Copy seq ordering bug fixed

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index bb4b58a..caa0321 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -300,7 +300,7 @@ public class AlignFrame
                              seq.findPosition(sg.getStartRes()) + "\t"\r
                              + seq.findPosition(sg.getEndRes()) + "\t"\r
                              +\r
-                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+                             seq.getSequence(sg.getStartRes(),\r
           sg.getEndRes() + 1) + "\n");\r
     }\r
 \r
@@ -397,13 +397,26 @@ public class AlignFrame
       return;\r
     }\r
 \r
+\r
     SequenceGroup sg = viewport.getSelectionGroup();\r
+    boolean allSequences = false;\r
+    if(sg.sequences.size()==viewport.alignment.getHeight())\r
+          allSequences = true;\r
+\r
     for (int i = 0; i < sg.sequences.size(); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.getAlignment().findIndex(seq);\r
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 \r
+      // If the cut affects all sequences, remove highlighted columns\r
+      if (allSequences)\r
+      {\r
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+                                                     sg.getEndRes() + 1);\r
+      }\r
+\r
+\r
       if (seq.getSequence().length() < 1)\r
       {\r
         viewport.getAlignment().deleteSequence(seq);\r
@@ -554,7 +567,9 @@ public class AlignFrame
 \r
     int start=0, end = viewport.alignment.getWidth();\r
 \r
-    if(viewport.getSelectionGroup()!=null)\r
+    if (viewport.getSelectionGroup() != null\r
+        && viewport.getSelectionGroup().sequences != null\r
+        && viewport.getSelectionGroup().sequences.size()>0)\r
     {\r
       seqs = viewport.getSelectionGroup().sequences;\r
       start = viewport.getSelectionGroup().getStartRes();\r
@@ -579,7 +594,7 @@ public class AlignFrame
         }\r
         j++;\r
       }\r
-      while(j < end);\r
+      while(j < end && j < jSize) ;\r
     }\r
 \r
     viewport.updateConservation();\r
@@ -979,8 +994,8 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
                                    HistoryItem.SORT));\r
     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
-    AlignmentSorter.sortGroups(viewport.getAlignment());\r
     alignPanel.repaint();\r
+\r
   }\r
 \r
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
@@ -1101,9 +1116,7 @@ public class AlignFrame
 \r
   protected void documentation_actionPerformed(ActionEvent e)\r
   {\r
-\r
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
-\r
+    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
   }\r
 \r
   protected void about_actionPerformed(ActionEvent e)\r
@@ -1121,7 +1134,7 @@ public class AlignFrame
         int y = 5, x = 7;\r
         g.setColor(Color.black);\r
         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
-        g.drawString("JalView - Release 2.0", 200, y += fh);\r
+        g.drawString("JalView - Release 2.01", 200, y += fh);\r
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
                      x, y += fh * 2);\r