Scroll implemented for applet editing
[jalview.git] / src / jalview / appletgui / SeqPanel.java
index 9ed48b2..e29f4e1 100755 (executable)
@@ -28,7 +28,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;\r
 \r
 public class SeqPanel\r
-    extends Panel\r
+    extends Panel implements MouseMotionListener, MouseListener\r
 {\r
 \r
   public SeqCanvas seqCanvas;\r
@@ -60,84 +60,42 @@ public class SeqPanel
 \r
     ap = p;\r
 \r
-    seqCanvas.addMouseMotionListener(new MouseMotionAdapter()\r
-    {\r
-      public void mouseMoved(MouseEvent evt)\r
-      {\r
-        doMouseMoved(evt);\r
-      }\r
-\r
-      public void mouseDragged(MouseEvent evt)\r
-      {\r
-        if (editingSeqs)\r
-        {\r
-          doMouseDragged(evt);\r
-        }\r
-        else\r
-        {\r
-          doMouseDraggedDefineMode(evt);\r
-        }\r
-      }\r
-    });\r
-\r
-    seqCanvas.addMouseListener(new MouseAdapter()\r
-    {\r
-      public void mouseReleased(MouseEvent evt)\r
-      {\r
-        if (editingSeqs)\r
-        {\r
-          doMouseReleased(evt);\r
-        }\r
-        else\r
-        {\r
-          doMouseReleasedDefineMode(evt);\r
-        }\r
-\r
-      }\r
-\r
-      public void mousePressed(MouseEvent evt)\r
-      {\r
-        if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
-        {\r
-          if (evt.isAltDown() || evt.isControlDown())\r
-          {\r
-            groupEditing = true;\r
-          }\r
+    seqCanvas.addMouseMotionListener(this);\r
+    seqCanvas.addMouseListener(this);\r
 \r
-          editingSeqs = true;\r
-          doMousePressed(evt);\r
-        }\r
-        else\r
-        {\r
-          doMousePressedDefineMode(evt);\r
-        }\r
-      }\r
+    seqCanvas.repaint();\r
+  }\r
 \r
-      public void mouseExited(MouseEvent evt)\r
-      {\r
-        if (editingSeqs)\r
-        {\r
-          return;\r
-        }\r
-        doMouseExitedDefineMode(evt);\r
 \r
-      }\r
+     public void mousePressed(MouseEvent evt)\r
+     {\r
+       if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+       {\r
+         if (evt.isAltDown() || evt.isControlDown())\r
+         {\r
+           groupEditing = true;\r
+         }\r
+\r
+         editingSeqs = true;\r
+         doMousePressed(evt);\r
+       }\r
+       else\r
+       {\r
+         doMousePressedDefineMode(evt);\r
+       }\r
+     }\r
 \r
-      public void mouseEntered(MouseEvent evt)\r
-      {\r
-        if (editingSeqs)\r
-        {\r
-          return;\r
-        }\r
-        doMouseEnteredDefineMode(evt);\r
-      }\r
+     public void mouseClicked(MouseEvent evt){}\r
 \r
-    });\r
-    seqCanvas.repaint();\r
-  }\r
 \r
-  public void doMouseReleased(MouseEvent evt)\r
+  public void mouseReleased(MouseEvent evt)\r
   {\r
+    if (!editingSeqs)\r
+    {\r
+      doMouseReleasedDefineMode(evt);\r
+      return;\r
+    }\r
+\r
 \r
     if (seqEditOccurred > -1)\r
     {\r
@@ -246,7 +204,7 @@ public class SeqPanel
     return;\r
   }\r
 \r
-  public void doMouseMoved(MouseEvent evt)\r
+  public void mouseMoved(MouseEvent evt)\r
   {\r
     int res = findRes(evt);\r
     int seq = findSeq(evt);\r
@@ -290,39 +248,66 @@ public class SeqPanel
       }\r
     }\r
 \r
-    ap.alignFrame.statusBar.setText(text.toString());\r
-\r
-    // use aa to see if the mouse pointer is on a\r
-    if (av.showSequenceFeatures)\r
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
     {\r
-      Vector features = sequence.getSequenceFeatures();\r
-      Enumeration e = features.elements();\r
-      StringBuffer sbuffer = new StringBuffer();\r
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+    }\r
+\r
 \r
-      while (e.hasMoreElements())\r
+    // use aa to see if the mouse pointer is on a\r
+    if (av.showSequenceFeatures\r
+        && sequence.getSequenceFeatures()!=null\r
+        && av.featuresDisplayed!=null)\r
+    {\r
+      int index = 0;\r
+      sequence.getSequenceFeatures();\r
+      boolean first = true;\r
+      while (index < sequence.getSequenceFeatures().length)\r
       {\r
-        SequenceFeature sf = (SequenceFeature) e.nextElement();\r
-        if (sf.getStart() <= sequence.findPosition(res) &&\r
+        SequenceFeature sf = sequence.getSequenceFeatures()[index];\r
+        if (sf.getBegin() <= sequence.findPosition(res) &&\r
             sf.getEnd() >= sequence.findPosition(res))\r
         {\r
-          if (sbuffer.length() > 0)\r
+          if(!av.featuresDisplayed.containsKey(sf.getType()))\r
+           {\r
+             index++;\r
+             continue;\r
+           }\r
+\r
+          if(first)\r
           {\r
-            sbuffer.append("; ");\r
+            text.append(" Sequence Feature:");\r
+            first = false;\r
           }\r
-          sbuffer.append(sf.getType() + " " + sf.getDescription());\r
-          if (sf.getStatus().length() > 0)\r
+\r
+          text.append(" "+sf.getType());\r
+\r
+          if(sf.getDescription()!=null)\r
+            text.append(" "+sf.getDescription());\r
+\r
+          if (sf.getStatus()!=null && sf.getStatus().length() > 0)\r
           {\r
-            sbuffer.append(" (" + sf.getStatus() + ")");\r
+            text.append(" (" + sf.getStatus() + ")");\r
           }\r
+          text.append("; ");\r
         }\r
 \r
+        index++;\r
+\r
       }\r
     }\r
 \r
+     ap.alignFrame.statusBar.setText(text.toString());\r
+\r
   }\r
 \r
-  public void doMouseDragged(MouseEvent evt)\r
+  public void mouseDragged(MouseEvent evt)\r
   {\r
+    if (!editingSeqs)\r
+    {\r
+      doMouseDraggedDefineMode(evt);\r
+      return;\r
+    }\r
 \r
     // If we're dragging we're editing\r
     int res = findRes(evt);\r
@@ -446,7 +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
@@ -455,18 +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,\r
-                        av.getStartRes(), av.getStartSeq(), 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
@@ -499,11 +491,20 @@ 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
     startWrapBlock=wrappedBlock;\r
 \r
+    if(seq==-1)\r
+      return;\r
+\r
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 \r
     if (sequence == null || res > sequence.getLength())\r
@@ -604,23 +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
@@ -631,121 +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
-      oldSeq += dragDirection;\r
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
 \r
-      if (stretchGroup.sequences.contains(nextSeq))\r
+      while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
       {\r
-        stretchGroup.deleteSequence(seq, false);\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
-      else\r
+\r
+      if(oldSeq < 0)\r
+        oldSeq = -1;\r
+\r
+\r
+      if(res>av.endRes || res<av.startRes\r
+          || y<av.startSeq || y>av.endSeq)\r
       {\r
-        if (seq != null)\r
-        {\r
-          stretchGroup.addSequence(seq, false);\r
-        }\r
-        stretchGroup.addSequence(nextSeq, false);\r
+        mouseExited(evt);\r
+      }\r
+\r
+      if (scrollThread != null)\r
+      {\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 doMouseEnteredDefineMode(MouseEvent e)\r
+  public void mouseExited(MouseEvent e)\r
   {\r
-    if (scrollThread != null)\r
+    if (av.getWrapAlignment())\r
     {\r
-      scrollThread.running = false;\r
+      return;\r
     }\r
-  }\r
 \r
-  public void doMouseExitedDefineMode(MouseEvent e)\r
-  {\r
-    if (mouseDragging)\r
+    if (mouseDragging && scrollThread==null)\r
     {\r
       scrollThread = new ScrollThread();\r
     }\r
@@ -777,6 +802,7 @@ public class SeqPanel
       running = true;\r
       while (running)\r
       {\r
+\r
         if (evt != null)\r
         {\r
 \r