From 5edb685cf52a607834a82c10cb4dd9c139e31dde Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 14 Mar 2017 16:41:33 +0000
Subject: [PATCH] JAL-2439 Fixes to out-by-one sequence indexing in gui
 classes

---
 src/jalview/appletgui/AlignmentPanel.java |    2 +-
 src/jalview/appletgui/IdCanvas.java       |    4 ++--
 src/jalview/appletgui/SeqCanvas.java      |    6 +++---
 src/jalview/gui/AlignmentPanel.java       |    3 ++-
 src/jalview/gui/IdCanvas.java             |    6 +++---
 src/jalview/gui/SeqCanvas.java            |    6 +++---
 6 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index af7e9cd..dd7c8fa 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -823,7 +823,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         av.setStartSeq(offy);
         av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
-                / av.getCharHeight());
+                / av.getCharHeight() - 1);
       }
     }
 
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 8f8ed35..18281d9 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -117,7 +117,7 @@ public class IdCanvas extends Panel
       }
       else
       {
-        transY = imgHeight - vertical * av.getCharHeight();
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
     else if (vertical < 0)
@@ -264,7 +264,7 @@ public class IdCanvas extends Panel
     {
       // Now draw the id strings
       SequenceI seq;
-      for (int i = starty; i < endy; i++)
+      for (int i = starty; i <= endy; i++)
       {
 
         seq = av.getAlignment().getSequenceAt(i);
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index fd74c4a..cd5aa74 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -252,7 +252,7 @@ public class SeqCanvas extends Panel
       }
       else
       {
-        transY = imgHeight - vertical * avcharHeight;
+        transY = imgHeight - ((vertical + 1) * avcharHeight);
       }
     }
     else if (vertical < 0)
@@ -613,7 +613,7 @@ public class SeqCanvas extends Panel
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
 
@@ -697,7 +697,7 @@ public class SeqCanvas extends Panel
         int bottom = -1;
         int alHeight = av.getAlignment().getHeight() - 1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * avcharWidth;
           sy = offset + ((i - startSeq) * avcharHeight);
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 552d166..631638f 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -801,7 +801,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         av.setStartSeq(offy);
         av.setEndSeq(offy
-                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
+                - 1);
       }
     }
 
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index c753cae..11bb14b 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -175,10 +175,10 @@ public class IdCanvas extends JPanel
       }
       else
       {
-        transY = imgHeight - (vertical * av.getCharHeight());
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
-    else if (vertical < 0)
+    else if (vertical < 0) // scroll up
     {
       es = ss - vertical;
 
@@ -354,7 +354,7 @@ public class IdCanvas extends JPanel
 
       SequenceI sequence;
       // Now draw the id strings
-      for (int i = starty; i < endy; i++)
+      for (int i = starty; i <= endy; i++)
       {
         sequence = av.getAlignment().getSequenceAt(i);
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 54d2be7..226e0df 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -306,7 +306,7 @@ public class SeqCanvas extends JComponent
       }
       else
       {
-        transY = imgHeight - (vertical * charHeight);
+        transY = imgHeight - ((vertical + 1) * charHeight);
       }
     }
     else if (vertical < 0)
@@ -719,7 +719,7 @@ public class SeqCanvas extends JComponent
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
       if (nextSeq == null)
@@ -803,7 +803,7 @@ public class SeqCanvas extends JComponent
         int top = -1;
         int bottom = -1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * charWidth;
           sy = offset + ((i - startSeq) * charHeight);
-- 
1.7.10.2