Allow specification of property / attribute for feature names. Fixes #…

…1089

src/main/java/org/broad/igv/feature/AbstractFeature.java

@@ -86,6 +86,11 @@ public String getName() {
         return name;
     }
 
+    public String getDisplayName(String property) {
+        String nm = getAttribute(property);
+        return nm == null ? getName() : nm;
+    }
+
     public boolean hasExons() {
         return false;
     }

src/main/java/org/broad/igv/feature/NamedFeature.java

@@ -34,4 +34,8 @@
 public interface  NamedFeature extends Feature {
 
     String getName();
+
+    default String getDisplayName(String property) {
+        return getName();
+    }
 }

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

@@ -5,7 +5,6 @@
 import org.broad.igv.feature.*;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.Sequence;
-import org.broad.igv.feature.genome.SequenceWrapper;
 import org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequence;
 import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
 import org.broad.igv.feature.gff.GFFFeatureSource;
@@ -70,7 +69,7 @@ private static FeatureTrack createGeneTrack(Genome genome, BufferedReader reader
                 if (props != null) {
                     geneFeatureTrack.setProperties(parser.getTrackProperties());
                 }
-                geneFeatureTrack.setUrl(annotationURL);
+                geneFeatureTrack.setFeatureInfoURL(annotationURL);
             }
         }
         return geneFeatureTrack;

src/main/java/org/broad/igv/feature/tribble/EncodePeakCodec.java

@@ -110,7 +110,7 @@ public BasicFeature decode(String nextLine) {
             strand = Strand.NONE;
         }
         feature.setStrand(strand);
-        
+
         // Store the remaining features in description string */
         Map<String, String> attributes = new LinkedHashMap<>();
         if (tokens.length > 6) attributes.put("signalValue", tokens[6]);

src/main/java/org/broad/igv/prefs/Constants.java

@@ -68,6 +68,8 @@ private Constants() {
     // Generic track options
     public static final String BYPASS_FILE_AUTO_DISCOVERY = "BYPASS_FILE_AUTO_DISCOVERY";
     public static final String TRACK_ATTRIBUTE_NAME_KEY = "TRACK_ATTRIBUTE_NAME_KEY";
+
+    public static final String FEATURE_NAME_PROPERTY = "FEATURE_NAME_PROPERTY";
     public static final String INITIAL_TRACK_HEIGHT = "15";
     public static final String COLOR_SCALE_KEY = "COLOR_SCALE_";
     public static final String TRACK_HEIGHT_KEY = "IGV.track.height";

src/main/java/org/broad/igv/renderer/IGVFeatureRenderer.java

@@ -140,7 +140,7 @@ public void render(List<IGVFeature> featureList,
             boolean alternateExonColor = (track instanceof FeatureTrack && ((FeatureTrack) track).isAlternateExonColor());
             Color trackPosColor = track.getColor();
             Color trackNegColor = alternateExonColor ? track.getColor() : track.getAltColor();
-
+            String featureNameProperty = track.getLabelField();
 
             for (IGVFeature feature : featureList) {
 
@@ -204,7 +204,7 @@ public void render(List<IGVFeature> featureList,
                     hasExons = bf.hasExons();
                 }
 
-                 // Add directional arrows and exons, if there is room.
+                // Add directional arrows and exons, if there is room.
                 int pixelYCenter = trackRectangle.y + NORMAL_STRAND_Y_OFFSET / 2;
 
                 if (hasExons) {
@@ -234,7 +234,7 @@ public void render(List<IGVFeature> featureList,
                                 Color peakColor = c == Color.cyan ? Color.red : Color.cyan;
                                 g2D.setColor(peakColor);
                                 int pw = Math.min(4, pixelWidth / 5);
-                                g2D.fillRect(peakPixelPosition - pw/2, pixelYCenter - thinBlockHeight/2 - 1, pw, thinBlockHeight + 2);
+                                g2D.fillRect(peakPixelPosition - pw / 2, pixelYCenter - thinBlockHeight / 2 - 1, pw, thinBlockHeight + 2);
                                 g2D.setColor(c);
                             }
                         } catch (NumberFormatException e) {
@@ -246,7 +246,10 @@ public void render(List<IGVFeature> featureList,
 
                 // Draw name , if there is room
                 if (displayMode != Track.DisplayMode.SQUISHED && track.isShowFeatureNames()) {
-                    String name = feature.getName();
+
+                    String name = featureNameProperty != null ?
+                            feature.getDisplayName(featureNameProperty) : feature.getName();
+
                     if (name != null) {
                         // Limit name display length
                         if (name.length() >= MAX_NAME_LENGTH) {
@@ -270,7 +273,7 @@ public void render(List<IGVFeature> featureList,
                         int verticalSpaceRequiredForText = textBaselineY - (int) trackRectangleY;
 
                         if (verticalSpaceRequiredForText <= trackRectangle.height) {
-                            lastNamePixelEnd = drawFeatureName(feature, track.getDisplayMode(), nameStart, nameEnd,
+                            lastNamePixelEnd = drawFeatureName(name, track.getDisplayMode(), nameStart, nameEnd,
                                     lastNamePixelEnd, fontGraphics, textBaselineY);
                         }
                     }
@@ -544,7 +547,7 @@ protected void drawStrandArrows(Strand strand,
 
         // Don't draw strand arrows for very small regions
         // Limit drawing to visible region, we don't really know the viewport pEnd,
-        if ((endX - startX)  < 6) {
+        if ((endX - startX) < 6) {
             return;
         }
 
@@ -579,19 +582,14 @@ protected void drawStrandArrows(Strand strand,
 
     }
 
-    final private int drawFeatureName(IGVFeature feature,
+    final private int drawFeatureName(String name,
                                       Track.DisplayMode mode,
                                       int pixelStart,
                                       int pixelEnd,
                                       int lastFeatureEndedAtPixelX,
                                       Graphics2D g2D,
                                       int textBaselineY) {
 
-        String name = feature.getName();
-        if (name == null) {
-            return lastFeatureEndedAtPixelX;
-        }
-
         FontMetrics fm = g2D.getFontMetrics();
         int fontSize = fm.getFont().getSize();
         int nameWidth = fm.stringWidth(name);
@@ -623,7 +621,7 @@ final private int drawFeatureName(IGVFeature feature,
      * @param locationScale
      * @param yOffset
      * @param trackRectangle
-     * @param idx  exon index
+     * @param idx            exon index
      */
     public void labelAminoAcids(int pStart, Graphics2D fontGraphics, double theOrigin,
                                 RenderContext context, IGVFeature gene, double locationScale,
@@ -632,16 +630,16 @@ public void labelAminoAcids(int pStart, Graphics2D fontGraphics, double theOrigi
         Genome genome = GenomeManager.getInstance().getCurrentGenome();
         Exon exon = gene.getExons().get(idx);
 
-        Exon prevExon = idx == 0 ? null : gene.getExons().get(idx-1);
-        Exon nextExon = (idx+1) < gene.getExons().size() ?gene.getExons().get(idx+1) : null;
+        Exon prevExon = idx == 0 ? null : gene.getExons().get(idx - 1);
+        Exon nextExon = (idx + 1) < gene.getExons().size() ? gene.getExons().get(idx + 1) : null;
 
         AminoAcidSequence aaSequence = exon.getAminoAcidSequence(genome, prevExon, nextExon);
 
         if ((aaSequence != null) && aaSequence.hasNonNullSequence()) {
             Rectangle aaRect = new Rectangle(pStart, yOffset - blockHeight / 2, 1, blockHeight);
 
             int aaSeqStartPosition = aaSequence.getStart();
-            boolean odd =  exon.getAminoAcidNumber(exon.getCdStart()) % 2 == 1;
+            boolean odd = exon.getAminoAcidNumber(exon.getCdStart()) % 2 == 1;
 
             for (CodonAA acid : aaSequence.getSequence()) {
                 if (acid != null) {
@@ -704,20 +702,20 @@ public String getDisplayName() {
     protected Color getFeatureColor(IGVFeature feature, Track track, Color defaultPosColor, Color defaultNegColor) {
 
         // Set color used to draw the feature
-         Color color = null;
+        Color color = null;
 
         // If an alt color is explicitly set use it for negative strand features;
-        if(feature.getStrand() == Strand.NEGATIVE) {
+        if (feature.getStrand() == Strand.NEGATIVE) {
             color = track.getExplicitAltColor();
         }
 
         // If color is explicitly set use it
-        if(color == null) {
-             color = track.getExplicitColor();
+        if (color == null) {
+            color = track.getExplicitColor();
         }
 
         // No explicitly set color, try the feature itself
-        if(color == null && track.isItemRGB()) {
+        if (color == null && track.isItemRGB()) {
             color = feature.getColor();
         }
 

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

@@ -75,7 +75,7 @@ public abstract class AbstractTrack implements Track {
 
     private String attributeKey;
     private String name;
-    private String url;
+    private String featureInfoURL;
     private boolean itemRGB = true;
 
     private boolean useScore;
@@ -150,12 +150,12 @@ public void setRendererClass(Class rc) {
         // Ignore by default
     }
 
-    public String getUrl() {
-        return url;
+    public String getFeatureInfoURL() {
+        return featureInfoURL;
     }
 
-    public void setUrl(String url) {
-        this.url = url;
+    public void setFeatureInfoURL(String featureInfoURL) {
+        this.featureInfoURL = featureInfoURL;
     }
 
     public void setUseScore(boolean useScore) {
@@ -193,11 +193,6 @@ public void setSampleId(String sampleId) {
         this.sampleId = sampleId;
     }
 
-    @Override
-    public boolean isFilterable() {
-        return true;   // True by default
-    }
-
     public void renderName(Graphics2D g2D, Rectangle trackRectangle, Rectangle visibleRectangle) {
 
         Rectangle rect = getDisplayableRect(trackRectangle, visibleRectangle);
@@ -503,10 +498,6 @@ public int getHeight() {
         return (height < 0) ? getDefaultHeight() : height;
     }
 
-    public boolean hasDataRange() {
-        return dataRange != null;
-    }
-
     public DataRange getDataRange() {
         if (dataRange == null) {
             // Use the color scale if there is one
@@ -679,7 +670,7 @@ public void setProperties(TrackProperties properties) {
             setWindowFunction(properties.getWindowingFunction());
         }
         if (properties.getUrl() != null) {
-            setUrl(properties.getUrl());
+            setFeatureInfoURL(properties.getUrl());
         }
 
         Map<String, String> attributes = properties.getAttributes();

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

@@ -59,8 +59,6 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import static org.broad.igv.feature.FeatureUtils.FEATURE_CENTER_COMPARATOR;
-
 /**
  * Track which displays features, typically showing regions of the genome
  * in a qualitative way. Features are rendered using the specified FeatureRenderer.
@@ -119,6 +117,7 @@ public class FeatureTrack extends AbstractTrack implements IGVEventObserver {
     private String trackLine = null;
 
     private boolean groupByStrand = false;
+    private String labelField;
 
     public FeatureTrack() {
 
@@ -445,7 +444,7 @@ public String getValueStringAt(String chr, double position, int mouseX, int mous
     private String getFeatureURL(IGVFeature igvFeature) {
         String url = igvFeature.getURL();
         if (url == null) {
-            String trackURL = getUrl();
+            String trackURL = getFeatureInfoURL();
             if (trackURL != null && igvFeature.getName() != null) {
                 String encodedID = StringUtils.encodeURL(igvFeature.getName());
                 url = trackURL.replaceAll("\\$\\$", encodedID);
@@ -454,6 +453,14 @@ private String getFeatureURL(IGVFeature igvFeature) {
         return url;
     }
 
+    @Override
+    public String getLabelField() {
+        return labelField;
+    }
+
+    public void setLabelField(String labelField) {
+        this.labelField = labelField;
+    }
 
     /**
      * Get all features which overlap the specified locus
@@ -1036,7 +1043,9 @@ public boolean isGroupByStrand() {
     @Override
     public void marshalXML(Document document, Element element) {
         element.setAttribute("groupByStrand", String.valueOf(groupByStrand));
-
+        if (labelField != null) {
+            element.setAttribute("featureNameProperty", labelField);
+        }
         super.marshalXML(document, element);
 
     }
@@ -1046,6 +1055,10 @@ public void unmarshalXML(Element element, Integer version) {
 
         super.unmarshalXML(element, version);
 
+        if (element.hasAttribute("featureNameProperty")) {
+            this.labelField = element.getAttribute("featureNameProperty");
+        }
+
         this.groupByStrand = "true".equals(element.getAttribute("groupByStrand"));
 
         NodeList tmp = element.getElementsByTagName("SequenceMatchSource");

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

@@ -62,11 +62,6 @@ public MutationTrack(ResourceLocator locator, String id, FeatureSource source) {
     public MutationTrack() {
     }
 
-    @Override
-    public boolean isFilterable() {
-        return true;   // Mutation tracks, unlike most FeatureTrack types, can be filtered
-    }
-
     @Override
     public void overlay(RenderContext context, Rectangle rect) {
         if (!context.getChr().equals(Globals.CHR_ALL) ||

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

@@ -84,7 +84,9 @@ enum DisplayMode {
      *
      * @return
      */
-    boolean isFilterable();
+    default boolean isFilterable() {
+        return true;
+    }
 
 
     /**
@@ -128,7 +130,7 @@ void renderAttributes(Graphics2D graphics, Rectangle trackRectangle, Rectangle v
 
     String getSample();
 
-    void setUrl(String url);
+    void setFeatureInfoURL(String featureInfoURL);
 
     ResourceLocator getResourceLocator();
 
@@ -182,8 +184,6 @@ default boolean isNumeric() {
      */
     void setDataRange(DataRange axisDefinition);
 
-    boolean hasDataRange();
-
     DataRange getDataRange();
 
     Color getColor();
@@ -276,6 +276,16 @@ default Color getExplicitAltColor() {
 
     default void setShowFeatureNames(boolean b) {}
 
+    /**
+     * Return the java property or attribute for the feature display name.  Default is "null", in which case the
+     * feature "name" property will be used.
+     *
+     * @return
+     */
+    default String getLabelField() {
+        return null;
+    }
+
     default void repaint() {
         IGV.getInstance().repaint(this);
     }

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

@@ -247,7 +247,10 @@ public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadE
 
                 for (Track track : newTracks) {
                     if (locator.getFeatureInfoURL() != null) {
-                        track.setUrl(locator.getFeatureInfoURL());
+                        track.setFeatureInfoURL(locator.getFeatureInfoURL());
+                    }
+                    if (locator.getLabelField() != null && track instanceof FeatureTrack) {
+                        ((FeatureTrack) track).setLabelField(locator.getLabelField());
                     }
                     if (tp != null) {
                         track.setProperties(tp);