From fa1b18fd88ff97d45a561afef3df4f2c023f0145 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 14 Dec 2004 11:22:30 +0000
Subject: [PATCH] Selection of sequences is continuous

---
 src/jalview/gui/SeqPanel.java |   85 +++++++++++++++++++++++++++--------------
 1 file changed, 57 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3680503..ad75942 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -39,7 +39,8 @@ public class SeqPanel extends JPanel
     addMouseMotionListener( new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
-      {  doMouseMoved(evt);   }
+      {   doMouseMoved(evt);    }
+
       public void mouseDragged(MouseEvent evt)
       {
         if(av.groupDefiningMode)
@@ -143,7 +144,6 @@ public class SeqPanel extends JPanel
 
       res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
 
-      System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
@@ -310,7 +310,7 @@ public class SeqPanel extends JPanel
 
   void updateConservation(int i)
   {
-    Alignment al = (Alignment) av.getAlignment();
+  /*  Alignment al = (Alignment) av.getAlignment();
     SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
     if(sg==null || !(sg.cs instanceof ConservationColourScheme))
       return;
@@ -324,28 +324,29 @@ public class SeqPanel extends JPanel
     c.verdict(false, 100);
     sg.setConservation(c);
     ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;
+    ccs.conserve = c;*/
   }
 
+  int oldSeq = -1;
 
   public void doMousePressedDefineMode(MouseEvent evt)
   {
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
     int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
+    oldSeq = seq;
 
     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)
+
+    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;
      }
 
-
-
     if(stretchGroup==null)
     {
       // define a new group here
@@ -355,23 +356,23 @@ public class SeqPanel extends JPanel
       sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
       av.setRubberbandGroup( sg );
       stretchGroup = sg;
-      System.out.println("new rubberband group");
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-        // edit the properties of existing group
+        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( av , this);
+        pop.show(this, evt.getX(), evt.getY());
+
+    // edit the properties of existing group
     }
 
     if(stretchGroup!=null && stretchGroup.getEndRes()==res)
-    {
       // Edit end res position of selected group
       changeEndRes = true;
-    }
-    if(stretchGroup!=null && stretchGroup.getStartRes()==res)
-    {
+
+   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
       // Edit end res position of selected group
       changeStartRes = true;
-    }
+
 
     seqCanvas.paintFlag = true;
     repaint();
@@ -385,7 +386,6 @@ public class SeqPanel extends JPanel
   boolean changeStartRes = false;
   SequenceGroup stretchGroup = null;
 
-
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
     changeEndRes = false;
@@ -393,13 +393,22 @@ public class SeqPanel extends JPanel
     stretchGroup = null;
   }
 
+
+  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    Sequence seq = (Sequence)av.getAlignment().getSequenceAt(
-                    evt.getY()/av.getCharHeight() + av.getStartSeq());
+    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+
+
+    if(stretchGroup.getEndRes()==res)
+      // Edit end res position of selected group
+      changeEndRes = true;
+
+    else if(stretchGroup.getStartRes()==res)
+      // Edit end res position of selected group
+      changeStartRes = true;
 
-   // SequenceGroup newSeqGroup = av.alignment.findGroup(seq);
 
     if(res<av.getStartRes())
       res = av.getStartRes();
@@ -417,20 +426,40 @@ public class SeqPanel extends JPanel
         stretchGroup.setStartRes( res );
     }
 
-   /* if(newSeqGroup != stretchGroup)
+
+    int dragDirection = 0;
+    if (y > oldSeq)
+      dragDirection = 1;
+    else if (y < oldSeq)
+      dragDirection = -1;
+
+    while (y != oldSeq)
     {
-      if(newSeqGroup !=null)
-        av.getAlignment().removeFromGroup(newSeqGroup, seq );
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-      if(stretchGroup!=null)
-        stretchGroup.addSequence( seq );
-    }*/
+      oldSeq += dragDirection;
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      if (stretchGroup.sequences.contains(nextSeq))
+      {
+        stretchGroup.deleteSequence(seq);
+        stretchGroup.deleteSequence(nextSeq);
+      }
+      else
+      {
+        stretchGroup.addSequence(seq);
+        stretchGroup.addSequence(nextSeq);
+      }
+    }
+    oldSeq = y;
 
     seqCanvas.paintFlag = true;
     repaint();
-
   }
 
+
 }
 
 
-- 
1.7.10.2