Stabilize 3-frame translation rows. Fixes #1420

igvteam · Dec 4, 2023 · c84524b · c84524b
1 parent 7d0c415
commit c84524b
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Showing 2 changed files with 13 additions and 13 deletions.
diff --git a/src/main/java/org/broad/igv/renderer/SequenceRenderer.java b/src/main/java/org/broad/igv/renderer/SequenceRenderer.java
@@ -377,21 +377,24 @@ public void draw(RenderContext context, int start, Rectangle trackRectangle, Seq
             AminoAcidSequence[] aa = strand == Strand.POSITIVE ? cache.posAA : cache.negAA;
 
             //only draw nucleotide lines the last time this is called
-            drawOneTranslation(context, bandRectangle, 0, shouldDrawLetters, fontSize,
-                    nucleotideLineXPositions, aa[0], strand);
+            int frame = start % 3;
+            drawOneTranslation(context, bandRectangle, frame, shouldDrawLetters, fontSize,
+                    nucleotideLineXPositions, aa[frame], strand);
 
             //rf 1
+            frame = (start + 1) % 3;
             bandRectangle.y = trackRectangle.y + heightAlreadyUsed;
             bandRectangle.height = idealHeightPerBand;
             heightAlreadyUsed += bandRectangle.height;
-            drawOneTranslation(context, bandRectangle, 1, shouldDrawLetters, fontSize,
-                    nucleotideLineXPositions, aa[1], strand);
+            drawOneTranslation(context, bandRectangle, frame, shouldDrawLetters, fontSize,
+                    nucleotideLineXPositions, aa[frame], strand);
 
             //rf 2
+            frame = (start + 2) % 3;
             bandRectangle.y = trackRectangle.y + heightAlreadyUsed;
             bandRectangle.height = trackRectangle.height - heightAlreadyUsed;
-            drawOneTranslation(context, bandRectangle, 2, shouldDrawLetters, fontSize,
-                    nucleotideLineXPositions, aa[2], strand);
+            drawOneTranslation(context, bandRectangle, frame, shouldDrawLetters, fontSize,
+                    nucleotideLineXPositions, aa[frame], strand);
 
             if (shouldDrawNucleotideLines) {
                 Graphics2D graphicsForNucleotideLines = context.getGraphic2DForColor(NUCLEOTIDE_SEPARATOR_COLOR);

diff --git a/src/main/java/org/broad/igv/track/SequenceTrack.java b/src/main/java/org/broad/igv/track/SequenceTrack.java
@@ -222,7 +222,7 @@ public void load(ReferenceFrame referenceFrame) {
         int start = (int) referenceFrame.getOrigin();
 
         Chromosome chromosome = currentGenome.getChromosome(chr);
-        if(chromosome == null) {
+        if (chromosome == null) {
             return;
         }
 
@@ -445,8 +445,6 @@ public static class SeqCache {
         public SeqCache(int start, byte[] seq) {
             this.start = start;
             this.seq = seq;
-            this.posAA = posAA;
-            this.negAA = negAA;
         }
 
         /**
@@ -455,10 +453,9 @@ public SeqCache(int start, byte[] seq) {
          * @param codonTable
          */
         public void refreshAminoAcids(CodonTable codonTable) {
-            int mod = start % 3;
-            int n1 = normalize3(3 - mod);
-            int n2 = normalize3(n1 + 1);
-            int n3 = normalize3(n2 + 1);
+            int n1 = start % 3;
+            int n2 = (start + 1) % 3;
+            int n3 = (start + 2) % 3;
 
             String sequence = new String(seq);
             AminoAcidSequence[] posAA = {