Add dialog to select tracks from hub

igvteam · Dec 2, 2023 · 68efeed · 68efeed
1 parent 2e1977a
commit 68efeed
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Showing 3 changed files with 54 additions and 21 deletions.
diff --git a/src/main/java/module-info.java b/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;

diff --git a/src/main/java/org/broad/igv/feature/genome/load/HubGenomeLoader.java b/src/main/java/org/broad/igv/feature/genome/load/HubGenomeLoader.java
@@ -1,13 +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.ui.TrackSelectionDialog;
+import org.broad.igv.ucsc.TrackSelectionDialog;
 
 import java.io.IOException;
-import java.util.Comparator;
-import java.util.List;
+import java.util.*;
 
 public class HubGenomeLoader extends GenomeLoader {
 
@@ -24,15 +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
@@ -42,13 +44,36 @@ public Genome loadGenome() throws IOException {
 
         GenomeConfig config = hub.getGenomeConfig(null);
 
-        // Select tracks
-        if(IGV.hasInstance()) {
+        // 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);

diff --git a/...rg/broad/igv/ui/TrackSelectionDialog.java → .../broad/igv/ucsc/TrackSelectionDialog.java b/...rg/broad/igv/ui/TrackSelectionDialog.java → .../broad/igv/ucsc/TrackSelectionDialog.java
@@ -1,23 +1,25 @@
-package org.broad.igv.ui;
+package org.broad.igv.ucsc;
 
+import com.jidesoft.swing.FontUtils;
 import org.broad.igv.feature.genome.load.TrackConfig;
-import org.broad.igv.ucsc.Hub;
-import org.broad.igv.ucsc.TrackConfigGroup;
+import org.broad.igv.ui.FontManager;
 import org.broad.igv.ui.util.HyperlinkFactory;
 
 import javax.swing.*;
 import javax.swing.border.Border;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 import java.util.List;
 
+/**
+ * Dialog to enable selection of track hub tracks prior to loading.  Might be generalized to other use cases, but
+ * for now focused on track hubs.
+ *
+ */
 public class TrackSelectionDialog extends JDialog {
 
-
     Map<JCheckBox, TrackConfig> configMap;
 
     public TrackSelectionDialog(List<TrackConfigGroup> groupedTrackConfigurations, Frame owner) {
@@ -35,6 +37,7 @@ void init(List<TrackConfigGroup> trackConfigurations) {
         configMap = new HashMap<>();
 
         JLabel headerMessage = new JLabel("Select tracks to load");
+        headerMessage.setFont(FontManager.getFont(Font.BOLD, 14));
         headerMessage.setHorizontalAlignment(SwingConstants.CENTER);
         headerMessage.setPreferredSize(new Dimension(300, 50));
         //   add(headerMessage, BorderLayout.NORTH);
@@ -113,8 +116,12 @@ JPanel categoryPanel(TrackConfigGroup configGroup) {
     public List<TrackConfig> getSelectedConfigs() {
         List<TrackConfig> selected = new ArrayList<>();
         for(Map.Entry<JCheckBox, TrackConfig> entry : configMap.entrySet()) {
+            final TrackConfig trackConfig = entry.getValue();
             if(entry.getKey().isSelected()) {
-                selected.add(entry.getValue());
+                trackConfig.visible = true;
+                selected.add(trackConfig);
+            } else {
+                trackConfig.visible = false;
             }
         }
         return selected;