X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=89e2086a1ebbd81a81e2f2286dc7071a3fc7455c;hb=7724430e3293cbb862d0c50c5308a3b3b0417cac;hp=8e70e35dbabe3e213ce0dfd303a4abbcad8794ae;hpb=3e3378e2ccfea39a2b161600c5a2029716acd1b7;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 8e70e35..89e2086 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -138,6 +138,24 @@ public class SeqPanel
    {
      seqCanvas.cursorX += dx;
      seqCanvas.cursorY += dy;
+     if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+     {
+       int original = seqCanvas.cursorX - dx;
+       int maxWidth = av.alignment.getWidth();
+
+       while(!av.colSel.isVisible(seqCanvas.cursorX)
+             && seqCanvas.cursorX<maxWidth
+             && seqCanvas.cursorX>0)
+       {
+         seqCanvas.cursorX += dx;
+       }
+
+       if(seqCanvas.cursorX>=maxWidth
+          || !av.colSel.isVisible(seqCanvas.cursorX) )
+       {
+         seqCanvas.cursorX = original;
+       }
+      }
      scrollToVisible();
    }
 
@@ -169,13 +187,13 @@ public class SeqPanel
        {
          ap.scrollUp(false);
        }
-       while (seqCanvas.cursorX < av.startRes)
+       while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
        {
 
          if (!ap.scrollRight(false))
            break;
        }
-       while (seqCanvas.cursorX > av.endRes)
+       while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
        {
          if (!ap.scrollRight(true))
            break;
@@ -197,7 +215,7 @@ public class SeqPanel
        SequenceGroup sg = av.selectionGroup;
        //Find the top and bottom of this group
        int min = av.alignment.getHeight(), max = 0;
-       for(int i=0; i<sg.getSize(false); i++)
+       for(int i=0; i<sg.getSize(); i++)
        {
          int index = av.alignment.findIndex( sg.getSequenceAt(i) );
          if(index > max)
@@ -233,7 +251,7 @@ public class SeqPanel
        else
        {
          // Now add any sequences between min and max
-         sg.getSequences(false).removeAllElements();
+         sg.getSequences(null).removeAllElements();
          for (int i = min; i < max; i++)
          {
            sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -712,24 +730,18 @@ public class SeqPanel
     boolean fixedColumns = false;
     SequenceGroup sg = av.getSelectionGroup();
 
+    SequenceI seq = av.alignment.getSequenceAt(startseq);
 
       if (!groupEditing && av.hasHiddenRows)
       {
-        if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
+        if (av.hiddenRepSequences!=null
+            && av.hiddenRepSequences.containsKey(seq))
         {
+          sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
           groupEditing = true;
-        }
-      }
-
-      //No group, but the sequence may represent a group
-      if (groupEditing
-          && sg == null
-          && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
-      {
-        groupEditing = false;
+          }
       }
 
-      SequenceI seq = av.alignment.getSequenceAt(startseq);
       StringBuffer message = new StringBuffer();
       if (groupEditing)
       {
@@ -758,7 +770,7 @@ public class SeqPanel
 
       //Are we editing within a selection group?
       if (groupEditing
-          || (sg != null && sg.getSequences(true).contains(seq)))
+          || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
       {
         fixedColumns = true;
 
@@ -766,9 +778,7 @@ public class SeqPanel
         //but the sequence represents a group
         if (sg == null)
         {
-          sg = new SequenceGroup(null, null, false, false, false, 0,
-                                 av.alignment.getWidth()-1);
-          sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+          sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
         }
 
         fixedLeft = sg.getStartRes();
@@ -827,7 +837,7 @@ public class SeqPanel
 
       if (groupEditing)
       {
-        Vector vseqs = sg.getSequences(true);
+        Vector vseqs = sg.getSequences(av.hiddenRepSequences);
         int g, groupSize = vseqs.size();
         SequenceI[] groupSeqs = new SequenceI[groupSize];
         for (g = 0; g < groupSeqs.length; g++)
@@ -875,7 +885,7 @@ public class SeqPanel
 
           if (!blank)
           {
-            if(sg.getSize(false) == av.alignment.getHeight()  )
+            if(sg.getSize() == av.alignment.getHeight()  )
             {
               if((av.hasHiddenColumns
                   && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
@@ -1127,7 +1137,7 @@ public class SeqPanel
       }
     }
 
-    else if (!stretchGroup.getSequences(false).contains(sequence)
+    else if (!stretchGroup.getSequences(null).contains(sequence)
              || stretchGroup.getStartRes() > res
              || stretchGroup.getEndRes() < res)
     {
@@ -1227,7 +1237,7 @@ public class SeqPanel
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
         ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-            stretchGroup.getSequences(true),
+            stretchGroup.getSequences(av.hiddenRepSequences),
             stretchGroup.getWidth());
       }
 
@@ -1337,7 +1347,7 @@ public class SeqPanel
 
           Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-          if (stretchGroup.getSequences(false).contains(nextSeq))
+          if (stretchGroup.getSequences(null).contains(nextSeq))
           {
               stretchGroup.deleteSequence(seq, false);
           }