From b9c2f4b60cd997cc03ab560cbf211331b3658968 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 18 Apr 2006 13:17:20 +0000
Subject: [PATCH] -1 from east scale, wrapped alignment

---
 src/jalview/appletgui/SeqCanvas.java |    6 +++---
 src/jalview/gui/SeqCanvas.java       |   11 +++++------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index f6ef577..c5b4324 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -141,7 +141,7 @@ public class SeqCanvas
           continue;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = seq.findPosition(index);
         break;
       }
       if (value != -1)
@@ -366,7 +366,7 @@ public class SeqCanvas
 
     while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
     {
-      endx = startRes + cWidth;
+      endx = startRes + cWidth -1;
 
       if (endx > al.getWidth())
       {
@@ -407,7 +407,7 @@ public class SeqCanvas
           if(annotations==null)
             annotations = new AnnotationPanel(av);
 
-          annotations.drawComponent( g, startRes, endx );
+          annotations.drawComponent( g, startRes, endx+1 );
           g.translate(0, -cHeight - ypos-4);
         }
         g.translate(-LABEL_WEST, 0);
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 99447a4..d9f7ebb 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -180,15 +180,14 @@ public class SeqCanvas extends JComponent
         if(av.hasHiddenColumns)
                 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
 
+        SequenceI seq;
         // EAST SCALE
         for (int i = 0; i < av.alignment.getHeight(); i++)
         {
-            SequenceI seq = av.alignment.getSequenceAt(i);
+            seq = av.alignment.getSequenceAt(i);
             int index = endx;
             int value = -1;
 
-
-
             while (index > startx)
             {
                 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
@@ -198,7 +197,7 @@ public class SeqCanvas extends JComponent
                     continue;
                 }
 
-                value = av.alignment.getSequenceAt(i).findPosition(index);
+                value = seq.findPosition(index);
 
                 break;
             }
@@ -441,7 +440,7 @@ public class SeqCanvas extends JComponent
 
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
         {
-          endx = startRes + cWidth;
+          endx = startRes + cWidth -1;
 
           if (endx > al.getWidth())
           {
@@ -492,7 +491,7 @@ public class SeqCanvas extends JComponent
               if(annotations==null)
                 annotations = new AnnotationPanel(av);
 
-              annotations.drawComponent( (Graphics2D) g, startRes, endx);
+              annotations.drawComponent( (Graphics2D) g, startRes, endx+1);
               g.translate(0, -cHeight - ypos);
             }
             g.setClip(clip);
-- 
1.7.10.2