Scroll implemented for applet editing

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index daff328..e29f4e1 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -255,7 +255,9 @@ public class SeqPanel
 \r
 \r
     // use aa to see if the mouse pointer is on a\r
-    if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)\r
+    if (av.showSequenceFeatures\r
+        && sequence.getSequenceFeatures()!=null\r
+        && av.featuresDisplayed!=null)\r
     {\r
       int index = 0;\r
       sequence.getSequenceFeatures();\r
@@ -429,7 +431,11 @@ public class SeqPanel
             }\r
             else\r
             {\r
-\r
+              if(scrollThread!=null)\r
+              {\r
+                scrollThread.running = false;\r
+                scrollThread = null;\r
+              }\r
               break;\r
             }\r
           }\r
@@ -438,17 +444,21 @@ public class SeqPanel
       }\r
     }\r
 \r
+    mouseDragging = true;\r
+    if (res > av.endRes || res < av.startRes)\r
+    {\r
+      mouseExited(evt);\r
+    }\r
+\r
+    if (scrollThread != null)\r
+      scrollThread.setEvent(evt);\r
+\r
+\r
     endEdit = res;\r
     lastres = res;\r
     seqCanvas.repaint();\r
   }\r
 \r
-  public void drawChars(int seqstart, int seqend, int start)\r
-  {\r
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,  0);\r
-    seqCanvas.repaint();\r
-  }\r
-\r
   public void insertChar(int j, int seq)\r
   {\r
     av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
@@ -481,6 +491,12 @@ public class SeqPanel
   int oldSeq = -1;\r
   public void doMousePressedDefineMode(MouseEvent evt)\r
   {\r
+    if (scrollThread != null)\r
+    {\r
+      scrollThread.running = false;\r
+      scrollThread = null;\r
+    }\r
+\r
     int res = findRes(evt);\r
     int seq = findSeq(evt);\r
     oldSeq = seq;\r
@@ -589,23 +605,25 @@ public class SeqPanel
 \r
   public void doMouseReleasedDefineMode(MouseEvent evt)\r
   {\r
-    if(mouseDragging)\r
-     {\r
-       stretchGroup.recalcConservation();\r
-       mouseDragging = false;\r
-     }\r
-\r
     if (stretchGroup == null)\r
     {\r
-      return;\r
+        return;\r
     }\r
 \r
     if(stretchGroup.cs!=null)\r
     {\r
+      if (stretchGroup.cs instanceof ClustalxColourScheme)\r
+      {\r
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
+            sequences,\r
+            stretchGroup.getWidth());\r
+      }\r
+\r
       if (stretchGroup.cs.conservationApplied())\r
       {\r
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
                                           stretchGroup.getName());\r
+        stretchGroup.recalcConservation();\r
       }\r
       else\r
       {\r
@@ -616,121 +634,143 @@ public class SeqPanel
     changeEndRes = false;\r
     changeStartRes = false;\r
     stretchGroup = null;\r
-    seqCanvas.repaint();\r
+    PaintRefresher.Refresh(av.alignment);\r
     ap.repaint();\r
   }\r
 \r
-  boolean remove = false;\r
   public void doMouseDraggedDefineMode(MouseEvent evt)\r
   {\r
     int res = findRes(evt);\r
     int y = findSeq(evt);\r
 \r
     if(wrappedBlock!=startWrapBlock)\r
-        return;\r
+      return;\r
 \r
-    if(y>=av.alignment.getHeight())\r
-      y = av.alignment.getHeight()-1;\r
+     if (stretchGroup == null)\r
+     {\r
+          return;\r
+     }\r
 \r
-    if (stretchGroup == null)\r
-    {\r
-      return;\r
-    }\r
+     mouseDragging = true;\r
 \r
-    if (res > av.alignment.getWidth())\r
-    {\r
-      res = av.alignment.getWidth() - 1;\r
-    }\r
 \r
-    if (stretchGroup.getEndRes() == res)\r
-    {\r
-      // Edit end res position of selected group\r
-      changeEndRes = true;\r
-    }\r
+      if(y > av.alignment.getHeight())\r
+      {\r
+        y = av.alignment.getHeight() -1;\r
+      }\r
 \r
-    else if (stretchGroup.getStartRes() == res)\r
-    {\r
-      // Edit start res position of selected group\r
-      changeStartRes = true;\r
-    }\r
+      if(res>av.alignment.getWidth())\r
+        res = av.alignment.getWidth()-1;\r
 \r
-    if (res < av.getStartRes())\r
-    {\r
-      res = av.getStartRes();\r
-    }\r
-    else if (res > av.getEndRes() && !av.getWrapAlignment())\r
-    {\r
-      res = av.getEndRes();\r
-    }\r
+      if (stretchGroup.getEndRes() == res)\r
+      {\r
+          // Edit end res position of selected group\r
+          changeEndRes = true;\r
+      }\r
+      else if (stretchGroup.getStartRes() == res)\r
+      {\r
+          // Edit start res position of selected group\r
+          changeStartRes = true;\r
+      }\r
 \r
-    if (changeEndRes)\r
-    {\r
-      if (res > stretchGroup.getStartRes() - 1)\r
+      if (res < 0)\r
       {\r
-        stretchGroup.setEndRes(res);\r
+          res = 0;\r
       }\r
-    }\r
-    else if (changeStartRes)\r
-    {\r
-      if (res < stretchGroup.getEndRes() + 1)\r
+\r
+      if (changeEndRes)\r
       {\r
-        stretchGroup.setStartRes(res);\r
+          if (res > (stretchGroup.getStartRes() - 1))\r
+          {\r
+              stretchGroup.setEndRes(res);\r
+          }\r
+      }\r
+      else if (changeStartRes)\r
+      {\r
+          if (res < (stretchGroup.getEndRes() + 1))\r
+          {\r
+              stretchGroup.setStartRes(res);\r
+          }\r
       }\r
-    }\r
 \r
-    int dragDirection = 0;\r
-    if (y > oldSeq)\r
-    {\r
-      dragDirection = 1;\r
-    }\r
-    else if (y < oldSeq)\r
-    {\r
-      dragDirection = -1;\r
-    }\r
+      int dragDirection = 0;\r
 \r
-    while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())\r
-    {\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
+      if (y > oldSeq)\r
+      {\r
+          dragDirection = 1;\r
+      }\r
+      else if (y < oldSeq)\r
+      {\r
+          dragDirection = -1;\r
+      }\r
+\r
+\r
+      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
+      {\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
+          oldSeq += dragDirection;\r
+\r
+          if(oldSeq<0)\r
+            break;\r
+\r
+          Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+          if (stretchGroup.sequences.contains(nextSeq))\r
+          {\r
+              stretchGroup.deleteSequence(seq, false);\r
+          }\r
+          else\r
+          {\r
+              if (seq != null)\r
+              {\r
+                  stretchGroup.addSequence(seq, false);\r
+              }\r
+\r
+              stretchGroup.addSequence(nextSeq, false);\r
+          }\r
+      }\r
 \r
-      oldSeq += dragDirection;\r
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+      if(oldSeq < 0)\r
+        oldSeq = -1;\r
 \r
-      if (stretchGroup.sequences.contains(nextSeq))\r
+\r
+      if(res>av.endRes || res<av.startRes\r
+          || y<av.startSeq || y>av.endSeq)\r
       {\r
-        stretchGroup.deleteSequence(seq, false);\r
+        mouseExited(evt);\r
       }\r
-      else\r
+\r
+      if (scrollThread != null)\r
       {\r
-        if (seq != null)\r
-        {\r
-          stretchGroup.addSequence(seq, false);\r
-        }\r
-        stretchGroup.addSequence(nextSeq, false);\r
+        scrollThread.setEvent(evt);\r
       }\r
+\r
+      seqCanvas.repaint();\r
     }\r
-    oldSeq = y;\r
-    mouseDragging = true;\r
-    if (scrollThread != null)\r
+\r
+    public void mouseEntered(MouseEvent e)\r
     {\r
-      scrollThread.setEvent(evt);\r
-    }\r
+      if (oldSeq < 0)\r
+        oldSeq = 0;\r
 \r
-    seqCanvas.repaint();\r
-  }\r
+      if (scrollThread != null)\r
+      {\r
+        scrollThread.running = false;\r
+        scrollThread = null;\r
+      }\r
+    }\r
 \r
-  public void mouseEntered(MouseEvent e)\r
+  public void mouseExited(MouseEvent e)\r
   {\r
-    if (editingSeqs && scrollThread != null)\r
+    if (av.getWrapAlignment())\r
     {\r
-      scrollThread.running = false;\r
+      return;\r
     }\r
-  }\r
 \r
-  public void mouseExited(MouseEvent e)\r
-  {\r
-    if (mouseDragging)\r
+    if (mouseDragging && scrollThread==null)\r
     {\r
       scrollThread = new ScrollThread();\r
     }\r
@@ -762,6 +802,7 @@ public class SeqPanel
       running = true;\r
       while (running)\r
       {\r
+\r
         if (evt != null)\r
         {\r
 \r