Recalc accelerated

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 0ae9ec2..a855f6f 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,21 +1,21 @@
 /*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.datamodel;\r
 \r
 import jalview.analysis.*;\r
@@ -28,244 +28,305 @@ import java.awt.*;
 \r
 import java.util.Vector;\r
 \r
-\r
-public class SequenceGroup {\r
-    String groupName;\r
-    Conservation conserve;\r
-    Vector aaFrequency;\r
-    boolean displayBoxes;\r
-    boolean displayText;\r
-    boolean colourText;\r
-    public Vector sequences = new Vector();\r
-    int width = -1;\r
-    public ColourSchemeI cs;\r
-    int startRes = 0;\r
-    int endRes = 0;\r
-    Color outlineColour = Color.black;\r
-\r
-    public SequenceGroup() {\r
-        groupName = "Group";\r
-        this.displayBoxes = true;\r
-        this.displayText = true;\r
-        this.colourText = false;\r
-        cs = null;\r
-    }\r
-\r
-    public SequenceGroup(String groupName, ColourSchemeI scheme,\r
-        boolean displayBoxes, boolean displayText, boolean colourText,\r
-        int start, int end) {\r
-        this.groupName = groupName;\r
-        this.displayBoxes = displayBoxes;\r
-        this.displayText = displayText;\r
-        this.colourText = colourText;\r
-        this.cs = scheme;\r
-        startRes = start;\r
-        endRes = end;\r
-    }\r
-\r
-    public boolean adjustForRemoveLeft(int col) {\r
-        // return value is true if the group still exists\r
-        if (startRes >= col) {\r
-            startRes = startRes - col;\r
-        }\r
-\r
-        if (endRes >= col) {\r
-            endRes = endRes - col;\r
-\r
-            if (startRes > endRes) {\r
-                startRes = 0;\r
-            }\r
-        } else {\r
-            // must delete this group!!\r
-            return false;\r
-        }\r
-\r
-        return true;\r
+public class SequenceGroup\r
+{\r
+  String groupName;\r
+  Conservation conserve;\r
+  Vector aaFrequency;\r
+  boolean displayBoxes;\r
+  boolean displayText;\r
+  boolean colourText;\r
+  public Vector sequences = new Vector();\r
+  int width = -1;\r
+  public ColourSchemeI cs;\r
+  int startRes = 0;\r
+  int endRes = 0;\r
+  Color outlineColour = Color.black;\r
+\r
+  public SequenceGroup()\r
+  {\r
+    groupName = "Group";\r
+    this.displayBoxes = true;\r
+    this.displayText = true;\r
+    this.colourText = false;\r
+    cs = null;\r
+  }\r
+\r
+  public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,\r
+                       boolean displayBoxes, boolean displayText,\r
+                       boolean colourText,\r
+                       int start, int end)\r
+  {\r
+    this.sequences = sequences;\r
+    this.groupName = groupName;\r
+    this.displayBoxes = displayBoxes;\r
+    this.displayText = displayText;\r
+    this.colourText = colourText;\r
+    this.cs = scheme;\r
+    startRes = start;\r
+    endRes = end;\r
+  }\r
+\r
+  public SequenceGroup(String groupName, ColourSchemeI scheme,\r
+                       boolean displayBoxes, boolean displayText,\r
+                       boolean colourText,\r
+                       int start, int end)\r
+  {\r
+    this.groupName = groupName;\r
+    this.displayBoxes = displayBoxes;\r
+    this.displayText = displayText;\r
+    this.colourText = colourText;\r
+    this.cs = scheme;\r
+    startRes = start;\r
+    endRes = end;\r
+  }\r
+\r
+  public boolean adjustForRemoveLeft(int col)\r
+  {\r
+    // return value is true if the group still exists\r
+    if (startRes >= col)\r
+    {\r
+      startRes = startRes - col;\r
     }\r
 \r
-    public boolean adjustForRemoveRight(int col) {\r
-        if (startRes > col) {\r
-            // delete this group\r
-            return false;\r
-        }\r
-\r
-        if (endRes >= col) {\r
-            endRes = col;\r
-        }\r
+    if (endRes >= col)\r
+    {\r
+      endRes = endRes - col;\r
 \r
-        return true;\r
+      if (startRes > endRes)\r
+      {\r
+        startRes = 0;\r
+      }\r
     }\r
-\r
-    public String getName() {\r
-        return groupName;\r
+    else\r
+    {\r
+      // must delete this group!!\r
+      return false;\r
     }\r
 \r
-    public void setName(String name) {\r
-        groupName = name;\r
-    }\r
+    return true;\r
+  }\r
 \r
-    public Conservation getConservation() {\r
-        return conserve;\r
+  public boolean adjustForRemoveRight(int col)\r
+  {\r
+    if (startRes > col)\r
+    {\r
+      // delete this group\r
+      return false;\r
     }\r
 \r
-    public void setConservation(Conservation c) {\r
-        conserve = c;\r
+    if (endRes >= col)\r
+    {\r
+      endRes = col;\r
     }\r
 \r
-    public void addSequence(SequenceI s) {\r
-        if (!sequences.contains(s)) {\r
-            sequences.addElement(s);\r
-        }\r
-\r
-        if (cs != null) {\r
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
-        }\r
+    return true;\r
+  }\r
 \r
-        if (cs instanceof ConservationColourScheme) {\r
-            recalcConservation();\r
-        }\r
-    }\r
+  public String getName()\r
+  {\r
+    return groupName;\r
+  }\r
 \r
-    void recalcConservation() {\r
-        Conservation c = new Conservation(groupName,\r
-                ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
-        c.calculate();\r
-        c.verdict(false, 25);\r
+  public void setName(String name)\r
+  {\r
+    groupName = name;\r
+  }\r
 \r
-        ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
-        ccs.conserve = c;\r
-    }\r
+  public Conservation getConservation()\r
+  {\r
+    return conserve;\r
+  }\r
 \r
-    public void addOrRemove(SequenceI s) {\r
-        if (sequences.contains(s)) {\r
-            deleteSequence(s);\r
-        } else {\r
-            addSequence(s);\r
-        }\r
-    }\r
+  public void setConservation(Conservation c)\r
+  {\r
+    conserve = c;\r
+  }\r
 \r
-    public void deleteSequence(SequenceI s) {\r
-        sequences.removeElement(s);\r
+  public void addSequence(SequenceI s, boolean recalc)\r
+  {\r
+    if (!sequences.contains(s))\r
+      sequences.addElement(s);\r
 \r
-        if (cs != null) {\r
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
-        }\r
+    if(recalc)\r
+      recalcConservation();\r
+  }\r
 \r
-        if (cs instanceof ConservationColourScheme) {\r
-            recalcConservation();\r
-        }\r
-    }\r
 \r
-    public int getStartRes() {\r
-        return startRes;\r
+  public void recalcConservation()\r
+  {\r
+    if (cs != null)\r
+    {\r
+      cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
     }\r
 \r
-    public int getEndRes() {\r
-        return endRes;\r
-    }\r
+    if ( cs  instanceof ConservationColourScheme)\r
+    {\r
+      Conservation c = new Conservation(groupName,\r
+                                        ResidueProperties.propHash, 3, sequences,\r
+                                        0, getWidth());\r
+      c.calculate();\r
+      c.verdict(false, 25);\r
 \r
-    public void setStartRes(int i) {\r
-        startRes = i;\r
+      ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+      ccs.conserve = c;\r
     }\r
+  }\r
 \r
-    public void setEndRes(int i) {\r
-        endRes = i;\r
+  public void addOrRemove(SequenceI s, boolean recalc)\r
+  {\r
+    if (sequences.contains(s))\r
+    {\r
+      deleteSequence(s, recalc);\r
     }\r
-\r
-    public int getSize() {\r
-        return sequences.size();\r
+    else\r
+    {\r
+      addSequence(s, recalc);\r
     }\r
-\r
-    public SequenceI getSequenceAt(int i) {\r
-        return (SequenceI) sequences.elementAt(i);\r
+  }\r
+\r
+  public void deleteSequence(SequenceI s, boolean recalc)\r
+  {\r
+    sequences.removeElement(s);\r
+    if(recalc)\r
+      recalcConservation();\r
+  }\r
+\r
+  public int getStartRes()\r
+  {\r
+    return startRes;\r
+  }\r
+\r
+  public int getEndRes()\r
+  {\r
+    return endRes;\r
+  }\r
+\r
+  public void setStartRes(int i)\r
+  {\r
+    startRes = i;\r
+  }\r
+\r
+  public void setEndRes(int i)\r
+  {\r
+    endRes = i;\r
+  }\r
+\r
+  public int getSize()\r
+  {\r
+    return sequences.size();\r
+  }\r
+\r
+  public SequenceI getSequenceAt(int i)\r
+  {\r
+    return (SequenceI) sequences.elementAt(i);\r
+  }\r
+\r
+  public void setColourText(boolean state)\r
+  {\r
+    colourText = state;\r
+  }\r
+\r
+  public boolean getColourText()\r
+  {\r
+    return colourText;\r
+  }\r
+\r
+  public void setDisplayText(boolean state)\r
+  {\r
+    displayText = state;\r
+  }\r
+\r
+  public boolean getDisplayText()\r
+  {\r
+    return displayText;\r
+  }\r
+\r
+  public void setDisplayBoxes(boolean state)\r
+  {\r
+    displayBoxes = state;\r
+  }\r
+\r
+  public boolean getDisplayBoxes()\r
+  {\r
+    return displayBoxes;\r
+  }\r
+\r
+  public int getWidth()\r
+  {\r
+    // MC This needs to get reset when characters are inserted and deleted\r
+    if (sequences.size() > 0)\r
+    {\r
+      width = ( (SequenceI) sequences.elementAt(0)).getLength();\r
     }\r
 \r
-    public void setColourText(boolean state) {\r
-        colourText = state;\r
-    }\r
+    for (int i = 1; i < sequences.size(); i++)\r
+    {\r
+      SequenceI seq = (SequenceI) sequences.elementAt(i);\r
 \r
-    public boolean getColourText() {\r
-        return colourText;\r
+      if (seq.getLength() > width)\r
+      {\r
+        width = seq.getLength();\r
+      }\r
     }\r
 \r
-    public void setDisplayText(boolean state) {\r
-        displayText = state;\r
+    return width;\r
+  }\r
+\r
+  public void setOutlineColour(Color c)\r
+  {\r
+    outlineColour = c;\r
+  }\r
+\r
+  public Color getOutlineColour()\r
+  {\r
+    return outlineColour;\r
+  }\r
+\r
+  /**\r
+   *\r
+   * returns the sequences in the group ordered by the ordering given by al\r
+   *\r
+   * @param al Alignment\r
+   * @return SequenceI[]\r
+   */\r
+  public SequenceI[] getSequencesInOrder(Alignment al)\r
+  {\r
+    int sz;\r
+    java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
+    SequenceI[] seqs = new SequenceI[sz = sequences.size()];\r
+\r
+    for (int i = 0; i < sz; i++)\r
+    {\r
+      SequenceI seq = (SequenceI) sequences.elementAt(i);\r
+      int index = al.findIndex(seq);\r
+      orderedSeqs.put(index + "", seq);\r
     }\r
 \r
-    public boolean getDisplayText() {\r
-        return displayText;\r
-    }\r
+    int index = 0;\r
 \r
-    public void setDisplayBoxes(boolean state) {\r
-        displayBoxes = state;\r
-    }\r
+    for (int i = 0; i < sz; i++)\r
+    {\r
+      SequenceI seq = null;\r
 \r
-    public boolean getDisplayBoxes() {\r
-        return displayBoxes;\r
-    }\r
+      while (seq == null)\r
+      {\r
+        if (orderedSeqs.containsKey(index + ""))\r
+        {\r
+          seq = (SequenceI) orderedSeqs.get(index + "");\r
+          index++;\r
 \r
-    public int getWidth() {\r
-        // MC This needs to get reset when characters are inserted and deleted\r
-        if (sequences.size() > 0) {\r
-            width = ((SequenceI) sequences.elementAt(0)).getLength();\r
+          break;\r
         }\r
-\r
-        for (int i = 1; i < sequences.size(); i++) {\r
-            SequenceI seq = (SequenceI) sequences.elementAt(i);\r
-\r
-            if (seq.getLength() > width) {\r
-                width = seq.getLength();\r
-            }\r
+        else\r
+        {\r
+          index++;\r
         }\r
+      }\r
 \r
-        return width;\r
-    }\r
-\r
-    public void setOutlineColour(Color c) {\r
-        outlineColour = c;\r
-    }\r
-\r
-    public Color getOutlineColour() {\r
-        return outlineColour;\r
+      seqs[index] = seq;\r
     }\r
 \r
-    /**\r
-     *\r
-     * returns the sequences in the group ordered by the ordering given by al\r
-     *\r
-     * @param al Alignment\r
-     * @return SequenceI[]\r
-     */\r
-    public SequenceI[] getSequencesInOrder(Alignment al) {\r
-        int sz;\r
-        java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
-        SequenceI[] seqs = new SequenceI[sz = sequences.size()];\r
-\r
-        for (int i = 0; i < sz; i++) {\r
-            SequenceI seq = (SequenceI) sequences.elementAt(i);\r
-            int index = al.findIndex(seq);\r
-            orderedSeqs.put(index + "", seq);\r
-        }\r
-\r
-        int index = 0;\r
-\r
-        for (int i = 0; i < sz; i++) {\r
-            SequenceI seq = null;\r
-\r
-            while (seq == null) {\r
-                if (orderedSeqs.containsKey(index + "")) {\r
-                    seq = (SequenceI) orderedSeqs.get(index + "");\r
-                    index++;\r
-\r
-                    break;\r
-                } else {\r
-                    index++;\r
-                }\r
-            }\r
-\r
-            seqs[index] = seq;\r
-        }\r
-\r
-        return seqs;\r
-    }\r
+    return seqs;\r
+  }\r
 }\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9bc4bc0..5c31931 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -558,7 +558,7 @@ public class AlignFrame
     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
          i++)\r
     {\r
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
     }\r
 \r
     sg.setEndRes(viewport.alignment.getWidth());\r
@@ -581,7 +581,7 @@ public class AlignFrame
     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
          i++)\r
     {\r
-      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\r
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
     }\r
 \r
     PaintRefresher.Refresh(null);\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index e30be30..c14da85 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -93,7 +93,6 @@ public class IdCanvas
     if (gg == null)\r
     {\r
       repaint();\r
-\r
       return;\r
     }\r
 \r
@@ -178,6 +177,10 @@ public class IdCanvas
 \r
   void drawIds(int starty, int endy)\r
   {\r
+    if(gg==null)\r
+      return;\r
+\r
+\r
     Color currentColor = Color.white;\r
     Color currentTextColor = Color.black;\r
 \r

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b8977c5..51bf824 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -580,21 +580,24 @@ public class Jalview2XML
           }\r
         }\r
 \r
+        Vector seqs = new Vector();\r
+        int[] ids = groups[i].getSeq();\r
+\r
+        for (int s = 0; s < ids.length; s++)\r
+        {\r
+          seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(\r
+              ids[s]));\r
+        }\r
+\r
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
-            SequenceGroup(groups[i].getName(),\r
+            SequenceGroup(seqs, groups[i].getName(),\r
                           cs, groups[i].getDisplayBoxes(),\r
                           groups[i].getDisplayText(), groups[i].getColourText(),\r
                           groups[i].getStart(), groups[i].getEnd());\r
+\r
         sg.setOutlineColour(new java.awt.Color(\r
             groups[i].getOutlineColour()));\r
 \r
-        int[] ids = groups[i].getSeq();\r
-\r
-        for (int s = 0; s < ids.length; s++)\r
-        {\r
-          sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt(\r
-              ids[s]));\r
-        }\r
 \r
         if (groups[i].getConsThreshold() != 0)\r
         {\r

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 0fc83c3..c89cd59 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -474,13 +474,13 @@ public class RotatableCanvas
     {\r
       if (av.getSelectionGroup() != null)\r
       {\r
-        av.getSelectionGroup().addOrRemove(found);\r
+        av.getSelectionGroup().addOrRemove(found, true);\r
         PaintRefresher.Refresh(this);\r
       }\r
       else\r
       {\r
         av.setSelectionGroup(new SequenceGroup());\r
-        av.getSelectionGroup().addOrRemove(found);\r
+        av.getSelectionGroup().addOrRemove(found, true);\r
         av.getSelectionGroup().setEndRes(av.alignment.getWidth());\r
       }\r
     }\r
@@ -570,7 +570,7 @@ public class RotatableCanvas
           if (!av.getSelectionGroup().sequences.contains(sp.sequence))\r
           {\r
             changedSel = true;\r
-            av.getSelectionGroup().addSequence(sp.sequence);\r
+            av.getSelectionGroup().addSequence(sp.sequence, true);\r
           }\r
         }\r
       }\r

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 250998f..551f262 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -77,7 +77,7 @@ public class ScalePanel
 \r
       for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
       {\r
-        sg.addSequence(av.alignment.getSequenceAt(i));\r
+        sg.addSequence(av.alignment.getSequenceAt(i), false);\r
       }\r
 \r
       sg.setStartRes(res);\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index f4d77c3..52d137b 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -570,7 +570,7 @@ public class SeqPanel
       SequenceGroup sg = new SequenceGroup();\r
       sg.setStartRes(res);\r
       sg.setEndRes(res);\r
-      sg.addSequence(sequence);\r
+      sg.addSequence(sequence, false);\r
       av.setSelectionGroup(sg);\r
       stretchGroup = sg;\r
 \r
@@ -620,11 +620,12 @@ public class SeqPanel
       return;\r
     }\r
 \r
+    stretchGroup.recalcConservation();\r
+\r
     if (stretchGroup.cs instanceof ClustalxColourScheme)\r
     {\r
       stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences,\r
                                                  av.alignment.getWidth());\r
-      repaint();\r
     }\r
     else if (stretchGroup.cs instanceof ConservationColourScheme)\r
     {\r
@@ -633,7 +634,6 @@ public class SeqPanel
       SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
                                         stretchGroup.getName());\r
 \r
-      repaint();\r
     }\r
     else\r
     {\r
@@ -644,6 +644,7 @@ public class SeqPanel
     changeEndRes = false;\r
     changeStartRes = false;\r
     stretchGroup = null;\r
+    repaint();\r
     ap.idPanel.repaint();\r
   }\r
 \r
@@ -720,17 +721,17 @@ public class SeqPanel
 \r
       if (stretchGroup.sequences.contains(nextSeq))\r
       {\r
-        stretchGroup.deleteSequence(seq);\r
-        stretchGroup.deleteSequence(nextSeq);\r
+        stretchGroup.deleteSequence(seq, false);\r
+        stretchGroup.deleteSequence(nextSeq, false);\r
       }\r
       else\r
       {\r
         if (seq != null)\r
         {\r
-          stretchGroup.addSequence(seq);\r
+          stretchGroup.addSequence(seq, false);\r
         }\r
 \r
-        stretchGroup.addSequence(nextSeq);\r
+        stretchGroup.addSequence(nextSeq, false);\r
       }\r
     }\r
 \r

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 12416ae..0f74faf 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -79,7 +79,7 @@ public class TreeCanvas
     }\r
 \r
     selected.setEndRes(av.alignment.getWidth());\r
-    selected.addOrRemove(sequence);\r
+    selected.addOrRemove(sequence, true);\r
 \r
     PaintRefresher.Refresh(this);\r
     repaint();\r
@@ -299,7 +299,7 @@ public class TreeCanvas
 \r
           if (sg != null)\r
           {\r
-            sg.addOrRemove(seq);\r
+            sg.addOrRemove(seq, true);\r
           }\r
         }\r
       }\r
@@ -561,21 +561,17 @@ public class TreeCanvas
           Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()\r
                                      .elementAt(i),\r
                                      new Vector());\r
-          SequenceGroup sg = null;\r
 \r
+         Vector sequences = new Vector();\r
           for (int j = 0; j < l.size(); j++)\r
           {\r
-            SequenceNode sn = (SequenceNode) l.elementAt(j);\r
+            sequences.add( (Sequence)((SequenceNode) l.elementAt(j)).element());\r
+          }\r
 \r
-            if (sg == null)\r
-            {\r
-              sg = new SequenceGroup("TreeGroup",\r
-                                     av.getGlobalColourScheme(), true, true,\r
-                                     false, 0, av.alignment.getWidth());\r
-            }\r
+          SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
+                           av.getGlobalColourScheme(), true, true,\r
+                           false, 0, av.alignment.getWidth());\r
 \r
-            sg.addSequence( (Sequence) sn.element());\r
-          }\r
 \r
           if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
           {\r