From 32a72d077d2371f4566688fbd103103d8505b27f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Nov 2006 15:46:50 +0000
Subject: [PATCH] IdMask must be Max seq end, not seq width

---
 src/jalview/appletgui/SeqCanvas.java |   15 ++++++++++++---
 src/jalview/gui/SeqCanvas.java       |   13 +++++++++++--
 2 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 4f32678..13a0ec8 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -355,13 +355,22 @@ public class SeqCanvas
    */
   String getMask()
   {
-    String mask = "00";
-    for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+    String mask = "0";
+    int maxWidth = 0;
+    int tmp;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      tmp = av.alignment.getSequenceAt(i).getEnd();
+      if (tmp > maxWidth)
+        maxWidth = tmp;
+    }
+
+    for (int i = maxWidth; i > 0; i /= 10)
     {
       mask += "0";
     }
     return mask;
-    }
+  }
 
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index aa98e76..1e66928 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -417,8 +417,17 @@ public class SeqCanvas extends JComponent
      */
     String getMask()
     {
-      String mask = "00";
-      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      String mask = "0";
+      int maxWidth = 0;
+      int tmp;
+      for(int i=0; i<av.alignment.getHeight(); i++)
+      {
+        tmp = av.alignment.getSequenceAt(i).getEnd();
+        if(tmp>maxWidth)
+          maxWidth = tmp;
+      }
+
+      for (int i = maxWidth; i > 0; i /= 10)
       {
         mask += "0";
       }
-- 
1.7.10.2