From 818c809792e06fb149946dd6e876e528d488eace Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Tue, 29 Aug 2023 22:50:05 -0700
Subject: [PATCH] Fix broken sashimi plot Filter sashimi plot menu to RNA-Seq
 experiments

---
 .../org/broad/igv/sam/AlignmentTrack.java     |  2 +-
 .../org/broad/igv/sam/AlignmentTrackMenu.java |  3 ++-
 .../broad/igv/sam/SpliceJunctionTrack.java    |  6 +++++
 .../org/broad/igv/sashimi/SashimiPlot.java    | 22 ++++++++++++-------
 4 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java
index 0af84ef622..1c8fa08b10 100644
--- a/src/main/java/org/broad/igv/sam/AlignmentTrack.java
+++ b/src/main/java/org/broad/igv/sam/AlignmentTrack.java
@@ -423,7 +423,7 @@ void setExperimentType(ExperimentType type) {
         }
     }
 
-    ExperimentType getExperimentType() {
+    public ExperimentType getExperimentType() {
         return experimentType;
     }
 
diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java b/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java
index 25fa117d86..26cbe2dff9 100644
--- a/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java
+++ b/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java
@@ -162,10 +162,11 @@ class AlignmentTrackMenu extends IGVPopupMenu {
             addInsertionItems(insertion);
         }
 
-        // Sashimi plot, probably should be depdenent on experimentType (RNA)
+        // Sashimi plot
         addSeparator();
         JMenuItem sashimi = new JMenuItem("Sashimi Plot");
         sashimi.addActionListener(e1 -> SashimiPlot.openSashimiPlot());
+        sashimi.setEnabled(alignmentTrack.getExperimentType() == AlignmentTrack.ExperimentType.RNA);
         add(sashimi);
 
         // Show alignments, coverage, splice junctions
diff --git a/src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java b/src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java
index be6ddec058..fa0902dbe9 100644
--- a/src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java
+++ b/src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java
@@ -33,6 +33,7 @@
 import org.broad.igv.feature.SpliceJunctionFeature;
 import org.broad.igv.renderer.DataRange;
 import org.broad.igv.renderer.GraphicUtils;
+import org.broad.igv.renderer.Renderer;
 import org.broad.igv.renderer.SpliceJunctionRenderer;
 import org.broad.igv.track.*;
 import org.broad.igv.ui.IGV;
@@ -95,6 +96,11 @@ public SpliceJunctionTrack() {
         this.renderer = new SpliceJunctionRenderer();
     }
 
+    @Override
+    public void setRenderer(Renderer renderer) {
+        this.renderer = renderer;
+    }
+
     @Override
     public String getSample() {
         if (sampleId != null) {
diff --git a/src/main/java/org/broad/igv/sashimi/SashimiPlot.java b/src/main/java/org/broad/igv/sashimi/SashimiPlot.java
index 78e7f1b33e..c0211c34e5 100644
--- a/src/main/java/org/broad/igv/sashimi/SashimiPlot.java
+++ b/src/main/java/org/broad/igv/sashimi/SashimiPlot.java
@@ -49,6 +49,7 @@
 import java.io.File;
 import java.util.List;
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * Window for displaying sashimi style junction plot
@@ -81,6 +82,8 @@ public class SashimiPlot extends JFrame implements IGVEventObserver {
 
     private static final List<Color> plotColors;
 
+    private Map<Object, SashimiJunctionRenderer> junctionRendererMap;
+
     static {
         ColorPalette palette = ColorUtilities.getDefaultPalette();
         plotColors = Arrays.asList(palette.getColors());
@@ -110,8 +113,11 @@ public SashimiPlot(ReferenceFrame iframe, Collection<? extends AlignmentTrack> a
         sashimiPanel.add(generateControlPanel(this.referenceFrame));
 
         spliceJunctionTracks = new ArrayList<>(alignmentTracks.size());
+
         int colorInd = 0;
 
+        junctionRendererMap = new HashMap<>();
+
         eventBus.subscribe(ViewChange.class, this);
 
         for (AlignmentTrack alignmentTrack : alignmentTracks) {
@@ -125,7 +131,9 @@ public SashimiPlot(ReferenceFrame iframe, Collection<? extends AlignmentTrack> a
             // Override expand/collpase setting -- expanded sashimi plots make no sense
             spliceJunctionTrack.setDisplayMode(Track.DisplayMode.COLLAPSED);
 
-            spliceJunctionTrack.setRenderer(new SashimiJunctionRenderer());
+            SashimiJunctionRenderer renderer = new SashimiJunctionRenderer();
+            spliceJunctionTrack.setRenderer(renderer);
+            junctionRendererMap.put(spliceJunctionTrack, renderer);
 
             Color color = plotColors.get(colorInd);
             colorInd = (colorInd + 1) % plotColors.size();
@@ -234,7 +242,7 @@ private void initSpliceJunctionComponent(TrackComponent<SpliceJunctionTrack> tra
     }
 
     private SashimiJunctionRenderer getRenderer(SpliceJunctionTrack spliceJunctionTrack) {
-        return (SashimiJunctionRenderer) spliceJunctionTrack.getRenderer();
+        return junctionRendererMap.get(spliceJunctionTrack);
     }
 
     @Override
@@ -649,13 +657,11 @@ public static void openSashimiPlot() {
             geneTrack = dlg.getSelectedTrack();
         }
 
-        Collection<AlignmentTrack> alignmentTracks = new ArrayList<AlignmentTrack>();
-        for (Track track : IGV.getInstance().getAllTracks()) {
-            if (track instanceof AlignmentTrack) {
-                alignmentTracks.add((AlignmentTrack) track);
-            }
-        }
 
+
+        Collection<AlignmentTrack> alignmentTracks =IGV.getInstance().getAlignmentTracks().stream()
+                .filter(t -> t.getExperimentType() == AlignmentTrack.ExperimentType.RNA).collect(Collectors.toList());
+;
         if (alignmentTracks.size() > 1) {
             TrackSelectionDialog<AlignmentTrack> alDlg =
                     new TrackSelectionDialog<AlignmentTrack>(IGV.getInstance().getMainFrame(), TrackSelectionDialog.SelectionMode.MULTIPLE, alignmentTracks);