X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=0bdcb55f4915cfd2f897950f624ea662c3df35f3;hb=08620e4438a99912019631c0b1c9deb341b76ae0;hp=832f795114c887b62869ab2f1e0bf5b882f6a377;hpb=dc6d9b88b36c704faa61bcd3ed29a9e2f510bc83;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 832f795..0bdcb55 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -80,6 +80,7 @@ public class AlignFrame
       }
     }
 
+
   }
 
   public void inputText_actionPerformed(ActionEvent e)
@@ -278,30 +279,55 @@ public class AlignFrame
       orderedSeqs.put(index + "", seq);
     }
 
-    int index = 0;
+    int index = 0, startRes, endRes;
+    char ch;
+
     for (int i = 0; i < sg.getSize(); i++)
     {
-      SequenceI seq = null;
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
+        SequenceI seq = null;
+
+        while (seq == null)
         {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-          break;
+            if (orderedSeqs.containsKey(index + ""))
+            {
+                seq = (SequenceI) orderedSeqs.get(index + "");
+                index++;
+
+                break;
+            }
+            else
+            {
+                index++;
+            }
         }
-        else
+
+        //FIND START RES
+        //Returns residue following index if gap
+        startRes = seq.findPosition(sg.getStartRes());
+
+        //FIND END RES
+        //Need to find the residue preceeding index if gap
+        endRes = 0;
+
+        for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
         {
-          index++;
+          ch = seq.getCharAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+
+        if(endRes>0)
+        {
+          endRes += seq.getStart() -1;
         }
-      }
 
-      copiedSequences.append(seq.getName() + "\t" +
-                             seq.findPosition(sg.getStartRes()) + "\t"
-                             + seq.findPosition(sg.getEndRes()) + "\t"
-                             +
-                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),
-          sg.getEndRes() + 1) + "\n");
+        copiedSequences.append(seq.getName() + "\t" +
+            startRes + "\t" +
+            endRes + "\t" +
+            seq.getSequence(sg.getStartRes(),
+                sg.getEndRes() + 1) + "\n");
     }
 
   }
@@ -397,13 +423,26 @@ public class AlignFrame
       return;
     }
 
+
     SequenceGroup sg = viewport.getSelectionGroup();
+    boolean allSequences = false;
+    if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+      // If the cut affects all sequences, remove highlighted columns
+      if (allSequences)
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+                                                     sg.getEndRes() + 1);
+      }
+
+
       if (seq.getSequence().length() < 1)
       {
         viewport.getAlignment().deleteSequence(seq);
@@ -554,7 +593,9 @@ public class AlignFrame
 
     int start=0, end = viewport.alignment.getWidth();
 
-    if(viewport.getSelectionGroup()!=null)
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size()>0)
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
@@ -579,7 +620,7 @@ public class AlignFrame
         }
         j++;
       }
-      while(j < end);
+      while(j < end && j < jSize) ;
     }
 
     viewport.updateConservation();
@@ -1053,7 +1094,21 @@ public class AlignFrame
     //are the sequences aligned?
     if (!viewport.alignment.isAligned())
     {
-      return;
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+
     }
 
     final TreePanel tp;
@@ -1101,9 +1156,7 @@ public class AlignFrame
 
   protected void documentation_actionPerformed(ActionEvent e)
   {
-
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org");
-
+    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
   }
 
   protected void about_actionPerformed(ActionEvent e)
@@ -1121,7 +1174,7 @@ public class AlignFrame
         int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalView - Release 2.0", 200, y += fh);
+        g.drawString("JalView - Release 2.02", 200, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
                      x, y += fh * 2);