support "displayMode" for json genomes. Fixes #1308 (#1386)

support "displayMode" for json genomes. Fixes #1308
igvteam · Sep 2, 2023 · a060dab · a060dab
1 parent 89a3195
commit a060dab
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Showing 3 changed files with 66 additions and 12 deletions.
diff --git a/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java b/src/main/java/org/broad/igv/feature/genome/load/JsonGenomeLoader.java
@@ -15,6 +15,8 @@
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.fasta.FastaBlockCompressedSequence;
 import org.broad.igv.feature.genome.fasta.FastaIndexedSequence;
+import org.broad.igv.track.Track;
+import org.broad.igv.track.TrackProperties;
 import org.broad.igv.track.TribbleFeatureSource;
 import org.broad.igv.ui.color.ColorUtilities;
 import org.broad.igv.util.FileUtils;
@@ -110,27 +112,56 @@ public Genome loadGenome() throws IOException {
                         res.setFormat(format.getAsString().toLowerCase());
                     }
 
+//                    JsonElement colorBy = obj.get("colorBy");
+//                    if (altColor != null) {
+//                        try {
+//                            properties.colorBy(ColorUtilities.stringToColor(colorBy.toString()));
+//                        } catch (Exception e) {
+//                            log.error("Error parsing color string: " + altColor.toString(), e);
+//                        }
+//                    }
+
+                    JsonElement infoURL = obj.get("infoURL");
+                    if (infoURL != null) {
+                        res.setFeatureInfoURL(infoURL.getAsString());
+                    }
+
+
+                    // Track properties
+                    TrackProperties properties = new TrackProperties();
                     JsonElement color = obj.get("color");
                     if (color != null) {
                         try {
-                            res.setColor(ColorUtilities.stringToColor(color.toString()));
+                            properties.setColor(ColorUtilities.stringToColor(color.toString()));
                         } catch (Exception e) {
-                            log.error("Error parsing color string: " + color.toString(), e);
+                            log.error("Error parsing color string: " + color, e);
+                        }
+                    }
+                    JsonElement altColor = obj.get("altColor");
+                    if (altColor != null) {
+                        try {
+                            properties.setAltColor(ColorUtilities.stringToColor(altColor.toString()));
+                        } catch (Exception e) {
+                            log.error("Error parsing color string: " + altColor, e);
+                        }
+                    }
+                    JsonElement displayMode = obj.get("displayMode");
+                    if (displayMode != null) {
+                        try {
+                            Track.DisplayMode dp = Track.DisplayMode.valueOf(stripQuotes(displayMode.toString()));
+                            properties.setDisplayMode(dp);
+                        } catch (Exception e) {
+                            log.error("Error parsing displayMode " + displayMode, e);
                         }
                     }
-
                     JsonElement vizwindow = obj.get("visibilityWindow");
                     if (vizwindow != null) {
-                        res.setVisibilityWindow(obj.get("visibilityWindow").getAsInt());
+                        properties.setFeatureVisibilityWindow(obj.get("visibilityWindow").getAsInt());
                     } else {
                         // If not explicitly set, assume whole chromosome viz window for annotations
-                        res.setVisibilityWindow(-1);
-                    }
-
-                    JsonElement infoURL = obj.get("infoURL");
-                    if (infoURL != null) {
-                        res.setFeatureInfoURL(infoURL.getAsString());
+                        properties.setFeatureVisibilityWindow(-1);
                     }
+                    res.setTrackProperties(properties);
 
                     JsonElement indexedElement = obj.get("indexed");
                     JsonElement hiddenElement = obj.get("hidden");
@@ -139,7 +170,6 @@ public Genome loadGenome() throws IOException {
                     if (indexedElement != null) {
                         res.setIndexed(indexed);
                     }
-
                     if (hidden) {
                         if (indexed || trackIndex != null) {
                             log.warn("Hidden tracks cannot be indexed.  Ignoring " + trackPath);
@@ -149,6 +179,7 @@ public Genome loadGenome() throws IOException {
                     } else {
                         tracks.add(res);
                     }
+
                 });
             }
 
@@ -267,6 +298,15 @@ private void addToFeatureDB(List<ResourceLocator> locators, Genome genome) {
         }
     }
 
+    private String stripQuotes(String str) {
+        if(str.startsWith("\"")) {
+            return str.substring(1, str.length() - 1);  // Assume also ends with
+        }
+        else {
+            return str;
+        }
+    }
+
     public static class GenomeDescriptor {
         String id;
         String name;

diff --git a/src/main/java/org/broad/igv/ui/IGV.java b/src/main/java/org/broad/igv/ui/IGV.java
@@ -1310,6 +1310,11 @@ public List<Track> load(ResourceLocator locator) throws DataLoadException {
                 track.setAttributeValue(Globals.TRACK_NAME_ATTRIBUTE, track.getName());
                 track.setAttributeValue(Globals.TRACK_DATA_FILE_ATTRIBUTE, fn);
                 track.setAttributeValue(Globals.TRACK_DATA_TYPE_ATTRIBUTE, track.getTrackType().toString());
+
+                TrackProperties properties = locator.getTrackProperties();
+                if(properties != null) {
+                    track.setProperties(properties);
+                }
             }
         }
         //revalidateTrackPanels();

diff --git a/src/main/java/org/broad/igv/util/ResourceLocator.java b/src/main/java/org/broad/igv/util/ResourceLocator.java
@@ -29,6 +29,7 @@
 import htsjdk.tribble.Tribble;
 import org.broad.igv.logging.LogManager;
 import org.broad.igv.logging.Logger;
+import org.broad.igv.track.TrackProperties;
 
 import java.awt.*;
 import java.io.File;
@@ -104,12 +105,13 @@ public class ResourceLocator {
      */
     public String format;
 
-
     /**
      * A UCSC style track line.  Overrides value in file, if any.
      */
     String trackLine;  //
 
+    TrackProperties trackProperties;
+
     /**
      * Color for features or data.  Somewhat redundant with trackLine.
      */
@@ -399,6 +401,13 @@ public String getTrackName() {
         }
     }
 
+    public TrackProperties getTrackProperties() {
+        return trackProperties;
+    }
+
+    public void setTrackProperties(TrackProperties trackProperties) {
+        this.trackProperties = trackProperties;
+    }
 
     public void setName(String name) {
         this.name = name;