From e224b72118c12cd77ae96f0f8d86c123e0416dc7 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 29 Apr 2016 10:44:30 +0100
Subject: [PATCH] JAL-192 scale origin relative to start of reference
 sequence, & deal gracefully with reference sequence being
 completely hidden

---
 src/jalview/gui/ScalePanel.java |   29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 7c8a1d7..e595e65 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -492,31 +492,38 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     gg.setColor(Color.black);
 
     int scalestartx = (startx / 10) * 10;
+
+    SequenceI refSeq = av.getAlignment().getSeqrep();
+    int refSp = 0, refEp = -1;
+    if (refSeq != null)
+    {
+      // find bounds and set origin appopriately
+      // locate first visible position for this sequence
+      int[] refbounds = av.getColumnSelection()
+              .locateVisibleBoundsOfSequence(refSeq);
+
+      refSp = refbounds[0] - 1;
+      refEp = refbounds[1] - 1;
+      scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
+    }
+
+
     int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
     int y = avCharHeight - fm.getDescent();
 
-    if ((scalestartx % 10) == 0)
+    if (refSeq == null && scalestartx % 10 == 0)
     {
       scalestartx += 5;
     }
 
     String string;
-    boolean isrgap = false;
-    char rc;
     int maxX = 0, refN, iadj;
-    SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = -1, refEp = -1;
-    if (refSeq != null)
-    {
-      refSp = refSeq.findIndex(refSeq.getStart()) - 1;
-      refEp = refSeq.findIndex(refSeq.getEnd()) - 1;
-    }
     // todo: add a 'reference origin column' to set column number relative to
     for (int i = scalestartx; i < endx; i += 5)
     {
-      if ((i % 10) == 0)
+      if (((i - refSp) % 10) == 0)
       {
         iadj = av.getColumnSelection().adjustForHiddenColumns(i) - 1;
         if (refSeq == null)
-- 
1.7.10.2