Track panel refactor

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

@@ -58,14 +58,18 @@ public static File downloadGenome(GenomeConfig c, boolean downloadSequence, bool
 
         // Create a directory for the data files (sequence and annotations)
         final File genomeDirectory = DirectoryManager.getGenomeCacheDirectory();
-        File dataDirectory = new File(genomeDirectory, config.getId());
-        if (dataDirectory.exists()) {
-            if (!dataDirectory.isDirectory()) {
-                throw new RuntimeException("Error downloading genome. " + dataDirectory.getAbsolutePath() + " exists and is not a directory.");
-            }
-        } else {
-            if (!dataDirectory.mkdir()) {
-                throw new RuntimeException("Error downloading genome.  Could not create directory: " + dataDirectory.getAbsolutePath());
+        File dataDirectory = null;
+
+        if(downloadSequence || downloadAnnotations) {
+            dataDirectory = new File(genomeDirectory, config.getId());
+            if (dataDirectory.exists()) {
+                if (!dataDirectory.isDirectory()) {
+                    throw new RuntimeException("Error downloading genome. " + dataDirectory.getAbsolutePath() + " exists and is not a directory.");
+                }
+            } else {
+                if (!dataDirectory.mkdir()) {
+                    throw new RuntimeException("Error downloading genome.  Could not create directory: " + dataDirectory.getAbsolutePath());
+                }
             }
         }
 

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

@@ -64,8 +64,6 @@
 import java.util.List;
 import java.util.stream.Stream;
 
-import static org.broad.igv.prefs.Constants.SHOW_SINGLE_TRACK_PANE_KEY;
-
 /**
  * @author jrobinso
  */
@@ -241,19 +239,19 @@ public void restoreGenomeTracks(Genome genome) {
         // Fetch the gene track, defined by .genome files.  In this format the genome data is encoded in the .genome file
         FeatureTrack geneFeatureTrack = genome.getGeneTrack();   // Can be null
         if (geneFeatureTrack != null) {
-            PanelName panelName = PreferencesManager.getPreferences().getAsBoolean(SHOW_SINGLE_TRACK_PANE_KEY) ?
-                    PanelName.DATA_PANEL : PanelName.FEATURE_PANEL;
             geneFeatureTrack.setAttributeValue(Globals.TRACK_NAME_ATTRIBUTE, geneFeatureTrack.getName());
             geneFeatureTrack.setAttributeValue(Globals.TRACK_DATA_FILE_ATTRIBUTE, "");
             geneFeatureTrack.setAttributeValue(Globals.TRACK_DATA_TYPE_ATTRIBUTE, geneFeatureTrack.getTrackType().toString());
-            IGV.getInstance().addTracks(Arrays.asList(geneFeatureTrack), panelName);
+            geneFeatureTrack.getResourceLocator().setPanelName(PanelName.ANNOTATION_PANEL.getName());
+            IGV.getInstance().addTracks(Arrays.asList(geneFeatureTrack));
         }
 
         List<ResourceLocator> resources = genome.getAnnotationResources();
         List<Track> annotationTracks = new ArrayList<>();
         if (resources != null) {
             for (ResourceLocator locator : resources) {
                 try {
+                    locator.setPanelName(PanelName.ANNOTATION_PANEL.getName());
                     List<Track> tracks = IGV.getInstance().load(locator);
                     annotationTracks.addAll(tracks);
                 } catch (DataLoadException e) {

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

@@ -239,9 +239,8 @@ public void setBlatDB(String blatDB) {
     }
 
     public String getUcsdID() {
-        return ucsdID;
+        return ucsdID == null ? id : ucsdID;
     }
-
     public void setUcsdID(String ucsdID) {
         this.ucsdID = ucsdID;
     }

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

@@ -19,7 +19,6 @@
 import javax.swing.*;
 import java.io.File;
 import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 import java.util.stream.Collectors;
 

src/main/java/org/broad/igv/session/IndexAwareSessionReader.java

@@ -122,11 +122,7 @@ public void loadSession(InputStream inputStream, Session session, String session
                     locator.setTrackLine(trackLine);
                     // Alignment tracks must be loaded synchronously
                     if (isAlignmentFile(locator.getPath())) {
-                        TrackPanel panel = igv.getPanelFor(locator);
-                        if (panel == null) {
-                            panel = igv.getTrackPanel(DATA_PANEL_NAME);
-                        }
-                        panel.addTracks(igv.load(locator));
+                        igv.addTracks(igv.load(locator));
                     } else {
                         aSync.add(locator);
                     }
@@ -233,8 +229,7 @@ private ResourceLocator parseResourceLine(String line) {
         String[] tokens = line.split("\\s+");
         if (tokens.length == 1) {
             locator = new ResourceLocator(tokens[0]);
-        }
-        else if (tokens.length >= 2) {
+        } else if (tokens.length >= 2) {
             // Might want to do some error checking here on
             // making sure file prefixes match and file extensions
             // indicate the index comes second.

src/main/java/org/broad/igv/session/UCSCSessionReader.java

@@ -112,11 +112,7 @@ public void loadSession(InputStream inputStream, Session session, String session
                     locator.setTrackLine(trackLine);
                     // Alignment tracks must be loaded synchronously
                     if (isAlignmentFile(locator.getPath())) {
-                        TrackPanel panel = igv.getPanelFor(locator);
-                        if (panel == null) {
-                            panel = igv.getTrackPanel(DATA_PANEL_NAME);
-                        }
-                        panel.addTracks(igv.load(locator));
+                        igv.addTracks(igv.load(locator));
                     } else {
                         aSync.add(locator);
                     }

src/main/java/org/broad/igv/tools/motiffinder/MotifFinderPlugin.java

@@ -80,7 +80,7 @@ static void handleDialogResult(MotifFinderDialog dialog) {
      */
     static List<Track> addTracksForPatterns(String[] pattern, String[] posTrackNames, String[] negTrackNames) {
         List<Track> trackList = generateTracksForPatterns(pattern, posTrackNames, negTrackNames);
-        IGV.getInstance().addTracks(trackList, PanelName.FEATURE_PANEL);
+        IGV.getInstance().addTracks(trackList);
         return trackList;
     }
 

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

@@ -103,7 +103,8 @@ private void okButtonActionPerformed(ActionEvent e) {
         TrackMenuUtils.changeRendererClass(Arrays.asList(newTrack), track0.getRenderer().getClass());
         newTrack.setDataRange(track0.getDataRange());
         newTrack.setColorScale(track0.getColorScale());
-        IGV.getInstance().addTracks(Arrays.asList(newTrack), PanelName.DATA_PANEL);
+
+        IGV.getInstance().addTracks(Arrays.asList(newTrack));
         this.setVisible(false);
 
     }

src/main/java/org/broad/igv/ucsc/hub/CollapsiblePanel.java

@@ -27,18 +27,18 @@ public class CollapsiblePanel extends JPanel {
     private final JLabel jlabel;
     private final List<SelectionBox> selectionBoxes;
     private final boolean autoselectDefaults;
-    private final TrackConfigContainer configGroup;
+    private final TrackConfigContainer configContainer;
     private JButton collapseButton;
     private JComponent content;
     private JPanel header;
     private ImageIcon openIcon;
     private ImageIcon closeIcon;
 
-    public CollapsiblePanel(TrackConfigContainer configGroup, boolean autoselectDefaults) {
+    public CollapsiblePanel(TrackConfigContainer configContainer, boolean autoselectDefaults) {
 
         Color backgroundColor = HEADER_BG;
 
-        this.configGroup = configGroup;
+        this.configContainer = configContainer;
         this.autoselectDefaults = autoselectDefaults;
 
         setLayout(new BorderLayout());
@@ -47,10 +47,10 @@ public CollapsiblePanel(TrackConfigContainer configGroup, boolean autoselectDefa
         trackPanel.setLayout(new BoxLayout(trackPanel, BoxLayout.Y_AXIS));
 
         // There is a (so far) intractable bug if a large # of JCheckboxes are created for this widget.
-        int totalTrackCount = configGroup.countTracks();
+        int totalTrackCount = configContainer.countTracks();
         SelectionBox.CheckboxType checkboxType = totalTrackCount < 1000 ? SelectionBox.CheckboxType.SWING : SelectionBox.CheckboxType.CUSTOM;
 
-        selectionBoxes = addSelectionBoxes(null, configGroup, trackPanel, checkboxType);
+        selectionBoxes = addSelectionBoxes(null, configContainer, trackPanel, checkboxType);
 
         boolean isSelected = false;
         int maxWidth = 0;
@@ -68,9 +68,9 @@ public CollapsiblePanel(TrackConfigContainer configGroup, boolean autoselectDefa
             selectionBox.setPreferredWidth(maxWidth);
         }
 
-        String label = configGroup.label + "   (" + selectionBoxes.size() + " tracks, " + selectionCount + " selected)";
+        String label = configContainer.label + "   (" + selectionBoxes.size() + " tracks, " + selectionCount + " selected)";
 
-        boolean isOpen = isSelected || configGroup.defaultOpen;
+        boolean isOpen = isSelected || configContainer.defaultOpen;
 
         this.content = trackPanel;
         this.openIcon = IconFactory.getInstance().getIcon(IconFactory.IconID.MINUS);
@@ -102,7 +102,7 @@ public CollapsiblePanel(TrackConfigContainer configGroup, boolean autoselectDefa
 
         this.add(header, BorderLayout.NORTH);
 
-        final JButton searchButton = createSearchButton("Search " + configGroup.label, selectionBoxes,
+        final JButton searchButton = createSearchButton("Search " + configContainer.label, selectionBoxes,
                 (selectedCount) -> {
                     this.updateLabel();
                     return null;
@@ -121,7 +121,9 @@ public CollapsiblePanel(TrackConfigContainer configGroup, boolean autoselectDefa
     public void resetSelectionBoxes(Set<String> loadedTrackPaths) {
         for (CollapsiblePanel.SelectionBox box : selectionBoxes) {
             final boolean isLoaded = loadedTrackPaths != null && loadedTrackPaths.contains(box.trackConfig.getUrl());
-            box.setSelected(isLoaded || (autoselectDefaults && box.trackConfig.getVisible() == true));
+            box.setSelected(
+                    isLoaded ||
+                    (autoselectDefaults && box.trackConfig.getVisible() == true) && configContainer.name.toLowerCase().equals("genes"));
             box.setEnabled(!isLoaded);
             updateLabel();
         }
@@ -134,7 +136,7 @@ public void updateLabel() {
                 count++;
             }
         }
-        String label = configGroup.label + "   (" + selectionBoxes.size() + " tracks, " + count + " selected)";
+        String label = configContainer.label + "   (" + selectionBoxes.size() + " tracks, " + count + " selected)";
         jlabel.setText(label);
     }
 
@@ -144,7 +146,7 @@ public void clearSelections() {
                 box.setSelected(false);
             }
         }
-        String label = configGroup.label + "   (" + selectionBoxes.size() + " tracks, 0 selected)";
+        String label = configContainer.label + "   (" + selectionBoxes.size() + " tracks, 0 selected)";
         jlabel.setText(label);
     }
 

src/main/java/org/broad/igv/ucsc/hub/Stanza.java

@@ -64,7 +64,7 @@ boolean hasProperty(String key) {
         return getProperty(key) != null;
     }
 
-    String format() {
+    String type() {
         String type = this.getOwnProperty("type");
         if (type != null) {
             // Trim extra bed qualifiers (e.g. bigBed + 4)

src/main/java/org/broad/igv/ucsc/hub/TrackDbHub.java

@@ -13,7 +13,7 @@ public class TrackDbHub {
 
 
     static Set supportedTypes = new HashSet(Arrays.asList("bigbed", "bigwig", "biggenepred", "vcftabix", "refgene",
-            "bam", "sampleinfo", "vcf.list", "ucscsnp", "bed", "tdf", "gff", "gff3", "gtf"));
+            "bam", "sampleinfo", "vcf.list", "ucscsnp", "bed", "tdf", "gff", "gff3", "gtf", "vcf"));
 
     static Set filterTracks = new HashSet(Arrays.asList("cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
             "cpgIslandExtUnmasked", "windowMasker"));
@@ -24,11 +24,15 @@ public class TrackDbHub {
             "squish", "SQUISHED",
             "dense", "COLLAPSED");
 
+    static Map<String, String> typeFormatMap = Map.of(
+            "vcftabix", "vcf"
+    );
+
+
     List<Stanza> trackStanzas;
     List<Stanza> groupStanzas;
     List<TrackConfigContainer> groupTrackConfigs;
 
-
     public TrackDbHub(List<Stanza> trackStanzas, List<Stanza> groupStanzas) {
         this.groupStanzas = groupStanzas;
         this.trackStanzas = trackStanzas;
@@ -100,7 +104,7 @@ public List<TrackConfigContainer> getGroupedTrackConfigurations(String hubName)
 
                 } else if (!filterTracks.contains(s.name) &&
                         s.hasProperty("bigDataUrl") &&
-                        supportedTypes.contains(s.format().toLowerCase())) {
+                        supportedTypes.contains(s.type().toLowerCase())) {
 
                     final TrackConfig trackConfig = getTrackConfig(s);
                     if (parent != null) {
@@ -123,19 +127,17 @@ public List<TrackConfigContainer> getGroupedTrackConfigurations(String hubName)
         return groupTrackConfigs;
     }
 
-
     private TrackConfig getTrackConfig(Stanza t) {
 
         String url = t.getProperty("bigDataUrl");
         TrackConfig config = new TrackConfig(url);
 
-        String format = t.format();
-        if (format != null) {
+        String type = t.type();
+        if (type != null) {
+            String format = typeFormatMap.containsKey(type) ? typeFormatMap.get(type) : type;
             config.setFormat(format.toLowerCase());
         }
 
-        config.setPanelName(IGV.DATA_PANEL_NAME);
-
         config.setId(t.getProperty("track"));
         config.setName(t.getProperty("shortLabel"));
 
@@ -154,7 +156,7 @@ private TrackConfig getTrackConfig(Stanza t) {
 
         if (t.hasProperty("bigDataIndex")) {
             config.setIndexURL(t.getProperty("bigDataIndex"));
-        } else if (t.format().equals("vcfTabix")) {
+        } else if (t.type().equals("vcfTabix")) {
             config.setIndexURL(t.getProperty("bigDataUrl") + ".tbi");
         }
 
@@ -181,7 +183,6 @@ private TrackConfig getTrackConfig(Stanza t) {
             config.setVisibilityWindow(vizWindow);
         }
 
-
         if (t.hasProperty("autoScale")) {
             config.setAutoscale(t.getProperty("autoScale").toLowerCase().equals("on"));
         }