Hidden representatives moved from sequence to viewport

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 24f2ddf..778142c 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -198,7 +198,7 @@ public class AlignmentSorter
             {\r
                 SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);\r
 \r
-                if (sg.getSize(false) > sg2.getSize(false))\r
+                if (sg.getSize() > sg2.getSize())\r
                 {\r
                     groups.insertElementAt(sg, j);\r
 \r

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index e24a6c0..c385ac8 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -22,7 +22,7 @@ public class Finder {
         this.alignment=alignment;
         this.selection = selection;
     }
-    
+
     public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {
         this(alignment, selectionGroup);
         this.seqIndex=seqIndex;
@@ -45,7 +45,7 @@ public class Finder {
         {
             int res = Integer.parseInt(searchString);
             found = true;
-            if (selection == null || selection.getSize(false) < 1)
+            if (selection == null || selection.getSize() < 1)
             {
               seq = (Sequence) alignment.getSequenceAt(0);
             }
@@ -65,10 +65,10 @@ public class Finder {
 
         int end = alignment.getHeight();
 
-        
+
         if (selection != null)
         {
-            if ((selection.getSize(false) < 1) ||
+            if ((selection.getSize() < 1) ||
                     ((selection.getEndRes() - selection.getStartRes()) < 2))
             {
                 selection = null;
@@ -79,7 +79,7 @@ public class Finder {
         {
             seq = (Sequence) alignment.getSequenceAt(seqIndex);
 
-            if ((selection != null) && !selection.getSequences(false).contains(seq))
+            if ((selection != null) && !selection.getSequences(null).contains(seq))
             {
                 seqIndex++;
                 resIndex = 0;
@@ -97,7 +97,7 @@ public class Finder {
             {
                 item = item.substring(0, selection.getEndRes() + 1);
             }
-            
+
             ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
             StringBuffer noGapsSB = new StringBuffer();
             int insertCount = 0;

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a1e99ff..0c0f562 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -106,7 +106,7 @@ public class APopupMenu
 \r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
 \r
-    if (sg != null && sg.getSize(false)>0)\r
+    if (sg != null && sg.getSize()>0)\r
     {\r
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
@@ -307,7 +307,7 @@ public class APopupMenu
       }\r
 \r
       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
-          description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange\r
           );\r
 \r
       ap.alignFrame.addHistoryItem(caseCommand);\r
@@ -529,7 +529,8 @@ public class APopupMenu
   protected void clustalColour_actionPerformed()\r
   {\r
     SequenceGroup sg = getGroup();\r
-    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());\r
+    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
+                                     ap.av.alignment.getWidth());\r
     refresh();\r
   }\r
 \r
@@ -589,7 +590,7 @@ public class APopupMenu
 \r
     if (abovePIDColour.getState())\r
     {\r
-      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                                ap.av.alignment.getWidth()));\r
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
           getGroup().getName());\r
@@ -617,7 +618,7 @@ public class APopupMenu
   {\r
     SequenceGroup sg = getGroup();\r
     sg.cs = new PIDColourScheme();\r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                              ap.av.alignment.getWidth()));\r
     refresh();\r
   }\r
@@ -628,7 +629,7 @@ public class APopupMenu
 \r
     sg.cs = new Blosum62ColourScheme();\r
 \r
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                              ap.av.alignment.getWidth()));\r
 \r
     refresh();\r
@@ -651,7 +652,7 @@ public class APopupMenu
 \r
       Conservation c = new Conservation("Group",\r
                                         ResidueProperties.propHash, 3,\r
-                                        sg.getSequences(true), 0,\r
+                                        sg.getSequences(ap.av.hiddenRepSequences), 0,\r
                                         ap.av.alignment.getWidth());\r
 \r
       c.calculate();\r
@@ -711,34 +712,33 @@ public class APopupMenu
   void hideSequences(boolean representGroup)\r
   {\r
     SequenceGroup sg = ap.av.getSelectionGroup();\r
-    if(sg==null || sg.getSize(false)<1)\r
+    if(sg==null || sg.getSize()<1)\r
     {\r
       ap.av.hideSequence(new SequenceI[]{seq});\r
       return;\r
     }\r
 \r
-    int gsize = sg.getSize(false);\r
-    SequenceI [] hseqs;\r
+    ap.av.setSelectionGroup(null);\r
 \r
-    hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+    if (representGroup)\r
+    {\r
+      ap.av.hideRepSequences(seq, sg);\r
 \r
-      int index = 0;\r
-      for(int i=0; i<gsize; i++)\r
-      {\r
-        if(representGroup && sg.getSequenceAt(i)!=seq)\r
-        {\r
-          seq.addHiddenSequence(sg.getSequenceAt(i));\r
-          hseqs[index++] = sg.getSequenceAt(i);\r
-        }\r
-        else if(!representGroup)\r
-        {\r
-          hseqs[index++] = sg.getSequenceAt(i);\r
-        }\r
-        }\r
+      return;\r
+    }\r
+\r
+    int gsize = sg.getSize();\r
+    SequenceI[] hseqs;\r
 \r
-      ap.av.hideSequence(hseqs);\r
+    hseqs = new SequenceI[gsize];\r
+\r
+    int index = 0;\r
+    for (int i = 0; i < gsize; i++)\r
+    {\r
+      hseqs[index++] = sg.getSequenceAt(i);\r
+    }\r
 \r
-      ap.av.setSelectionGroup(null);\r
+    ap.av.hideSequence(hseqs);\r
     }\r
 \r
 }\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 9fdf1c8..147e035 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -337,7 +337,7 @@ public class AlignFrame extends Frame implements ActionListener,
 \r
         if(toggleSeqs)\r
         {\r
-          if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+          if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
           {\r
             hide = true;\r
             viewport.hideAllSelectedSeqs();\r
@@ -916,13 +916,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
       {\r
         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-        if (!sg.getSequences(false).contains(seq))\r
+        if (!sg.getSequences(null).contains(seq))\r
         {\r
           continue;\r
         }\r
 \r
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
-        if (sg.getSequences(false).contains(temp))\r
+        if (sg.getSequences(null).contains(temp))\r
         {\r
           continue;\r
         }\r
@@ -936,13 +936,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
       {\r
         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-        if (!sg.getSequences(true).contains(seq))\r
+        if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
         {\r
           continue;\r
         }\r
 \r
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
-        if (sg.getSequences(true).contains(temp))\r
+        if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
         {\r
           continue;\r
         }\r
@@ -967,7 +967,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceGroup sg = viewport.getSelectionGroup();\r
     copiedSequences = new StringBuffer();\r
     Hashtable orderedSeqs = new Hashtable();\r
-    for (int i = 0; i < sg.getSize(false); i++)\r
+    for (int i = 0; i < sg.getSize(); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.alignment.findIndex(seq);\r
@@ -996,7 +996,7 @@ public void itemStateChanged(ItemEvent evt)
       copiedHiddenColumns = null;\r
 \r
 \r
-    for (int i = 0; i < sg.getSize(false); i++)\r
+    for (int i = 0; i < sg.getSize(); i++)\r
     {\r
         SequenceI seq = null;\r
 \r
@@ -1161,7 +1161,7 @@ public void itemStateChanged(ItemEvent evt)
 \r
     Vector seqs = new Vector();\r
     SequenceI seq;\r
-    for (int i = 0; i < sg.getSize(false); i++)\r
+    for (int i = 0; i < sg.getSize(); i++)\r
     {\r
       seq = sg.getSequenceAt(i);\r
       seqs.addElement(seq);\r
@@ -1169,7 +1169,7 @@ public void itemStateChanged(ItemEvent evt)
 \r
 \r
    // If the cut affects all sequences, remove highlighted columns\r
-   if (sg.getSize(false) == viewport.alignment.getHeight())\r
+   if (sg.getSize() == viewport.alignment.getHeight())\r
    {\r
      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
          sg.getEndRes() + 1);\r
@@ -1267,7 +1267,7 @@ public void itemStateChanged(ItemEvent evt)
 \r
       SequenceI [] seqs;\r
       if(viewport.getSelectionGroup()!=null)\r
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
       else\r
         seqs = viewport.alignment.getSequencesArray();\r
 \r
@@ -1326,7 +1326,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceI[] seqs;\r
     if (viewport.getSelectionGroup() != null)\r
     {\r
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
       start = viewport.getSelectionGroup().getStartRes();\r
       end = viewport.getSelectionGroup().getEndRes();\r
     }\r
@@ -1365,7 +1365,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceI[] seqs;\r
     if (viewport.getSelectionGroup() != null)\r
     {\r
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
       start = viewport.getSelectionGroup().getStartRes();\r
       end = viewport.getSelectionGroup().getEndRes();\r
     }\r
@@ -1557,7 +1557,9 @@ public void itemStateChanged(ItemEvent evt)
         }\r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
-          sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
+          sg.cs = new ClustalxColourScheme(\r
+              sg.getSequences(viewport.hiddenRepSequences),\r
+              sg.getWidth());\r
         }\r
         else\r
         {\r
@@ -1577,7 +1579,8 @@ public void itemStateChanged(ItemEvent evt)
             || cs instanceof Blosum62ColourScheme)\r
         {\r
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
+          sg.cs.setConsensus(AAFrequency.calculate(\r
+              sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
         }\r
         else\r
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
@@ -1586,7 +1589,7 @@ public void itemStateChanged(ItemEvent evt)
         {\r
           Conservation c = new Conservation("Group",\r
                                             ResidueProperties.propHash, 3,\r
-                                            sg.getSequences(true), 0,\r
+                                            sg.getSequences(viewport.hiddenRepSequences), 0,\r
                                             viewport.alignment.getWidth() - 1);\r
           c.calculate();\r
           c.verdict(false, viewport.ConsPercGaps);\r
@@ -1692,7 +1695,7 @@ public void itemStateChanged(ItemEvent evt)
   public void pairwiseAlignmentMenuItem_actionPerformed()\r
   {\r
     if (viewport.getSelectionGroup()!=null\r
-        && viewport.getSelectionGroup().getSize(false) > 1)\r
+        && viewport.getSelectionGroup().getSize() > 1)\r
     {\r
       Frame frame = new Frame();\r
       frame.add(new PairwiseAlignPanel(alignPanel));\r
@@ -1722,8 +1725,8 @@ public void itemStateChanged(ItemEvent evt)
     }\r
 \r
     if ( (viewport.getSelectionGroup() != null &&\r
-          viewport.getSelectionGroup().getSize(false) < 4 &&\r
-          viewport.getSelectionGroup().getSize(false) > 0)\r
+          viewport.getSelectionGroup().getSize() < 4 &&\r
+          viewport.getSelectionGroup().getSize() > 0)\r
         || viewport.getAlignment().getHeight() < 4)\r
     {\r
       return;\r
@@ -1782,7 +1785,7 @@ public void itemStateChanged(ItemEvent evt)
     }\r
 \r
     if ( (viewport.getSelectionGroup() != null &&\r
-          viewport.getSelectionGroup().getSize(false) > 1)\r
+          viewport.getSelectionGroup().getSize() > 1)\r
       || (viewport.getSelectionGroup() == null\r
           && viewport.alignment.getHeight() > 1))\r
     {\r

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ad7113a..88a0b0f 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -111,6 +111,8 @@ public class AlignViewport
 \r
   String sequenceSetID;\r
 \r
+  Hashtable hiddenRepSequences;\r
+\r
   public AlignViewport(AlignmentI al, JalviewLite applet)\r
   {\r
     this.applet = applet;\r
@@ -951,6 +953,33 @@ public class AlignViewport
     hasHiddenColumns = true;\r
   }\r
 \r
+  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)\r
+  {\r
+    int sSize = sg.getSize();\r
+    if(sSize < 2)\r
+      return;\r
+\r
+    if(hiddenRepSequences==null)\r
+      hiddenRepSequences = new Hashtable();\r
+\r
+     hiddenRepSequences.put(repSequence, sg);\r
+\r
+    //Hide all sequences except the repSequence\r
+    SequenceI [] seqs = new SequenceI[sSize-1];\r
+    int index = 0;\r
+    for(int i=0; i<sSize; i++)\r
+      if(sg.getSequenceAt(i)!=repSequence)\r
+      {\r
+        if(index==sSize-1)\r
+          return;\r
+\r
+        seqs[index++] = sg.getSequenceAt(i);\r
+      }\r
+\r
+    hideSequence(seqs);\r
+\r
+    }\r
+\r
   public void hideAllSelectedSeqs()\r
   {\r
     if (selectionGroup == null)\r
@@ -997,7 +1026,7 @@ public class AlignViewport
         selectionGroup = new SequenceGroup();\r
         selectionGroup.setEndRes(alignment.getWidth()-1);\r
       }\r
-      Vector tmp = alignment.getHiddenSequences().showAll();\r
+      Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);\r
       for(int t=0; t<tmp.size(); t++)\r
       {\r
         selectionGroup.addSequence(\r
@@ -1006,7 +1035,8 @@ public class AlignViewport
       }\r
       firePropertyChange("alignment", null, alignment.getSequences());\r
       hasHiddenRows = false;\r
-    }\r
+      hiddenRepSequences = null;\r
+      }\r
   }\r
 \r
   public int adjustForHiddenSeqs(int alignmentIndex)\r
@@ -1047,7 +1077,7 @@ public class AlignViewport
     int start = 0, end = 0;\r
     if(selectedRegionOnly && selectionGroup!=null)\r
     {\r
-      iSize = selectionGroup.getSize(false);\r
+      iSize = selectionGroup.getSize();\r
       seqs = selectionGroup.getSequencesInOrder(alignment);\r
       start = selectionGroup.getStartRes();\r
       end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor\r
@@ -1142,7 +1172,7 @@ public class AlignViewport
     int start = 0, end = 0;\r
     if(selectedRegionOnly && selectionGroup!=null)\r
     {\r
-      iSize = selectionGroup.getSize(false);\r
+      iSize = selectionGroup.getSize();\r
       seqs = selectionGroup.getSequencesInOrder(alignment);\r
       start = selectionGroup.getStartRes();\r
       end = selectionGroup.getEndRes()+1;\r
@@ -1310,7 +1340,7 @@ public class AlignViewport
       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
       {\r
         ((ClustalxColourScheme)sg.cs).resetClustalX(\r
-            sg.getSequences(true), sg.getWidth());\r
+            sg.getSequences(hiddenRepSequences), sg.getWidth());\r
       }\r
       sg.recalcConservation();\r
     }\r

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 7ee9f54..830eeeb 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -149,7 +149,7 @@ public class Finder extends Panel implements ActionListener
       int res = Integer.parseInt(searchString);\r
       found = true;\r
 \r
-      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
       {\r
         seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
       }\r
@@ -172,7 +172,7 @@ public class Finder extends Panel implements ActionListener
     SequenceGroup selection = av.getSelectionGroup();\r
     if (selection != null)\r
     {\r
-      if (selection.getSize(false) < 1 ||\r
+      if (selection.getSize() < 1 ||\r
           (selection.getEndRes() - selection.getStartRes() < 2))\r
       {\r
         selection = null;\r
@@ -184,7 +184,7 @@ public class Finder extends Panel implements ActionListener
 \r
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
 \r
-      if (selection != null && !selection.getSequences(false).contains(seq))\r
+      if (selection != null && !selection.getSequences(null).contains(seq))\r
       {\r
         seqIndex++;\r
         resIndex = 0;\r

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 3bf6639..a1bc873 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -59,7 +59,7 @@ public class IdCanvas
       gg.setColor(Color.white);\r
     }\r
     else if (av.getSelectionGroup() != null &&\r
-             av.getSelectionGroup().getSequences(false).contains(s))\r
+             av.getSelectionGroup().getSequences(null).contains(s))\r
     {\r
       gg.setColor(Color.lightGray);\r
       gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
@@ -260,7 +260,7 @@ public class IdCanvas
           currentTextColor = Color.white;\r
         }\r
         else if ( (av.getSelectionGroup() != null) &&\r
-                 av.getSelectionGroup().getSequences(false).contains(seq))\r
+                 av.getSelectionGroup().getSequences(null).contains(seq))\r
         {\r
           currentColor = Color.lightGray;\r
           currentTextColor = Color.black;\r

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 792c906..480f719 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -60,7 +60,7 @@ public class PairwiseAlignPanel
 
     float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
-    int count = ap.av.getSelectionGroup().getSize(false);
+    int count = ap.av.getSelectionGroup().getSize();
     String type=(ap.av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
     Sequence seq;
 

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index fd85ce7..2e8811a 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -103,7 +103,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 \r
       int start, end;\r
 \r
-      if ( (sg != null) && (sg.getSize(false) >= 1))\r
+      if ( (sg != null) && (sg.getSize() >= 1))\r
       {\r
          originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
          start = sg.getStartRes();\r

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index f411a63..36e0859 100755 (executable)
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -382,7 +382,7 @@ public class RotatableCanvas
 \r
       if (av.getSelectionGroup() != null)\r
       {\r
-        if (av.getSelectionGroup().getSequences(false).contains( ( (SequencePoint) points.\r
+        if (av.getSelectionGroup().getSequences(null).contains( ( (SequencePoint) points.\r
             elementAt(i)).sequence))\r
         {\r
           g.setColor(Color.gray);\r
@@ -577,7 +577,7 @@ public class RotatableCanvas
       {\r
         if (av != null)\r
         {\r
-          if (!av.getSelectionGroup().getSequences(false).contains(sp.sequence))\r
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))\r
           {\r
             av.getSelectionGroup().addSequence(sp.sequence, true);\r
           }\r

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index bfa0531..9cde175 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -112,7 +112,7 @@ public class ScalePanel
             av.hideColumns(res, res);\r
             if (av.getSelectionGroup() != null\r
                 &&\r
-                av.getSelectionGroup().getSize(false) == av.alignment.getHeight())\r
+                av.getSelectionGroup().getSize() == av.alignment.getHeight())\r
               av.setSelectionGroup(null);\r
 \r
             ap.repaint();\r

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index dc7911d..3af9fb9 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -671,12 +671,12 @@ public class SeqCanvas
            }\r
 \r
            if ( (sx <= (endRes - startRes) * av.charWidth) &&\r
-               group.getSequences(false).\r
+               group.getSequences(null).\r
                contains(av.alignment.getSequenceAt(i)))\r
            {\r
              if ( (bottom == -1) &&\r
              (i >= alHeight ||\r
-                 !group.getSequences(false).contains(\r
+                 !group.getSequences(null).contains(\r
                      av.alignment.getSequenceAt(i + 1))))\r
              {\r
                bottom = sy + av.charHeight;\r
@@ -685,7 +685,7 @@ public class SeqCanvas
              if (!inGroup)\r
              {\r
                if ( ( (top == -1) && (i == 0)) ||\r
-                   !group.getSequences(false).contains(\r
+                   !group.getSequences(null).contains(\r
                        av.alignment.getSequenceAt(i - 1)))\r
                {\r
                  top = sy;\r

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index feda697..89e2086 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -215,7 +215,7 @@ public class SeqPanel
        SequenceGroup sg = av.selectionGroup;\r
        //Find the top and bottom of this group\r
        int min = av.alignment.getHeight(), max = 0;\r
-       for(int i=0; i<sg.getSize(false); i++)\r
+       for(int i=0; i<sg.getSize(); i++)\r
        {\r
          int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
          if(index > max)\r
@@ -251,7 +251,7 @@ public class SeqPanel
        else\r
        {\r
          // Now add any sequences between min and max\r
-         sg.getSequences(false).removeAllElements();\r
+         sg.getSequences(null).removeAllElements();\r
          for (int i = min; i < max; i++)\r
          {\r
            sg.addSequence(av.alignment.getSequenceAt(i), false);\r
@@ -730,24 +730,18 @@ public class SeqPanel
     boolean fixedColumns = false;\r
     SequenceGroup sg = av.getSelectionGroup();\r
 \r
+    SequenceI seq = av.alignment.getSequenceAt(startseq);\r
 \r
       if (!groupEditing && av.hasHiddenRows)\r
       {\r
-        if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
+        if (av.hiddenRepSequences!=null\r
+            && av.hiddenRepSequences.containsKey(seq))\r
         {\r
+          sg = (SequenceGroup)av.hiddenRepSequences.get(seq);\r
           groupEditing = true;\r
-        }\r
-      }\r
-\r
-      //No group, but the sequence may represent a group\r
-      if (groupEditing\r
-          && sg == null\r
-          && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)\r
-      {\r
-        groupEditing = false;\r
+          }\r
       }\r
 \r
-      SequenceI seq = av.alignment.getSequenceAt(startseq);\r
       StringBuffer message = new StringBuffer();\r
       if (groupEditing)\r
       {\r
@@ -776,7 +770,7 @@ public class SeqPanel
 \r
       //Are we editing within a selection group?\r
       if (groupEditing\r
-          || (sg != null && sg.getSequences(true).contains(seq)))\r
+          || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))\r
       {\r
         fixedColumns = true;\r
 \r
@@ -784,9 +778,7 @@ public class SeqPanel
         //but the sequence represents a group\r
         if (sg == null)\r
         {\r
-          sg = new SequenceGroup(null, null, false, false, false, 0,\r
-                                 av.alignment.getWidth()-1);\r
-          sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
+          sg = (SequenceGroup) av.hiddenRepSequences.get(seq);\r
         }\r
 \r
         fixedLeft = sg.getStartRes();\r
@@ -845,7 +837,7 @@ public class SeqPanel
 \r
       if (groupEditing)\r
       {\r
-        Vector vseqs = sg.getSequences(true);\r
+        Vector vseqs = sg.getSequences(av.hiddenRepSequences);\r
         int g, groupSize = vseqs.size();\r
         SequenceI[] groupSeqs = new SequenceI[groupSize];\r
         for (g = 0; g < groupSeqs.length; g++)\r
@@ -893,7 +885,7 @@ public class SeqPanel
 \r
           if (!blank)\r
           {\r
-            if(sg.getSize(false) == av.alignment.getHeight()  )\r
+            if(sg.getSize() == av.alignment.getHeight()  )\r
             {\r
               if((av.hasHiddenColumns\r
                   && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
@@ -1145,7 +1137,7 @@ public class SeqPanel
       }\r
     }\r
 \r
-    else if (!stretchGroup.getSequences(false).contains(sequence)\r
+    else if (!stretchGroup.getSequences(null).contains(sequence)\r
              || stretchGroup.getStartRes() > res\r
              || stretchGroup.getEndRes() < res)\r
     {\r
@@ -1245,7 +1237,7 @@ public class SeqPanel
       if (stretchGroup.cs instanceof ClustalxColourScheme)\r
       {\r
         ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
-            stretchGroup.getSequences(true),\r
+            stretchGroup.getSequences(av.hiddenRepSequences),\r
             stretchGroup.getWidth());\r
       }\r
 \r
@@ -1355,7 +1347,7 @@ public class SeqPanel
 \r
           Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 \r
-          if (stretchGroup.getSequences(false).contains(nextSeq))\r
+          if (stretchGroup.getSequences(null).contains(nextSeq))\r
           {\r
               stretchGroup.deleteSequence(seq, false);\r
           }\r

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 0d80535..2801351 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -185,7 +185,7 @@ public class TreeCanvas
       // Colour selected leaves differently\r
       SequenceGroup selected = av.getSelectionGroup();\r
       if (selected != null &&\r
-          selected.getSequences(false).contains( (SequenceI) node.element()))\r
+          selected.getSequences(null).contains( (SequenceI) node.element()))\r
       {\r
         g.setColor(Color.gray);\r
 \r
@@ -584,7 +584,7 @@ public class TreeCanvas
             {\r
             Conservation c = new Conservation("Group",\r
                                               ResidueProperties.propHash, 3,\r
-                                              sg.getSequences(false),\r
+                                              sg.getSequences(null),\r
                                               sg.getStartRes(),\r
                                               sg.getEndRes());\r
 \r

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 9a2db89..552a5f8 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -203,7 +203,7 @@ public class Alignment implements AlignmentI
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.getSequences(false).contains(s))
+            if (sg.getSequences(null).contains(s))
             {
                 return sg;
             }
@@ -227,14 +227,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.getSequences(false)==null)
+            if(sg==null || sg.getSequences(null)==null)
             {
               this.deleteGroup(sg);
               gSize--;
               continue;
             }
 
-            if (sg.getSequences(false).contains(s))
+            if (sg.getSequences(null).contains(s))
             {
                 temp.addElement(sg);
             }
@@ -259,9 +259,7 @@ public class Alignment implements AlignmentI
         {
           if(hiddenSequences.getSize()>0)
           {
-            //We're not going to make groups of
-            //Hidden sequences
-            int i, iSize = sg.getSize(false);
+            int i, iSize = sg.getSize();
             for (i = 0; i < iSize; i++)
             {
               if (!sequences.contains(sg.getSequenceAt(i)))
@@ -272,7 +270,7 @@ public class Alignment implements AlignmentI
               }
             }
 
-            if (sg.getSize(true) < 1)
+            if (sg.getSize() < 1)
               return;
           }
 
@@ -660,34 +658,6 @@ public class Alignment implements AlignmentI
     {
       return hiddenSequences;
     }
-    SequenceI [] getVisibleAndRepresentedSeqs()
-    {
-      if(hiddenSequences==null || hiddenSequences.getSize()<1)
-        return getSequencesArray();
-
-      Vector seqs = new Vector();
-      SequenceI seq;
-      SequenceGroup hidden;
-      for (int i = 0; i < sequences.size(); i++)
-      {
-        seq = (SequenceI) sequences.elementAt(i);
-        seqs.addElement(seq);
-        hidden = seq.getHiddenSequences();
-        if(hidden!=null)
-        {
-          for(int j=0; j<hidden.getSize(false); j++)
-          {
-            seqs.addElement(hidden.getSequenceAt(j));
-          }
-        }
-      }
-      SequenceI [] result = new SequenceI[seqs.size()];
-      for(int i=0; i<seqs.size(); i++)
-        result[i] = (SequenceI)seqs.elementAt(i);
-
-      return result;
-
-    }
 
   public CigarArray getCompactAlignment()
   {

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9d9fa81..9491329 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -121,14 +121,14 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);\r
   }\r
 \r
-  public Vector showAll()\r
+  public Vector showAll(Hashtable hiddenReps)\r
   {\r
    Vector revealedSeqs = new Vector();\r
    for(int i=0; i<hiddenSequences.length; i++)\r
     {\r
       if(hiddenSequences[i]!=null)\r
       {\r
-        Vector tmp = showSequence(i);\r
+        Vector tmp = showSequence(i, hiddenReps);\r
         for (int t = 0; t < tmp.size(); t++)\r
           revealedSeqs.addElement(tmp.elementAt(t));\r
       }\r
@@ -136,18 +136,17 @@ public class HiddenSequences
     return revealedSeqs;\r
   }\r
 \r
-  public Vector showSequence(int alignmentIndex)\r
+  public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)\r
   {\r
     Vector revealedSeqs = new Vector();\r
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);\r
-    if(repSequence!=null\r
-       && repSequence.getHiddenSequences()==null\r
-       && alignmentIndex>0)\r
-      repSequence = alignment.getSequenceAt(alignmentIndex-1);\r
-\r
-    if(repSequence!=null\r
-       && repSequence.getHiddenSequences()==null)\r
-      repSequence = null;\r
+    if(repSequence !=null &&\r
+       hiddenReps!=null\r
+       && hiddenReps.containsKey(repSequence))\r
+    {\r
+      hiddenReps.remove(repSequence);\r
+      revealedSeqs.addElement(repSequence);\r
+    }\r
 \r
     int start = adjustForHiddenSeqs(alignmentIndex-1);\r
     int end = adjustForHiddenSeqs(alignmentIndex);\r
@@ -168,11 +167,6 @@ public class HiddenSequences
          }\r
          else\r
            System.out.println(seq.getName()+" has been deleted whilst hidden");\r
-\r
-         if (repSequence != null)\r
-         {\r
-           repSequence.showHiddenSequence(seq);\r
-         }\r
       }\r
 \r
     }\r

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 39d6880..02fc543 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -30,7 +30,6 @@ import java.util.*;
  */
 public class Sequence implements SequenceI
 {
-  
   SequenceI datasetSequence;
   String name;
   private char [] sequence;
@@ -48,10 +47,6 @@ public class Sequence implements SequenceI
   /** DOCUMENT ME!! */
   public SequenceFeature[] sequenceFeatures;
 
-  /** This array holds hidden sequences
-   * of which this sequence is the representitive member of a group
-   */
-  SequenceGroup hiddenSequences;
 
   /**
    * Creates a new Sequence object.
@@ -690,32 +685,11 @@ public class Sequence implements SequenceI
     this.annotation.addElement(annotation);
   }
 
-  public SequenceGroup getHiddenSequences()
-  {
-    return hiddenSequences;
-  }
 
-  public void addHiddenSequence(SequenceI seq)
-  {
-    if (hiddenSequences == null)
-    {
-      hiddenSequences = new SequenceGroup();
-    }
-    hiddenSequences.addSequence(seq, false);
-  }
-
-  public void showHiddenSequence(SequenceI seq)
-  {
-    hiddenSequences.deleteSequence(seq, false);
-    if (hiddenSequences.getSize(false) < 1)
-    {
-      hiddenSequences = null;
-    }
-  }
   /**
    * test if this is a valid candidate for another
-   * sequence's dataset sequence. 
-   * 
+   * sequence's dataset sequence.
+   *
    */
   private boolean isValidDatasetSequence() {
       if (datasetSequence!=null)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index f640ebb..76a350f 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -178,25 +178,27 @@ public class SequenceGroup
       return eres;\r
     }\r
 \r
-    public Vector getSequences(boolean includeHidden)\r
+    public Vector getSequences(Hashtable hiddenReps)\r
     {\r
-      if(!includeHidden)\r
+      if(hiddenReps == null)\r
         return sequences;\r
       else\r
       {\r
         Vector allSequences = new Vector();\r
-        SequenceI seq;\r
+        SequenceI seq, seq2;\r
         for (int i = 0; i < sequences.size(); i++)\r
         {\r
           seq = (SequenceI) sequences.elementAt(i);\r
           allSequences.addElement(seq);\r
-          if (seq.getHiddenSequences() != null)\r
+          if (hiddenReps.containsKey(seq) )\r
           {\r
-            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)\r
+            SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);\r
+            for (int h = 0; h < hsg.getSize(); h++)\r
             {\r
-              allSequences.addElement(\r
-                  seq.getHiddenSequences().getSequenceAt(h)\r
-                  );\r
+              seq2 = hsg.getSequenceAt(h);\r
+              if (seq2 != seq\r
+                  && !allSequences.contains(seq2))\r
+                allSequences.addElement(seq2);\r
             }\r
           }\r
         }\r
@@ -205,9 +207,9 @@ public class SequenceGroup
       }\r
     }\r
 \r
-    public SequenceI[] getSequencesAsArray(boolean includeHidden)\r
+    public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)\r
     {\r
-      Vector tmp = getSequences(includeHidden);\r
+      Vector tmp = getSequences(hiddenReps);\r
       if(tmp==null)\r
         return null;\r
       SequenceI [] result = new SequenceI[tmp.size()];\r
@@ -452,24 +454,9 @@ public class SequenceGroup
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public int getSize(boolean includeHidden)\r
+    public int getSize()\r
     {\r
-      if(!includeHidden)\r
         return sequences.size();\r
-      else\r
-      {\r
-        int total = sequences.size();\r
-        SequenceI seq;\r
-        for (int i = 0; i < sequences.size(); i++)\r
-        {\r
-          seq = (SequenceI) sequences.elementAt(i);\r
-          if (seq.getHiddenSequences() != null)\r
-          {\r
-            total += seq.getHiddenSequences().getSize(false);\r
-          }\r
-        }\r
-        return total;\r
-      }\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index c5fdbda..96c6cbf 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -259,12 +259,7 @@ public interface SequenceI
 
     public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
-    public SequenceGroup getHiddenSequences();
 
-    public void addHiddenSequence(SequenceI seq);
-
-    public void showHiddenSequence(SequenceI seq);
-    
     /**
      * Derive a sequence (using this one's dataset or as the dataset)
      * @return duplicate sequence with valid dataset sequence

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bb722a5..1f2b37b 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -310,7 +310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               SequenceGroup sg = viewport.getSelectionGroup();
               if (toggleSeqs)
               {
-                if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
                 {
                   hideSelSequences_actionPerformed(null);
                   hide = true;
@@ -1082,14 +1082,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -1104,14 +1104,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
 
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -1435,7 +1435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     Vector seqs = new Vector();
     SequenceI seq;
-    for (int i = 0; i < sg.getSize(false); i++)
+    for (int i = 0; i < sg.getSize(); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
@@ -1443,7 +1443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
    // If the cut affects all sequences, remove highlighted columns
-   if (sg.getSize(false) == viewport.alignment.getHeight())
+   if (sg.getSize() == viewport.alignment.getHeight())
    {
      viewport.getColumnSelection().removeElements(sg.getStartRes(),
          sg.getEndRes() + 1);
@@ -1608,7 +1608,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       SequenceI [] seqs;
       if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       else
         seqs = viewport.alignment.getSequencesArray();
 
@@ -1671,7 +1671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -1715,7 +1715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
@@ -2230,7 +2230,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -2255,7 +2255,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 viewport.getIgnoreGapsConsensus());
 
          sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(true), sg.getStartRes(),
+             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
              sg.getEndRes()+1));
        }
         else
@@ -2266,7 +2266,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true),
+                                            sg.getSequences(viewport.hiddenRepSequences),
                                             sg.getStartRes(),
                                             sg.getEndRes()+1);
           c.calculate();
@@ -2518,7 +2518,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ( (viewport.getSelectionGroup() == null) ||
-        (viewport.getSelectionGroup().getSize(false) < 2))
+        (viewport.getSelectionGroup().getSize() < 2))
     {
       JOptionPane.showInternalMessageDialog(this,
                                             "You must select at least 2 sequences.",
@@ -2541,8 +2541,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if ( ( (viewport.getSelectionGroup() != null) &&
-          (viewport.getSelectionGroup().getSize(false) < 4) &&
-          (viewport.getSelectionGroup().getSize(false) > 0)) ||
+          (viewport.getSelectionGroup().getSize() < 4) &&
+          (viewport.getSelectionGroup().getSize() > 0)) ||
         (viewport.getAlignment().getHeight() < 4))
     {
       JOptionPane.showInternalMessageDialog(this,
@@ -2622,7 +2622,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     TreePanel tp;
 
     if (viewport.getSelectionGroup() != null) {
-      if (viewport.getSelectionGroup().getSize(false) < 3) {
+      if (viewport.getSelectionGroup().getSize() < 3) {
         JOptionPane.showMessageDialog(Desktop.desktop,
                                       "You need to have more than two sequences selected to build a tree!",
                                       "Not enough sequences",
@@ -2634,9 +2634,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      while (s < sg.getSize(false))
+      while (s < sg.getSize())
       {
-        if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
+        if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
             sg.getEndRes())
         {
           JOptionPane.showMessageDialog(Desktop.desktop,
@@ -2779,7 +2779,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignmentView msa = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 1))
+        (viewport.getSelectionGroup().getSize() > 1))
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       /*SequenceGroup seqs = viewport.getSelectionGroup();
@@ -2821,7 +2821,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    AlignmentView seqs = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 0))
+        (viewport.getSelectionGroup().getSize() > 0))
     {
       seqs = viewport.getAlignmentView(true);
     }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 05ba166..be7f8f4 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -120,6 +120,8 @@ public class AlignViewport
 
     boolean rightAlignIds = false;
 
+    Hashtable hiddenRepSequences;
+
 
     /**
      * Creates a new AlignViewport object.
@@ -1262,6 +1264,33 @@ public class AlignViewport
       hasHiddenColumns = true;
     }
 
+    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+    {
+      int sSize = sg.getSize();
+      if(sSize < 2)
+        return;
+
+      if(hiddenRepSequences==null)
+        hiddenRepSequences = new Hashtable();
+
+       hiddenRepSequences.put(repSequence, sg);
+
+      //Hide all sequences except the repSequence
+      SequenceI [] seqs = new SequenceI[sSize-1];
+      int index = 0;
+      for(int i=0; i<sSize; i++)
+        if(sg.getSequenceAt(i)!=repSequence)
+        {
+          if(index==sSize-1)
+            return;
+
+          seqs[index++] = sg.getSequenceAt(i);
+        }
+
+      hideSequence(seqs);
+
+    }
+
     public void hideAllSelectedSeqs()
     {
       if (selectionGroup == null)
@@ -1279,8 +1308,9 @@ public class AlignViewport
       if(seq!=null)
       {
         for (int i = 0; i < seq.length; i++)
+        {
           alignment.getHiddenSequences().hideSequence(seq[i]);
-
+        }
         hasHiddenRows = true;
         firePropertyChange("alignment", null, alignment.getSequences());
       }
@@ -1288,7 +1318,8 @@ public class AlignViewport
 
     public void showSequence(int index)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index
+          , hiddenRepSequences);
       if(tmp.size()>0)
       {
         if(selectionGroup==null)
@@ -1332,7 +1363,7 @@ public class AlignViewport
           selectionGroup = new SequenceGroup();
           selectionGroup.setEndRes(alignment.getWidth()-1);
         }
-        Vector tmp = alignment.getHiddenSequences().showAll();
+        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
         for(int t=0; t<tmp.size(); t++)
         {
           selectionGroup.addSequence(
@@ -1341,9 +1372,12 @@ public class AlignViewport
         }
         firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
+        hiddenRepSequences = null;
       }
     }
 
+
+
     public void invertColumnSelection()
     {
       for(int i=0; i<alignment.getWidth(); i++)
@@ -1357,9 +1391,7 @@ public class AlignViewport
             colSel.addElement(i);
           }
         }
-
       }
-
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1400,7 +1432,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
@@ -1495,7 +1527,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes()+1;
@@ -1605,7 +1637,7 @@ public class AlignViewport
         if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
         {
           ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(hiddenRepSequences), sg.getWidth());
         }
         sg.recalcConservation();
       }

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 1574d03..4047ac8 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -719,7 +719,7 @@ public class AlignmentPanel extends GAlignmentPanel
     {\r
       seq = av.getAlignment().getSequenceAt(i);\r
       if ( (av.getSelectionGroup() != null) &&\r
-          av.getSelectionGroup().getSequences(false).contains(seq))\r
+          av.getSelectionGroup().getSequences(null).contains(seq))\r
       {\r
         currentColor = Color.gray;\r
         currentTextColor = Color.black;\r

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 7acd374..a3a2396 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -579,9 +579,9 @@ public class FeatureSettings extends JPanel
     int iSize;\r
 \r
     if(af.getViewport().getSelectionGroup()!=null\r
-      && af.getViewport().getSelectionGroup().getSize(false)>0)\r
+      && af.getViewport().getSelectionGroup().getSize()>0)\r
     {\r
-      iSize = af.getViewport().getSelectionGroup().getSize(false);\r
+      iSize = af.getViewport().getSelectionGroup().getSize();\r
       dataset = new SequenceI[iSize];\r
       seqs = af.getViewport().getSelectionGroup().\r
           getSequencesInOrder(\r

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index f3a0d45..0e340dc 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -172,7 +172,7 @@ public class Finder extends GFinder
         {\r
             int res = Integer.parseInt(searchString);\r
             found = true;\r
-            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
             {\r
               seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
             }\r
@@ -195,7 +195,7 @@ public class Finder extends GFinder
 \r
         if (selection != null)\r
         {\r
-            if ((selection.getSize(false) < 1) ||\r
+            if ((selection.getSize() < 1) ||\r
                     ((selection.getEndRes() - selection.getStartRes()) < 2))\r
             {\r
                 selection = null;\r
@@ -206,7 +206,7 @@ public class Finder extends GFinder
         {\r
             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
 \r
-            if ((selection != null) && !selection.getSequences(false).contains(seq))\r
+            if ((selection != null) && !selection.getSequences(null).contains(seq))\r
             {\r
                 seqIndex++;\r
                 resIndex = 0;\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index d1f130b..168b50d 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -82,7 +82,7 @@ public class IdCanvas extends JPanel
             gg.setColor(Color.white);\r
         }\r
         else if ((av.getSelectionGroup() != null) &&\r
-                av.getSelectionGroup().getSequences(false).contains(s))\r
+                av.getSelectionGroup().getSequences(null).contains(s))\r
         {\r
             gg.setColor(Color.lightGray);\r
             gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),\r
@@ -271,14 +271,14 @@ public class IdCanvas extends JPanel
             {\r
               for (int i = starty; i < alheight; i++)\r
               {\r
+                SequenceI s = av.alignment.getSequenceAt(i);\r
                 if (av.hasHiddenRows)\r
                 {\r
-                  setHiddenFont(i);\r
+                  setHiddenFont(s);\r
                 }\r
                 else\r
                   gg.setFont(italic);\r
 \r
-                SequenceI s = av.alignment.getSequenceAt(i);\r
                 drawIdString(gg, s, i, 0, ypos);\r
               }\r
 \r
@@ -310,7 +310,7 @@ public class IdCanvas extends JPanel
 \r
               if (av.hasHiddenRows)\r
               {\r
-                setHiddenFont(i);\r
+                setHiddenFont(sequence);\r
               }\r
 \r
                 // Selected sequence colours\r
@@ -321,7 +321,7 @@ public class IdCanvas extends JPanel
                   currentTextColor = Color.white;\r
                 }\r
                 else if ( (av.getSelectionGroup() != null) &&\r
-                         av.getSelectionGroup().getSequences(false).contains(\r
+                         av.getSelectionGroup().getSequences(null).contains(\r
                              sequence))\r
                 {\r
                   currentColor = Color.lightGray;\r
@@ -419,7 +419,7 @@ public class IdCanvas extends JPanel
         }\r
     }\r
 \r
-    void setHiddenFont(int i)\r
+    void setHiddenFont(SequenceI seq)\r
     {\r
       Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
                              av.getFont().getSize());\r
@@ -427,8 +427,8 @@ public class IdCanvas extends JPanel
                            av.getFont().getSize());\r
 \r
 \r
-      if (av.alignment.getSequenceAt(i)!=null\r
-          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
+      if (av.hiddenRepSequences!=null &&\r
+          av.hiddenRepSequences.containsKey(seq))\r
         gg.setFont(bold);\r
       else\r
         gg.setFont(italic);\r

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f1f7db1..6652aea 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -263,16 +263,20 @@ public class Jalview2XML
             {
               jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 
-              if(jal.getSequenceAt(i).getHiddenSequences()!=null)
+              if(av.hiddenRepSequences!=null
+              && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
               {
-                jalview.datamodel.SequenceI [] reps =
-                    jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
+                jalview.datamodel.SequenceI[] reps =
+                    ( (jalview.datamodel.SequenceGroup)
+                     av.hiddenRepSequences.get(
+                         jal.getSequenceAt(i))).getSequencesInOrder(jal);
 
                 for(int h=0; h<reps.length; h++)
                 {
-                  jseq.addHiddenSequences(
-                      jal.findIndex(reps[h])
-                      );
+                  if (reps[h] != jal.getSequenceAt(i))
+                    jseq.addHiddenSequences(
+                        jal.findIndex(reps[h])
+                        );
                 }
               }
             }
@@ -574,7 +578,7 @@ public class Jalview2XML
                 groups[i].setTextCol2(sg.textColour2.getRGB());
                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 
-                for (int s = 0; s < sg.getSize(false); s++)
+                for (int s = 0; s < sg.getSize(); s++)
                 {
                     jalview.datamodel.Sequence seq =
                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
@@ -1301,7 +1305,7 @@ public class Jalview2XML
                 if (groups[i].getConsThreshold() != 0)
                 {
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
+                            ResidueProperties.propHash, 3, sg.getSequences(null), 0,
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
@@ -1362,12 +1366,17 @@ public class Jalview2XML
         {
           for(int s=0; s<JSEQ.length; s++)
           {
+            jalview.datamodel.SequenceGroup hidden =
+                new jalview.datamodel.SequenceGroup();
+
             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
             {
-              al.getSequenceAt(s).addHiddenSequence(
-                  al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
+              hidden.addSequence(
+                  al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
+                  , false
                   );
             }
+            af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
           }
 
           jalview.datamodel.SequenceI [] hseqs = new

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 62f6df0..393b192 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -338,7 +338,7 @@ public class Jalview2XML_V1
                 if (groups[i].getConsThreshold() != 0)\r
                 {\r
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
-                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
+                            ResidueProperties.propHash, 3, sg.getSequences(null), 0,\r
                             sg.getWidth() - 1);\r
                     c.calculate();\r
                     c.verdict(false, 25);\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 21be086..9ed81ab 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -180,7 +180,7 @@ public class PopupMenu extends JPopupMenu
           add(menuItem);\r
 \r
           if(ap.av.getSelectionGroup() !=null\r
-             && ap.av.getSelectionGroup().getSize(false)>1)\r
+             && ap.av.getSelectionGroup().getSize()>1)\r
           {\r
             menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
             menuItem.addActionListener(new java.awt.event.ActionListener()\r
@@ -718,7 +718,7 @@ public class PopupMenu extends JPopupMenu
     protected void clustalColour_actionPerformed(ActionEvent e)\r
     {\r
         SequenceGroup sg = getGroup();\r
-        sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
+        sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
                 ap.av.alignment.getWidth());\r
         refresh();\r
     }\r
@@ -825,7 +825,7 @@ public class PopupMenu extends JPopupMenu
         if (abovePIDColour.isSelected())\r
         {\r
           sg.cs.setConsensus(AAFrequency.calculate(\r
-              sg.getSequences(true), sg.getStartRes(),\r
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
               sg.getEndRes() + 1));\r
 \r
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
@@ -872,7 +872,7 @@ public class PopupMenu extends JPopupMenu
     {\r
         SequenceGroup sg = getGroup();\r
         sg.cs = new PIDColourScheme();\r
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
                                                  sg.getStartRes(),\r
                                                  sg.getEndRes() + 1));\r
         refresh();\r
@@ -889,7 +889,7 @@ public class PopupMenu extends JPopupMenu
 \r
         sg.cs = new Blosum62ColourScheme();\r
 \r
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
                                                  sg.getStartRes(),\r
                                                  sg.getEndRes() + 1));\r
 \r
@@ -922,7 +922,7 @@ public class PopupMenu extends JPopupMenu
         {\r
             Conservation c = new Conservation("Group",\r
                     ResidueProperties.propHash, 3,\r
-                    sg.getSequences(true),\r
+                    sg.getSequences(ap.av.hiddenRepSequences),\r
                     sg.getStartRes(),\r
                     sg.getEndRes() + 1);\r
 \r
@@ -1124,34 +1124,33 @@ public class PopupMenu extends JPopupMenu
     void hideSequences(boolean representGroup)\r
     {\r
       SequenceGroup sg = ap.av.getSelectionGroup();\r
-      if(sg==null || sg.getSize(false)<1)\r
+      if(sg==null || sg.getSize()<1)\r
       {\r
         ap.av.hideSequence(new SequenceI[]{sequence});\r
         return;\r
       }\r
 \r
-      int gsize = sg.getSize(false);\r
-      SequenceI [] hseqs;\r
+      ap.av.setSelectionGroup(null);\r
 \r
-      hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+      if (representGroup)\r
+      {\r
+        ap.av.hideRepSequences(sequence, sg);\r
 \r
-        int index = 0;\r
-        for(int i=0; i<gsize; i++)\r
-        {\r
-          if(representGroup && sg.getSequenceAt(i)!=sequence)\r
-          {\r
-            sequence.addHiddenSequence(sg.getSequenceAt(i));\r
-            hseqs[index++] = sg.getSequenceAt(i);\r
-          }\r
-          else if(!representGroup)\r
-          {\r
-            hseqs[index++] = sg.getSequenceAt(i);\r
-          }\r
-        }\r
+        return;\r
+      }\r
 \r
-        ap.av.hideSequence(hseqs);\r
+      int gsize = sg.getSize();\r
+      SequenceI[] hseqs;\r
 \r
-        ap.av.setSelectionGroup(null);\r
+      hseqs = new SequenceI[gsize];\r
+\r
+      int index = 0;\r
+      for (int i = 0; i < gsize; i++)\r
+      {\r
+        hseqs[index++] = sg.getSequenceAt(i);\r
+      }\r
+\r
+      ap.av.hideSequence(hseqs);\r
     }\r
 \r
   public void copy_actionPerformed(ActionEvent e)\r
@@ -1226,7 +1225,8 @@ public class PopupMenu extends JPopupMenu
       }\r
 \r
       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
-          description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
+          startEnd, caseChange\r
           );\r
 \r
       ap.alignFrame.addHistoryItem(caseCommand);\r
@@ -1335,7 +1335,7 @@ public class PopupMenu extends JPopupMenu
     if(sg==null)\r
       return;\r
 \r
-    int gSize= sg.getSize(false);\r
+    int gSize= sg.getSize();\r
     SequenceI [] seqs = new SequenceI[gSize];\r
     SequenceFeature [] features = new SequenceFeature[gSize];\r
 \r

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index e7a580e..4ca114d 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -125,7 +125,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 \r
         int start, end;\r
 \r
-        if ( (sg != null) && (sg.getSize(false) >= 1))\r
+        if ( (sg != null) && (sg.getSize() >= 1))\r
         {\r
            originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
            start = sg.getStartRes();\r

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index be1d3f5..5a963ec 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -429,7 +429,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 \r
             if (av.getSelectionGroup() != null)\r
             {\r
-                if (av.getSelectionGroup().getSequences(false).contains(\r
+                if (av.getSelectionGroup().getSequences(null).contains(\r
                             ((SequencePoint) points.elementAt(i)).sequence))\r
                 {\r
                     g.setColor(Color.gray);\r
@@ -706,7 +706,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
             {\r
                 if (av != null)\r
                 {\r
-                    if (!av.getSelectionGroup().getSequences(false).contains(sp.sequence))\r
+                    if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))\r
                     {\r
                         av.getSelectionGroup().addSequence(sp.sequence, true);\r
                     }\r

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 99b8620..32283ce 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -119,7 +119,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener, MouseList
               {\r
                 av.hideColumns(res, res);\r
                 if(av.getSelectionGroup()!=null\r
-                   && av.getSelectionGroup().getSize(false)==av.alignment.getHeight())\r
+                   && av.getSelectionGroup().getSize()==av.alignment.getHeight())\r
                   av.setSelectionGroup(null);\r
 \r
                 ap.repaint();\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8a873a2..5b89ca1 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -763,11 +763,11 @@ public class SeqCanvas extends JComponent
                     }\r
 \r
                     if ( (sx <= (endRes-startRes)*av.charWidth) &&\r
-                            group.getSequences(false).\r
+                            group.getSequences(null).\r
                             contains(av.alignment.getSequenceAt(i)))\r
                     {\r
                         if ((bottom == -1) &&\r
-                                !group.getSequences(false).contains(\r
+                                !group.getSequences(null).contains(\r
                                     av.alignment.getSequenceAt(i + 1)))\r
                         {\r
                             bottom = sy + av.charHeight;\r
@@ -776,7 +776,7 @@ public class SeqCanvas extends JComponent
                         if (!inGroup)\r
                         {\r
                             if (((top == -1) && (i == 0)) ||\r
-                                    !group.getSequences(false).contains(\r
+                                    !group.getSequences(null).contains(\r
                                         av.alignment.getSequenceAt(i - 1)))\r
                             {\r
                                 top = sy;\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bc9adfe..675325a 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -366,7 +366,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         SequenceGroup sg = av.selectionGroup;\r
         //Find the top and bottom of this group\r
         int min = av.alignment.getHeight(), max = 0;\r
-        for(int i=0; i<sg.getSize(false); i++)\r
+        for(int i=0; i<sg.getSize(); i++)\r
         {\r
           int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
           if(index > max)\r
@@ -402,7 +402,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         else\r
         {\r
           // Now add any sequences between min and max\r
-          sg.getSequences(false).clear();\r
+          sg.getSequences(null).clear();\r
           for (int i = min; i < max; i++)\r
           {\r
             sg.addSequence(av.alignment.getSequenceAt(i), false);\r
@@ -809,24 +809,20 @@ public class SeqPanel extends JPanel implements MouseListener,
       boolean fixedColumns = false;\r
       SequenceGroup sg = av.getSelectionGroup();\r
 \r
+      SequenceI seq = av.alignment.getSequenceAt(startseq);\r
 \r
+      //No group, but the sequence may represent a group\r
         if (!groupEditing && av.hasHiddenRows)\r
         {\r
-          if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
+          if (av.hiddenRepSequences!=null\r
+              && av.hiddenRepSequences.containsKey(seq))\r
           {\r
+            sg = (SequenceGroup)av.hiddenRepSequences.get(seq);\r
             groupEditing = true;\r
           }\r
         }\r
 \r
-        //No group, but the sequence may represent a group\r
-        if (groupEditing\r
-            && sg == null\r
-            && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)\r
-        {\r
-          groupEditing = false;\r
-        }\r
 \r
-        SequenceI seq = av.alignment.getSequenceAt(startseq);\r
         StringBuffer message = new StringBuffer();\r
         if (groupEditing)\r
         {\r
@@ -855,7 +851,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 \r
         //Are we editing within a selection group?\r
         if (groupEditing\r
-            || (sg != null && sg.getSequences(true).contains(seq)))\r
+            || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))\r
         {\r
           fixedColumns = true;\r
 \r
@@ -863,9 +859,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           //but the sequence represents a group\r
           if (sg == null)\r
           {\r
-            sg = new SequenceGroup(null, null, false, false, false, 0,\r
-                                   av.alignment.getWidth()-1);\r
-            sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
+            sg = (SequenceGroup) av.hiddenRepSequences.get(seq);\r
           }\r
 \r
           fixedLeft = sg.getStartRes();\r
@@ -924,7 +918,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 \r
         if (groupEditing)\r
         {\r
-          Vector vseqs = sg.getSequences(true);\r
+          Vector vseqs = sg.getSequences(av.hiddenRepSequences);\r
           int g, groupSize = vseqs.size();\r
           SequenceI[] groupSeqs = new SequenceI[groupSize];\r
           for (g = 0; g < groupSeqs.length; g++)\r
@@ -972,7 +966,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 \r
             if (!blank)\r
             {\r
-              if(sg.getSize(false) == av.alignment.getHeight()  )\r
+              if(sg.getSize() == av.alignment.getHeight()  )\r
               {\r
                 if((av.hasHiddenColumns\r
                     && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
@@ -1221,7 +1215,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );\r
       if(evt.getClickCount()>1)\r
       {\r
-        if (av.getSelectionGroup().getSize(false) == 1\r
+        if (av.getSelectionGroup().getSize() == 1\r
             && av.getSelectionGroup().getEndRes()\r
             - av.getSelectionGroup().getStartRes() < 2)\r
           av.setSelectionGroup(null);\r
@@ -1327,7 +1321,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 stretchGroup = null;\r
             }\r
         }\r
-        else if (!stretchGroup.getSequences(false).contains(sequence) ||\r
+        else if (!stretchGroup.getSequences(null).contains(sequence) ||\r
                 (stretchGroup.getStartRes() > res) ||\r
                 (stretchGroup.getEndRes() < res))\r
         {\r
@@ -1442,7 +1436,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           if (stretchGroup.cs instanceof ClustalxColourScheme)\r
           {\r
             ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
-                stretchGroup.getSequences(true),\r
+                stretchGroup.getSequences(av.hiddenRepSequences),\r
                 stretchGroup.getWidth());\r
           }\r
 \r
@@ -1549,7 +1543,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 \r
             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 \r
-            if (stretchGroup.getSequences(false).contains(nextSeq))\r
+            if (stretchGroup.getSequences(null).contains(nextSeq))\r
             {\r
                 stretchGroup.deleteSequence(seq, false);\r
             }\r

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7fdb33c..f338492 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -238,7 +238,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       SequenceGroup selected = av.getSelectionGroup();
 
       if ( (selected != null) &&
-          selected.getSequences(false).contains( (SequenceI) node.element()))
+          selected.getSequences(null).contains( (SequenceI) node.element()))
       {
         g.setColor(Color.gray);
 
@@ -850,7 +850,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(false),
+                                            sg.getSequences(null),
                                             sg.getStartRes(), sg.getEndRes());
 
           c.calculate();