From 733e0fec094b381464807e6e167bf3b91dda3ed8 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Mon, 27 Nov 2023 19:38:03 -0800
Subject: [PATCH] Stabilize 3-frame translation rows.  Fixes #1420

---
 .../org/broad/igv/renderer/SequenceRenderer.java  | 15 +++++++++------
 .../java/org/broad/igv/track/SequenceTrack.java   | 11 ++++-------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/main/java/org/broad/igv/renderer/SequenceRenderer.java b/src/main/java/org/broad/igv/renderer/SequenceRenderer.java
index 6d0b1c3a79..451a6802c2 100644
--- 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
index afcfe29bbf..4d11c7d747 100644
--- 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 = {