X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=45bcf66d4c7bbb62c62229db86ad53007fe25719;hb=9961a60fb0e1ab87e60dc301485b00d058abf9e5;hp=aa98e76cdef6b2c32069cea96d313b2c5a9992be;hpb=987c0089ccb8885a1bf768d74ee3858859b489f5;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index aa98e76..45bcf66 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -418,7 +418,16 @@ public class SeqCanvas extends JComponent
     String getMask()
     {
       String mask = "00";
-      for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+      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";
       }
@@ -466,7 +475,7 @@ public class SeqCanvas extends JComponent
 
         int endx;
         int ypos = hgap;
-        int maxwidth = av.alignment.getWidth();
+        int maxwidth = av.alignment.getWidth()-1;
 
         if(av.hasHiddenColumns)
           maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;
@@ -560,8 +569,6 @@ public class SeqCanvas extends JComponent
             g.translate(-LABEL_WEST, 0);
 
             ypos += cHeight+getAnnotationHeight()+hgap;
-            if(av.showAnnotation)
-              ypos -= 3;
 
             startRes += cWidth;
         }
@@ -756,11 +763,11 @@ public class SeqCanvas extends JComponent
                     }
 
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&
-                            group.getSequences(false).
+                            group.getSequences(null).
                             contains(av.alignment.getSequenceAt(i)))
                     {
                         if ((bottom == -1) &&
-                                !group.getSequences(false).contains(
+                                !group.getSequences(null).contains(
                                     av.alignment.getSequenceAt(i + 1)))
                         {
                             bottom = sy + av.charHeight;
@@ -769,7 +776,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)
                         {
                             if (((top == -1) && (i == 0)) ||
-                                    !group.getSequences(false).contains(
+                                    !group.getSequences(null).contains(
                                         av.alignment.getSequenceAt(i - 1)))
                             {
                                 top = sy;