From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 16 Sep 2015 17:38:24 +0000 (+0100)
Subject: JAL-1486 off-by-one error bugfix
X-Git-Tag: Release_2_10_0~401
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b61d853baef9db35859efb45d331becfdd11e61d;p=jalview.git

JAL-1486 off-by-one error bugfix
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 88271b9..360cf6b 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1309,19 +1309,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     int startPos = aligmentStartEnd[0];
     int endPos = aligmentStartEnd[1];
 
-    int[] lowestRange = new int[2];
-    int[] higestRange = new int[2];
+    int[] lowestRange = new int[] { -1, -1 };
+    int[] higestRange = new int[] { -1, -1 };
 
     for (int[] hiddenCol : hiddenCols)
     {
-      // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
     }
-    // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
-    // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
 
-    if (lowestRange[0] == 0 && lowestRange[1] == 0)
+    if (lowestRange[0] == -1 && lowestRange[1] == -1)
     {
       startPos = aligmentStartEnd[0];
     }
@@ -1330,27 +1327,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       startPos = lowestRange[1] + 1;
     }
 
-    if (higestRange[0] == 0 && higestRange[1] == 0)
+    if (higestRange[0] == -1 && higestRange[1] == -1)
     {
       endPos = aligmentStartEnd[1];
     }
     else
     {
-      endPos = higestRange[0];
+      endPos = higestRange[0] - 1;
     }
 
-    // System.out.println("Export range : " + minPos + " - " + maxPos);
+    // System.out.println("Export range : " + startPos + " - " + endPos);
     return new int[] { startPos, endPos };
   }
 
   public static void main(String[] args)
   {
     ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-    hiddenCols.add(new int[] { 0, 4 });
+    hiddenCols.add(new int[] { 0, 0 });
     hiddenCols.add(new int[] { 6, 9 });
     hiddenCols.add(new int[] { 11, 12 });
     hiddenCols.add(new int[] { 33, 33 });
-    hiddenCols.add(new int[] { 45, 50 });
+    hiddenCols.add(new int[] { 50, 50 });
 
     int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
     // System.out.println("Export range : " + x[0] + " - " + x[1]);
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index ebca31b..4ec077f 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -107,7 +107,6 @@ public class FormatAdapter extends AppletFormatAdapter
       {
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
-
         if (startEnd != null)
         {
           startIndex = startEnd[0];
@@ -127,9 +126,7 @@ public class FormatAdapter extends AppletFormatAdapter
           }
 
           startRes = seqs[i].findPosition(startIndex);
-          startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
-                  : startRes;
-          endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+          endRes = seqs[i].findPosition(endIndex);
         }
 
         tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],