X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=147e035ff6ea6bfa293f607472d1b2ac7b919cb4;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=9fdf1c80e4f9f6939a55bc431fc6afac4d14d06f;hpb=dbcfef03ad3d2853eda62c727978a160fc347f58;p=jalview.git

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