Reduced jar size by 20%

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

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9c3a1e8..2f06d64 100755 (executable)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -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
+    seqCanvas.addMouseMotionListener(this);\r
+    seqCanvas.addMouseListener(this);\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
-\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
@@ -161,16 +119,26 @@ public class SeqPanel
 \r
   if (av.wrapAlignment)\r
   {\r
+\r
+    int hgap = av.charHeight;\r
+    if (av.scaleAboveWrapped)\r
+      hgap += av.charHeight;\r
+\r
+    int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+        + hgap + seqCanvas.getAnnotationHeight();\r
+\r
       int y = evt.getY();\r
-      y -= (2 * av.charHeight);\r
+      y -= hgap;\r
       x -= seqCanvas.LABEL_WEST;\r
 \r
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-      int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);\r
-      wrappedBlock = y/chunkHeight;\r
-      wrappedBlock += av.getStartRes()/cwidth;\r
 \r
-      res = wrappedBlock*cwidth   +   x / av.getCharWidth();\r
+      int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
+\r
+      wrappedBlock = y / cHeight;\r
+      wrappedBlock += av.getStartRes() / cwidth;\r
+\r
+      res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
   }\r
   else\r
   {\r
@@ -183,14 +151,22 @@ public class SeqPanel
 \r
  int findSeq(MouseEvent evt)\r
  {\r
+\r
    int seq = 0;\r
    int y = evt.getY();\r
 \r
    if (av.wrapAlignment)\r
    {\r
-     y -= (2 * av.charHeight);\r
-     int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-     seq = ( (y % chunkHeight) / av.getCharHeight());\r
+     int hgap = av.charHeight;\r
+     if (av.scaleAboveWrapped)\r
+       hgap += av.charHeight;\r
+\r
+     int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+         + hgap + seqCanvas.getAnnotationHeight();\r
+\r
+       y -= hgap;\r
+\r
+     seq = ( (y % cHeight) / av.getCharHeight());\r
    }\r
    else\r
    {\r
@@ -228,7 +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
@@ -272,39 +248,52 @@ public class SeqPanel
       }\r
     }\r
 \r
-    ap.alignFrame.statusBar.setText(text.toString());\r
+    if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+    {\r
+      seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+    }\r
+\r
 \r
     // use aa to see if the mouse pointer is on a\r
-    if (av.showSequenceFeatures)\r
+    if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)\r
     {\r
       Vector features = sequence.getSequenceFeatures();\r
       Enumeration e = features.elements();\r
-      StringBuffer sbuffer = new StringBuffer();\r
-\r
+      boolean first = true;\r
       while (e.hasMoreElements())\r
       {\r
         SequenceFeature sf = (SequenceFeature) e.nextElement();\r
-        if (sf.getStart() <= sequence.findPosition(res) &&\r
+        if (sf.getBegin() <= sequence.findPosition(res) &&\r
             sf.getEnd() >= sequence.findPosition(res))\r
         {\r
-          if (sbuffer.length() > 0)\r
+          if(first)\r
           {\r
-            sbuffer.append("; ");\r
+            text.append(" Sequence Feature: ");\r
+            first = false;\r
           }\r
-          sbuffer.append(sf.getType() + " " + sf.getDescription());\r
+\r
+          text.append(sf.getDescription());\r
           if (sf.getStatus().length() > 0)\r
           {\r
-            sbuffer.append(" (" + sf.getStatus() + ")");\r
+            text.append(" (" + sf.getStatus() + ")");\r
           }\r
+          text.append("; ");\r
         }\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
@@ -486,6 +475,9 @@ public class SeqPanel
     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
@@ -717,15 +709,15 @@ public class SeqPanel
     seqCanvas.repaint();\r
   }\r
 \r
-  public void doMouseEnteredDefineMode(MouseEvent e)\r
+  public void mouseEntered(MouseEvent e)\r
   {\r
-    if (scrollThread != null)\r
+    if (editingSeqs && scrollThread != null)\r
     {\r
       scrollThread.running = false;\r
     }\r
   }\r
 \r
-  public void doMouseExitedDefineMode(MouseEvent e)\r
+  public void mouseExited(MouseEvent e)\r
   {\r
     if (mouseDragging)\r
     {\r