From f3030a08d2a57edf262374d822502c5aaafc0406 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 10 Dec 2004 14:37:09 +0000
Subject: [PATCH] Addition of rubberband

---
 src/jalview/gui/SeqPanel.java |  150 +++++++++++++----------------------------
 1 file changed, 48 insertions(+), 102 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ebcbc76..3680503 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -328,142 +328,78 @@ public class SeqPanel extends JPanel
   }
 
 
-  public void setColourScheme(ColourSchemeI cs, boolean showConservation)
+  public void doMousePressedDefineMode(MouseEvent evt)
   {
-    seqCanvas.paintFlag = true;
-    if (av.getSelection().size() == 0)
-    {
-      seqCanvas.globalColorScheme = cs;
-      for (int i = 0; i < av.alignment.getGroups().size();i++)
-      {
-        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
-        sg.cs = cs;
-        if(!showConservation
-            && !(sg.cs instanceof Blosum62ColourScheme)
-            && sg.cs instanceof ConservationColourScheme)
-         {
-           // remove ConservationColouring from existing Conservation group
-           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-           sg.cs = ccs.cs;
-         }
-         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
-         {
-           // add ConservationColouring to new group
-           Conservation c = sg.getConservation();
-           Alignment al = (Alignment) av.getAlignment();
-           c = new Conservation("All", al.cons,
-                                ResidueProperties.propHash, 3, sg.sequences, 0,
-                                al.getWidth() );
-           c.calculate();
-           c.verdict(false, 100);
-           sg.setConservation(c);
-           sg.cs = new ConservationColourScheme(sg);
-         }
-      }
-    }
-    else
-    {
-      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
+    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
+    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
 
-      if( isNewSelection(sg) )
-      {
-        sg = av.getAlignment().addGroup();
-        for (int i=0; i < av.getSelection().size(); i++)
-        {
-          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
-              sel.sequenceAt(i)),
-                                       (Sequence) av.sel.sequenceAt(i));
-          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
-        }
-      }
+    stretchGroup = av.getRubberbandGroup();
+    if(stretchGroup == null)
+        stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
+      else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
+            || stretchGroup.getStartRes()<res
+            || stretchGroup.getEndRes()>res)
+     {
+       System.out.println(stretchGroup.getStartRes()+" "+stretchGroup.getEndRes()+" "+res);
+       stretchGroup = null;
+     }
 
 
-      sg.cs = cs;
 
-      // Selection is made, we only want to change the conservationColour for selected group
-      if(  showConservation
-           && !(sg.cs instanceof ConservationColourScheme)
-           && !(sg.cs instanceof Blosum62ColourScheme))
-      {
-        Conservation c = sg.getConservation();
-        Alignment al = (Alignment) av.getAlignment();
-
-        c = new Conservation("All", al.cons,
-                             ResidueProperties.propHash, 3, sg.sequences, 0,
-                             al.getWidth() );
-        c.calculate();
-        c.verdict(false, 100);
-        sg.setConservation(c);
-        sg.cs = new ConservationColourScheme(sg);
+    if(stretchGroup==null)
+    {
+      // define a new group here
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(res);
+      sg.setEndRes(res);
+      sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
+      av.setRubberbandGroup( sg );
+      stretchGroup = sg;
+      System.out.println("new rubberband group");
     }
-    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
+    else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-      sg.cs = ccs.cs;
+        // edit the properties of existing group
     }
-   }
-   repaint();
-  }
-
-  boolean isNewSelection(SequenceGroup sg)
-  {
-    if(sg==null)
-      return true;
-
-    if(sg.getSize()!=av.getSelection().size())
-      return true;
-
-    for(int i=0; i<sg.getSize(); i++)
-     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
-       return true;
-
-    return false;
-  }
 
-
-  public ColourSchemeI getColourScheme()
-  {
-    if(av.getSelection().size()>0)
-       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
-    else
-      return seqCanvas.globalColorScheme;
-  }
-
-  public void doMousePressedDefineMode(MouseEvent evt)
-  {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
-
-    stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
-
-    if(stretchGroup!=null  && stretchGroup.getEndRes()==res)
+    if(stretchGroup!=null && stretchGroup.getEndRes()==res)
     {
       // Edit end res position of selected group
       changeEndRes = true;
     }
-    else if(stretchGroup!=null  && stretchGroup.getStartRes()==res)
+    if(stretchGroup!=null && stretchGroup.getStartRes()==res)
     {
       // Edit end res position of selected group
       changeStartRes = true;
     }
 
+    seqCanvas.paintFlag = true;
+    repaint();
+
 
   }
 
+  boolean changeEndSeq = false;
+  boolean changeStartSeq = false;
   boolean changeEndRes = false;
   boolean changeStartRes = false;
   SequenceGroup stretchGroup = null;
 
+
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
     changeEndRes = false;
     changeStartRes = false;
+    stretchGroup = null;
   }
 
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    Sequence seq = (Sequence)av.getAlignment().getSequenceAt(
+                    evt.getY()/av.getCharHeight() + av.getStartSeq());
+
+   // SequenceGroup newSeqGroup = av.alignment.findGroup(seq);
 
     if(res<av.getStartRes())
       res = av.getStartRes();
@@ -480,6 +416,16 @@ public class SeqPanel extends JPanel
       if(res<stretchGroup.getEndRes()+1)
         stretchGroup.setStartRes( res );
     }
+
+   /* if(newSeqGroup != stretchGroup)
+    {
+      if(newSeqGroup !=null)
+        av.getAlignment().removeFromGroup(newSeqGroup, seq );
+
+      if(stretchGroup!=null)
+        stretchGroup.addSequence( seq );
+    }*/
+
     seqCanvas.paintFlag = true;
     repaint();
 
-- 
1.7.10.2