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authorjprocter <jprocter@compbio.dundee.ac.uk>
Wed, 29 Aug 2012 15:27:17 +0000 (16:27 +0100)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Wed, 29 Aug 2012 15:27:17 +0000 (16:27 +0100)
src/jalview/gui/AnnotationLabels.java patch | blob | history

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 665537c..319dcf4 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -144,7 +144,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   void getSelectedRow(int y)
   {
     int height = 0;
-    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
     selectedRow = -2;
     if (aa != null)
     {
@@ -176,7 +177,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void actionPerformed(ActionEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
     if (evt.getActionCommand().equals(ADDNEW))
     {
@@ -245,8 +247,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     ap.validateAnnotationDimensions(false);
     ap.addNotify();
     ap.repaint();
-    //validate();
-    //ap.paintAlignment(true);
+    // validate();
+    // ap.paintAlignment(true);
   }
 
   /**
@@ -312,7 +314,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       {
         end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
       }
-      AlignmentAnnotation endAA = ap.av.getAlignment().getAlignmentAnnotation()[end];
+      AlignmentAnnotation endAA = ap.av.getAlignment()
+              .getAlignmentAnnotation()[end];
 
       ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
       ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
@@ -405,40 +408,51 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (selectedRow > -1
             && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
     {
-      AlignmentAnnotation aa = ap.av.getAlignment().getAlignmentAnnotation()[selectedRow];
-      
+      AlignmentAnnotation aa = ap.av.getAlignment()
+              .getAlignmentAnnotation()[selectedRow];
+
       StringBuffer desc = new StringBuffer();
       if (aa.description != null
               && !aa.description.equals("New description"))
       {
-        // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips
+        // TODO: we could refactor and merge this code with the code in
+        // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+        // tooltips
         desc.append(aa.getDescription(true).trim());
         // check to see if the description is an html fragment.
-        if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("<html>")<0))
+        if (desc.length() < 6
+                || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
         {
           // clean the description ready for embedding in html
-          desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("&lt;"));        
+          desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+                  .replaceAll("&lt;"));
           desc.insert(0, "<html>");
-        } else {
-               // remove terminating html if any
-               int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("</html>");
-               if (i>-1) {
-                 desc.setLength(desc.length()-7+i);
-               }
+        }
+        else
+        {
+          // remove terminating html if any
+          int i = desc.substring(desc.length() - 7).toLowerCase()
+                  .lastIndexOf("</html>");
+          if (i > -1)
+          {
+            desc.setLength(desc.length() - 7 + i);
+          }
         }
         if (aa.hasScore())
         {
           desc.append("<br/>");
         }
-        
-        
-      } else {
+
+      }
+      else
+      {
         // begin the tooltip's html fragment
         desc.append("<html>");
       }
       if (aa.hasScore())
       {
-        // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value).
+        // TODO: limit precision of score to avoid noise from imprecise doubles
+        // (64.7 becomes 64.7+/some tiny value).
         desc.append(" Score: " + aa.score);
       }
 
@@ -461,7 +475,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
       if (selectedRow > -1 && selectedRow < aa.length)
@@ -470,7 +485,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (evt.getClickCount() >= 2)
           {
-            // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
+            // todo: make the ap scroll to the selection - not necessary, first
+            // click highlights/scrolls, second selects
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
             ap.av.setSelectionGroup(// new SequenceGroup(
             aa[selectedRow].groupRef); // );
@@ -638,7 +654,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           {
             public void actionPerformed(ActionEvent e)
             {
-              
+
               // TODO: pass on reference
               // to ap
               // so the