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 25b74b6..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
@@ -544,16 +557,34 @@ public class AlignFrame
 \r
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    addHistoryItem(new HistoryItem("Remove Gaps",\r
-                                   viewport.alignment,\r
+    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
                                    HistoryItem.HIDE));\r
+\r
     SequenceI current;\r
     int jSize;\r
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+\r
+    Vector seqs=null;\r
+\r
+    int start=0, end = viewport.alignment.getWidth();\r
+\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
+      end = viewport.getSelectionGroup().getEndRes();\r
+    }\r
+    else\r
+      seqs = viewport.alignment.getSequences();\r
+\r
+    for (int i = 0; i <seqs.size(); i++)\r
     {\r
-      current = viewport.getAlignment().getSequenceAt(i);\r
+      current = (SequenceI)seqs.elementAt(i);\r
       jSize = current.getLength();\r
-      for (int j = 0; j < jSize; j++)\r
+\r
+      int j = start;\r
+      do\r
       {\r
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
         {\r
@@ -561,13 +592,17 @@ public class AlignFrame
           j--;\r
           jSize--;\r
         }\r
+        j++;\r
       }\r
+      while(j < end && j < jSize) ;\r
     }\r
+\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
     alignPanel.repaint();\r
   }\r
 \r
+\r
   public void findMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     Finder finder = new Finder(alignPanel);\r
@@ -749,10 +784,6 @@ public class AlignFrame
       {\r
         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
       }\r
-      else if (cs instanceof ScoreColourScheme)\r
-      {\r
-        ( (ScoreColourScheme) cs).setThreshold(threshold);\r
-      }\r
 \r
       viewport.setGlobalColourScheme(cs);\r
     }\r
@@ -760,10 +791,6 @@ public class AlignFrame
     {\r
       ( (ResidueColourScheme) cs).setThreshold(0);\r
     }\r
-    else if (cs instanceof ScoreColourScheme)\r
-    {\r
-      ( (ScoreColourScheme) cs).setThreshold(0);\r
-    }\r
 \r
     if (viewport.getConservationSelected())\r
     {\r
@@ -804,9 +831,16 @@ public class AlignFrame
       {\r
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 \r
+        if(cs==null)\r
+        {\r
+          sg.cs = null;\r
+          continue;\r
+        }\r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
+          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
+          sg.cs = cxs;\r
         }\r
         else\r
         {\r
@@ -827,10 +861,6 @@ public class AlignFrame
           {\r
             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
           }\r
-          else if (sg.cs instanceof ScoreColourScheme)\r
-          {\r
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-          }\r
 \r
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
         }\r
@@ -964,8 +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
@@ -1086,9 +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
@@ -1106,7 +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