Selection of sequences is continuous

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