substring(0, 3);
-           String n1 = accension.substring(4, 7);
-           String n2 = accension.substring(7, 10);
-           String n3 = accension.substring(10, 13);
-           return "https://hgdownload.soe.ucsc.edu/hubs/" + prefix + "/" + n1 + "/" + n2 + "/" + n3 + "/" + accension + "/hub.txt";
-       } else {
-           return null;
-       }
+        if (accension.startsWith("GCF") || accension.startsWith("GCA") && accension.length() >= 13) {
+            String prefix = accension.substring(0, 3);
+            String n1 = accension.substring(4, 7);
+            String n2 = accension.substring(7, 10);
+            String n3 = accension.substring(10, 13);
+            return "https://hgdownload.soe.ucsc.edu/hubs/" + prefix + "/" + n1 + "/" + n2 + "/" + n3 + "/" + accension + "/hub.txt";
+        } else {
+            return null;
+        }
     }
 
     @Override
@@ -38,6 +44,38 @@ public Genome loadGenome() throws IOException {
 
         GenomeConfig config = hub.getGenomeConfig(null);
 
+        // Potentially override default tracks from hub with user selections
+
+        // Check previous selections for this hub first
+        String key = "hub:" + this.hubURL;
+        if (PreferencesManager.getPreferences().hasExplicitValue(key)) {
+            List<TrackConfig> selectedTracks = new ArrayList<>();
+            Set<String> selectedTrackNames = new HashSet<>(Arrays.asList(PreferencesManager.getPreferences().get(key).split(",")));
+            List<TrackConfigGroup> trackConfigGroups = hub.getGroupedTrackConfigurations();
+            for (TrackConfigGroup group : trackConfigGroups) {
+                for (TrackConfig trackConfig : group.tracks) {
+                    if (selectedTrackNames.contains(trackConfig.name)) {
+                        selectedTracks.add(trackConfig);
+                    }
+                }
+            }
+            selectedTracks.sort((o1, o2) -> o1.order - o2.order);
+            config.tracks = selectedTracks;
+        }
+
+        // If running in interactive mode opend dialog to set tracks.
+        else if (IGV.hasInstance() && !Globals.isBatch() && !Globals.isHeadless() && !Globals.isTesting()) {
+            TrackSelectionDialog dlg = new TrackSelectionDialog(hub.getGroupedTrackConfigurations(), IGV.getInstance().getMainFrame());
+            dlg.setVisible(true);
+            List<TrackConfig> selectedTracks = dlg.getSelectedConfigs();
+            selectedTracks.sort((o1, o2) -> o1.order - o2.order);
+            config.tracks = selectedTracks;
+
+            // Remember selections in user preferences
+            List<String> names = selectedTracks.stream().map((trackConfig) -> trackConfig.name).toList();
+            PreferencesManager.getPreferences().put(key, String.join(",", names));
+        }
+
         return new Genome(config);
 
     }

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

@@ -31,6 +31,7 @@ public class TrackConfig {
     public Integer visibilityWindow;
     public Boolean indexed;
     public Boolean hidden;
+    public String html;
 
     public TrackConfig() {
     }

src/main/java/org/broad/igv/ucsc/Hub.java

@@ -114,6 +114,7 @@ private static List<Hub.Stanza> loadStanzas(String url) throws IOException {
         List<Stanza> nodes = new ArrayList<>();
         Stanza currentNode = null;
         boolean startNewNode = true;
+        int order = 0;
         try (BufferedReader br = ParsingUtils.openBufferedReader(url)) {
             String line;
             while ((line = br.readLine()) != null) {
@@ -130,7 +131,7 @@ private static List<Hub.Stanza> loadStanzas(String url) throws IOException {
                     if (startNewNode) {
                         // Start a new node -- indent is currently ignored as igv.js does not support sub-tracks,
                         // so track stanzas are flattened
-                        Stanza newNode = new Stanza(key, value);
+                        Stanza newNode = new Stanza(++order, key, value);
                         nodes.add(newNode);
                         currentNode = newNode;
                         startNewNode = false;
@@ -259,11 +260,12 @@ shortLabel Chromosome Band (Ideogram)
         return config;
     }
 
-    List<TrackConfigGroup> getGroupedTrackConfigurations() {
+    public List<TrackConfigGroup> getGroupedTrackConfigurations() {
 
         // Organize track configs by group
         LinkedHashMap<String, List<TrackConfig>> trackConfigMap = new LinkedHashMap<>();
-        for (TrackConfig c : this.getTracksConfigs(null)) {
+        java.util.function.Function<Stanza, Boolean> filter = (stanza -> !stanza.name.equals("cytoBandIdeo"));
+        for (TrackConfig c : this.getTracksConfigs(filter)) {
             String groupName = c.group != null ? c.group : "other";
             if (!trackConfigMap.containsKey(groupName)) {
                 trackConfigMap.put(groupName, new ArrayList<>());
@@ -329,6 +331,12 @@ TrackConfig getTrackConfig(Stanza t) {
             config.description = t.getProperty("longLabel");
         }
 
+        if(t.hasProperty("html")) {
+            config.html = this.baseURL + t.getProperty("html");
+        }
+
+        config.visible = !("hide".equals(t.getProperty("visibility")));
+
         if (t.hasProperty("autoScale")) {
             config.autoscale = t.getProperty("autoScale").toLowerCase().equals("on");
         }
@@ -388,12 +396,14 @@ static class Stanza {
 
         private final String type;
         private final String name;
+        private final int order;
 
         private Map<String, String> properties;
 
         Stanza parent;
 
-        Stanza(String type, String name) {
+        Stanza(int order, String type, String name) {
+            this.order = order;
             this.type = type;
             this.name = name;
             this.properties = new HashMap<>();