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[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 35c5aef..8e7141b 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,10 @@ public class SeqPanel extends JPanel
   // if character is inserted or deleted, we will need to recalculate the conservation\r
   int seqEditOccurred = -1;\r
 \r
+  ScrollThread scrollThread = null;\r
+  boolean mouseDragging = false;\r
+\r
+\r
   public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
     this.av         = avp;\r
 \r
@@ -75,6 +79,21 @@ public class SeqPanel extends JPanel
         else\r
           doMousePressedDefineMode(evt);\r
       }\r
+      public void mouseExited(MouseEvent evt)\r
+      {\r
+        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
+                  evt.isControlDown())\r
+                return;\r
+              doMouseExitedDefineMode(evt);\r
+\r
+      }\r
+      public void mouseEntered(MouseEvent evt)\r
+      {\r
+        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
+            evt.isControlDown())\r
+          return;\r
+        doMouseEnteredDefineMode(evt);\r
+      }\r
 \r
     });\r
     repaint();\r
@@ -369,15 +388,19 @@ public class SeqPanel extends JPanel
     oldSeq = seq;\r
 \r
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
-    if(res>sequence.getLength())\r
+\r
+    if(sequence==null || res>sequence.getLength())\r
       return;\r
 \r
-    stretchGroup = av.getRubberbandGroup();\r
+    stretchGroup = av.getSelectionGroup();\r
 \r
     if(stretchGroup == null)\r
      {\r
        stretchGroup = av.alignment.findGroup( sequence );\r
-       av.setRubberbandGroup( stretchGroup );\r
+       if(res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
+         av.setSelectionGroup(stretchGroup);\r
+       else\r
+         stretchGroup = null;\r
      }\r
 \r
     else if(!stretchGroup.sequences.contains(sequence)\r
@@ -394,7 +417,7 @@ public class SeqPanel extends JPanel
                allGroups[i].getEndRes() >= res)\r
            {\r
              stretchGroup = allGroups[i];\r
-             av.setRubberbandGroup(stretchGroup);\r
+             av.setSelectionGroup(stretchGroup);\r
              break;\r
            }\r
      }\r
@@ -406,7 +429,7 @@ public class SeqPanel extends JPanel
       sg.setStartRes(res);\r
       sg.setEndRes(res);\r
       sg.addSequence( sequence );\r
-      av.setRubberbandGroup( sg );\r
+      av.setSelectionGroup( sg );\r
       stretchGroup = sg;\r
 \r
       if(av.getConservationSelected())\r
@@ -450,6 +473,8 @@ public class SeqPanel extends JPanel
 \r
   public void doMouseReleasedDefineMode(MouseEvent evt)\r
   {\r
+    mouseDragging = false;\r
+\r
     if(stretchGroup==null)\r
       return;\r
 \r
@@ -464,13 +489,6 @@ public class SeqPanel extends JPanel
     {\r
       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
 \r
-      Conservation c = new Conservation("Group",\r
-                                        ResidueProperties.propHash, 3, stretchGroup.sequences, 0,\r
-                                        av.alignment.getWidth() );\r
-\r
-       c.calculate();\r
-       c.verdict(false, 100);\r
-       ccs = new ConservationColourScheme(c, ccs.cs);\r
 \r
        stretchGroup.cs = ccs;\r
 \r
@@ -496,6 +514,7 @@ public class SeqPanel extends JPanel
     changeEndRes = false;\r
     changeStartRes = false;\r
     stretchGroup = null;\r
+    ap.idPanel.repaint();\r
   }\r
 \r
 \r
@@ -533,14 +552,13 @@ public class SeqPanel extends JPanel
         stretchGroup.setStartRes( res );\r
     }\r
 \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
+    while (y != oldSeq && oldSeq>0)\r
     {\r
       // This routine ensures we don't skip any sequences, as the\r
       // selection is quite slow.\r
@@ -561,11 +579,83 @@ public class SeqPanel extends JPanel
       }\r
     }\r
     oldSeq = y;\r
+    mouseDragging = true;\r
+    if(scrollThread!=null)\r
+      scrollThread.setEvent(evt);\r
 \r
     seqCanvas.paintFlag = true;\r
     repaint();\r
   }\r
 \r
+  public void doMouseEnteredDefineMode(MouseEvent e)\r
+  {\r
+    if (scrollThread != null)\r
+      scrollThread.running = false;\r
+  }\r
+\r
+  public void doMouseExitedDefineMode(MouseEvent e)\r
+  {\r
+    if (av.getWrapAlignment())\r
+      return;\r
+\r
+    if(mouseDragging)\r
+      scrollThread = new ScrollThread();\r
+\r
+  }\r
+  // this class allows scrolling off the bottom of the visible alignment\r
+  class ScrollThread extends Thread\r
+  {\r
+    MouseEvent evt;\r
+    boolean running = false;\r
+    public ScrollThread()\r
+    {\r
+      start();\r
+    }\r
+\r
+    public void setEvent(MouseEvent e)\r
+    {\r
+      evt = e;\r
+    }\r
+\r
+    public void stopScrolling()\r
+    {\r
+      running = false;\r
+    }\r
+\r
+    public void run()\r
+    {\r
+      running = true;\r
+      while (running)\r
+      {\r
+        if(evt!=null)\r
+        {\r
+\r
+          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+            running = ap.scrollUp(true);\r
+\r
+          if (mouseDragging && evt.getY() >= getHeight() &&\r
+              av.alignment.getHeight() > av.getEndSeq())\r
+            running = ap.scrollUp(false);\r
+\r
+          if (mouseDragging && evt.getX() < 0)\r
+            running = ap.scrollRight(true);\r
+\r
+          else if (mouseDragging && evt.getX() >= getWidth())\r
+            running = ap.scrollRight(false);\r
+        }\r
+\r
+        ap.repaint();\r
+        try\r
+        {\r
+          Thread.sleep(75);\r
+        }\r
+        catch (Exception ex)\r
+        {}\r
+      }\r
+    }\r
+}\r
+\r
+\r
 \r
 }\r
 \r