X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=ba8c6abe4d5b490ad9861c6685e3802cc418fa54;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=c7e94323cbb98b1b6c11913a1b0d58e15cc58148;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index c7e9432..ba8c6ab 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,33 +1,49 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
 
 public class SeqPanel extends Panel implements MouseMotionListener,
         MouseListener, SequenceListener
@@ -143,10 +159,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setCursorPosition()
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
-    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
     scrollToVisible();
   }
 
@@ -154,19 +170,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
-    if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+    if (av.hasHiddenColumns()
+            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
-      int maxWidth = av.alignment.getWidth();
+      int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.colSel.isVisible(seqCanvas.cursorX)
+      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.colSel.isVisible(seqCanvas.cursorX))
+              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -180,18 +197,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       seqCanvas.cursorX = 0;
     }
-    else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+    else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
     {
-      seqCanvas.cursorX = av.alignment.getWidth() - 1;
+      seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
     }
 
     if (seqCanvas.cursorY < 0)
     {
       seqCanvas.cursorY = 0;
     }
-    else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+    else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
     {
-      seqCanvas.cursorY = av.alignment.getHeight() - 1;
+      seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
     }
 
     endEditing();
@@ -209,7 +226,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       {
         ap.scrollUp(false);
       }
-      while (seqCanvas.cursorX < av.colSel
+      while (seqCanvas.cursorX < av.getColumnSelection()
               .adjustForHiddenColumns(av.startRes))
       {
 
@@ -218,7 +235,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           break;
         }
       }
-      while (seqCanvas.cursorX > av.colSel
+      while (seqCanvas.cursorX > av.getColumnSelection()
               .adjustForHiddenColumns(av.endRes))
       {
         if (!ap.scrollRight(true))
@@ -227,7 +244,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
       }
     }
-    setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
 
     seqCanvas.repaint();
@@ -235,17 +252,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
     {
-      SequenceGroup sg = av.selectionGroup;
+      SequenceGroup sg = av.getSelectionGroup();
       // Find the top and bottom of this group
-      int min = av.alignment.getHeight(), max = 0;
+      int min = av.getAlignment().getHeight(), max = 0;
       for (int i = 0; i < sg.getSize(); i++)
       {
-        int index = av.alignment.findIndex(sg.getSequenceAt(i));
+        int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
         if (index > max)
         {
           max = index;
@@ -287,10 +304,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       else
       {
         // Now add any sequences between min and max
-        sg.getSequences(null).removeAllElements();
+        sg.clear();
         for (int i = min; i < max; i++)
         {
-          sg.addSequence(av.alignment.getSequenceAt(i), false);
+          sg.addSequence(av.getAlignment().getSequenceAt(i), false);
         }
       }
     }
@@ -344,26 +361,36 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   int getKeyboardNo1()
   {
-    if (keyboardNo1 == null)
-      return 1;
-    else
+    try
+    {
+      if (keyboardNo1 != null)
+      {
+        int value = Integer.parseInt(keyboardNo1.toString());
+        keyboardNo1 = null;
+        return value;
+      }
+    } catch (Exception x)
     {
-      int value = Integer.parseInt(keyboardNo1.toString());
-      keyboardNo1 = null;
-      return value;
     }
+    keyboardNo1 = null;
+    return 1;
   }
 
   int getKeyboardNo2()
   {
-    if (keyboardNo2 == null)
-      return 1;
-    else
+    try
+    {
+      if (keyboardNo2 != null)
+      {
+        int value = Integer.parseInt(keyboardNo2.toString());
+        keyboardNo2 = null;
+        return value;
+      }
+    } catch (Exception x)
     {
-      int value = Integer.parseInt(keyboardNo2.toString());
-      keyboardNo2 = null;
-      return value;
     }
+    keyboardNo2 = null;
+    return 1;
   }
 
   void setStatusMessage(SequenceI sequence, int res, int seq)
@@ -372,7 +399,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
             + sequence.getName());
 
     Object obj = null;
-    if (av.alignment.isNucleotide())
+    if (av.getAlignment().isNucleotide())
     {
       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
               + "");
@@ -455,10 +482,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   public void mouseClicked(MouseEvent evt)
   {
-    SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+    SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
     if (evt.getClickCount() > 1)
     {
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1
+      if (av.getSelectionGroup() != null
+              && av.getSelectionGroup().getSize() == 1
               && av.getSelectionGroup().getEndRes()
                       - av.getSelectionGroup().getStartRes() < 2)
       {
@@ -543,7 +571,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       res = (x / av.getCharWidth()) + av.getStartRes();
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
@@ -581,8 +609,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(),
-              av.alignment.getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+              .getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -590,8 +618,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
-              av.alignment.getHeight() - 1);
+      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+              .getAlignment().getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -632,7 +660,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     String tmp = sequence.hashCode() + index + "";
     if (lastMessage == null || !lastMessage.equals(tmp))
+    {
       ssm.mouseOverSequence(sequence, index, pos, av);
+    }
 
     lastMessage = tmp;
   }
@@ -682,13 +712,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     int respos = sequence.findPosition(res);
     if (ssm != null)
+    {
       mouseOverSequence(sequence, res, respos);
+    }
 
     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
             + sequence.getName());
 
     Object obj = null;
-    if (av.alignment.isNucleotide())
+    if (av.getAlignment().isNucleotide())
     {
       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
               + "");
@@ -717,7 +749,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     ap.alignFrame.statusBar.setText(text.toString());
 
     StringBuffer tooltipText = new StringBuffer();
-    SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+    SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
     if (groups != null)
     {
       for (int g = 0; g < groups.length; g++)
@@ -797,7 +829,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                         .containsKey(features[i].featureGroup)
                 && !((Boolean) seqCanvas.fr.featureGroups
                         .get(features[i].featureGroup)).booleanValue())
+        {
           continue;
+        }
 
         if ((features[i].getBegin() <= res)
                 && (features[i].getEnd() >= res))
@@ -916,14 +950,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     boolean fixedColumns = false;
     SequenceGroup sg = av.getSelectionGroup();
 
-    SequenceI seq = av.alignment.getSequenceAt(startseq);
+    SequenceI seq = av.getAlignment().getSequenceAt(startseq);
 
-    if (!groupEditing && av.hasHiddenRows)
+    if (!groupEditing && av.hasHiddenRows())
     {
-      if (av.hiddenRepSequences != null
-              && av.hiddenRepSequences.containsKey(seq))
+      if (av.isHiddenRepSequence(seq))
       {
-        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        sg = av.getRepresentedSequences(seq);
         groupEditing = true;
       }
     }
@@ -931,15 +964,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     StringBuffer message = new StringBuffer();
     if (groupEditing)
     {
-      message.append("Edit group:");
+      message.append(MessageManager.getString("action.edit_group")).append(":");
       if (editCommand == null)
       {
-        editCommand = new EditCommand("Edit Group");
+        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
       }
     }
     else
     {
-      message.append("Edit sequence: " + seq.getName());
+      message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
       String label = seq.getName();
       if (label.length() > 10)
       {
@@ -947,7 +980,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand("Edit " + label);
+        editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
       }
     }
 
@@ -965,7 +998,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     // Are we editing within a selection group?
     if (groupEditing
-            || (sg != null && sg.getSequences(av.hiddenRepSequences)
+            || (sg != null && sg.getSequences(av.getHiddenRepSequences())
                     .contains(seq)))
     {
       fixedColumns = true;
@@ -974,14 +1007,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       // but the sequence represents a group
       if (sg == null)
       {
-        if (av.hiddenRepSequences == null
-                || !av.hiddenRepSequences.containsKey(seq))
+        if (!av.isHiddenRepSequence(seq))
         {
           endEditing();
           return;
         }
 
-        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        sg = av.getRepresentedSequences(seq);
       }
 
       fixedLeft = sg.getStartRes();
@@ -1008,7 +1040,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       fixedColumns = true;
       int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
@@ -1038,13 +1070,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (groupEditing)
     {
-      Vector vseqs = sg.getSequences(av.hiddenRepSequences);
-      int g, groupSize = vseqs.size();
-      SequenceI[] groupSeqs = new SequenceI[groupSize];
-      for (g = 0; g < groupSeqs.length; g++)
-      {
-        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
-      }
+      SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
+              .toArray(new SequenceI[0]);
 
       // drag to right
       if (insertGap)
@@ -1052,9 +1079,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         // If the user has selected the whole sequence, and is dragging to
         // the right, we can still extend the alignment and selectionGroup
         if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
-                && sg.getEndRes() == av.alignment.getWidth() - 1)
+                && sg.getEndRes() == av.getAlignment().getWidth() - 1)
         {
-          sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+          sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
           fixedRight = sg.getEndRes();
         }
 
@@ -1066,12 +1093,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           blank = true;
 
-          for (g = 0; g < groupSize; g++)
+          for (SequenceI gs : groupSeqs)
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(groupSeqs[g]
-                      .getCharAt(fixedRight - j)))
+              if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
+                      - j)))
               {
                 blank = false;
                 break;
@@ -1086,19 +1113,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
         if (!blank)
         {
-          if (sg.getSize() == av.alignment.getHeight())
+          if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns && startres < av.getColumnSelection()
-                    .getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns() && startres < av
+                    .getColumnSelection().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
             }
 
-            int alWidth = av.alignment.getWidth();
-            if (av.hasHiddenRows)
+            int alWidth = av.getAlignment().getWidth();
+            if (av.hasHiddenRows())
             {
-              int hwidth = av.alignment.getHiddenSequences().getWidth();
+              int hwidth = av.getAlignment().getHiddenSequences()
+                      .getWidth();
               if (hwidth > alWidth)
               {
                 alWidth = hwidth;
@@ -1123,16 +1151,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         // / Are we able to delete?
         // ie are all columns blank?
 
-        for (g = 0; g < groupSize; g++)
+        for (SequenceI gs : groupSeqs)
         {
           for (int j = startres; j < lastres; j++)
           {
-            if (groupSeqs[g].getLength() <= j)
+            if (gs.getLength() <= j)
             {
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+            if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1154,8 +1182,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
-                  startres, startres - lastres, av.alignment, true);
+          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
+                  startres, startres - lastres, av.getAlignment(), true);
         }
       }
       else
@@ -1170,8 +1198,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
-                  startres, lastres - startres, av.alignment, true);
+          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
+                  startres, lastres - startres, av.getAlignment(), true);
         }
 
       }
@@ -1192,8 +1220,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres, av.alignment, true);
+          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
+          { seq }, lastres, startres - lastres, av.getAlignment(), true);
         }
       }
       else
@@ -1227,8 +1255,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
           if (max > 0)
           {
-            editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
-            { seq }, startres, max, av.alignment, true);
+            editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
+            { seq }, startres, max, av.getAlignment(), true);
           }
         }
       }
@@ -1263,22 +1291,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
-            av.alignment, true);
+    editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
+            av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
-            true);
+    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
+            av.getAlignment(), true);
 
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
-            true);
+    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
+            av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
-            av.alignment, true);
+    editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
+            av.getAlignment(), true);
   }
 
   // ////////////////////////////////////////
@@ -1302,7 +1330,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
     if (sequence == null || res > sequence.getLength())
     {
@@ -1313,7 +1341,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (stretchGroup == null)
     {
-      stretchGroup = av.alignment.findGroup(sequence);
+      stretchGroup = av.getAlignment().findGroup(sequence);
       if (stretchGroup != null && res > stretchGroup.getStartRes()
               && res < stretchGroup.getEndRes())
       {
@@ -1331,7 +1359,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       stretchGroup = null;
 
-      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+      SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
 
       if (allGroups != null)
       {
@@ -1419,28 +1447,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
+    stretchGroup.recalcConservation(); // always do this - annotation has own
+                                       // state
     if (stretchGroup.cs != null)
     {
-      if (stretchGroup.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-                stretchGroup.getSequences(av.hiddenRepSequences),
-                stretchGroup.getWidth());
-      }
-
-      if (stretchGroup.cs instanceof Blosum62ColourScheme
-              || stretchGroup.cs instanceof PIDColourScheme
-              || stretchGroup.cs.conservationApplied()
-              || stretchGroup.cs.getThreshold() > 0)
-      {
-        stretchGroup.recalcConservation();
-      }
+      stretchGroup.cs.alignmentChanged(stretchGroup,
+              av.getHiddenRepSequences());
 
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                 stretchGroup.getName());
-        stretchGroup.recalcConservation();
       }
       else
       {
@@ -1473,14 +1490,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     mouseDragging = true;
 
-    if (y > av.alignment.getHeight())
+    if (y > av.getAlignment().getHeight())
     {
-      y = av.alignment.getHeight() - 1;
+      y = av.getAlignment().getHeight() - 1;
     }
 
-    if (res >= av.alignment.getWidth())
+    if (res >= av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
     if (stretchGroup.getEndRes() == res)
@@ -1525,7 +1542,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       dragDirection = -1;
     }
 
-    while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    while ((y != oldSeq) && (oldSeq > -1)
+            && (y < av.getAlignment().getHeight()))
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -1662,7 +1680,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           }
 
           if (mouseDragging && evt.getY() >= getSize().height
-                  && av.alignment.getHeight() > av.getEndSeq())
+                  && av.getAlignment().getHeight() > av.getEndSeq())
           {
             running = ap.scrollUp(false);
           }
@@ -1709,12 +1727,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // rules are: colsel is copied if there is a real intersection between
     // sequence selection
     boolean repaint = false, copycolsel = true;
-    if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+    if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
     {
       SequenceGroup sgroup = null;
-      if (seqsel != null && seqsel.getSize()>0)
+      if (seqsel != null && seqsel.getSize() > 0)
       {
-        if (av.alignment == null)
+        if (av.getAlignment() == null)
         {
           System.out
                   .println("Selection message: alignviewport av SeqSetId="
@@ -1723,8 +1741,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                           + " 's alignment is NULL! returning immediatly.");
           return;
         }
-        sgroup = seqsel.intersect(av.alignment,
-                (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+        sgroup = seqsel.intersect(av.getAlignment(),
+                (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
         if ((sgroup == null || sgroup.getSize() == 0)
                 && (colsel == null || colsel.size() == 0))
         {
@@ -1740,35 +1758,39 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       {
         av.setSelectionGroup(null);
       }
-      repaint = av.isSelectionGroupChanged();
+      repaint = av.isSelectionGroupChanged(true);
     }
-    if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+    if (copycolsel
+            && (av.getColumnSelection() == null || !av
+                    .isColSelChanged(true)))
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
       if (colsel == null || colsel.size() == 0)
       {
-        if (av.colSel != null)
+        if (av.getColumnSelection() != null)
         {
-          av.colSel.clear();
+          av.getColumnSelection().clear();
         }
       }
       else
       {
         // TODO: shift colSel according to the intersecting sequences
-        if (av.colSel == null)
+        if (av.getColumnSelection() == null)
         {
-          av.colSel = new ColumnSelection(colsel);
+          av.setColumnSelection(new ColumnSelection(colsel));
         }
         else
         {
-          av.colSel.setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel);
         }
       }
-      repaint |= av.isColSelChanged();
+      repaint |= av.isColSelChanged(true);
     }
-    if (copycolsel && av.hasHiddenColumns
-            && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+    if (copycolsel
+            && av.hasHiddenColumns()
+            && (av.getColumnSelection() == null || av.getColumnSelection()
+                    .getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }
@@ -1781,35 +1803,40 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   /**
    * scroll to the given row/column - or nearest visible location
+   * 
    * @param row
    * @param column
    */
   public void scrollTo(int row, int column)
   {
-    
-    row = row<0 ? ap.av.startSeq : row;
-    column = column<0 ? ap.av.startRes : column;
-    ap.scrollTo(row, row, column, true, true);
+
+    row = row < 0 ? ap.av.startSeq : row;
+    column = column < 0 ? ap.av.startRes : column;
+    ap.scrollTo(column, column, row, true, true);
   }
+
   /**
    * scroll to the given row - or nearest visible location
+   * 
    * @param row
    */
   public void scrollToRow(int row)
   {
-    
-    row = row<0 ? ap.av.startSeq : row;
-    ap.scrollTo(row, row, ap.av.startRes, true, true);
+
+    row = row < 0 ? ap.av.startSeq : row;
+    ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
   }
+
   /**
    * scroll to the given column - or nearest visible location
+   * 
    * @param column
    */
   public void scrollToColumn(int column)
   {
-    
-    column = column<0 ? ap.av.startRes : column;
-    ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+
+    column = column < 0 ? ap.av.startRes : column;
+    ap.scrollTo(column, column, ap.av.startSeq, true, true);
   }
 
 }