apply jalview code style

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 18bda61..b77fab6 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -73,6 +73,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   Font font = new Font("Arial", Font.PLAIN, 11);
 
+  private boolean hasHiddenRows;
+
   /**
    * Creates a new AnnotationLabels object.
    * 
@@ -102,8 +104,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     {
     }
 
-    BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
-            .getWidth(this), BufferedImage.TYPE_INT_RGB);
+    BufferedImage bi = new BufferedImage(temp.getHeight(this),
+            temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
     Graphics2D g = (Graphics2D) bi.getGraphics();
     g.rotate(Math.toRadians(90));
     g.drawImage(temp, 0, -bi.getWidth(this), this);
@@ -130,15 +132,23 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     repaint();
   }
 
+  /**
+   * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+   * y
+   * 
+   * @param y
+   *          coordinate position to search for a row
+   */
   void getSelectedRow(int y)
   {
     int height = 0;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
+    selectedRow = -2;
     if (aa != null)
     {
       for (int i = 0; i < aa.length; i++)
       {
+        selectedRow = -1;
         if (!aa[i].visible)
         {
           continue;
@@ -250,7 +260,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "       Annotation Name ",
-            "Annotation Description ", "Edit Annotation Name/Description");
+            "Annotation Description ", "Edit Annotation Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -298,6 +309,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       // Swap these annotations
       AlignmentAnnotation startAA = ap.av.alignment
               .getAlignmentAnnotation()[start];
+      if (end == -1)
+      {
+        end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+      }
       AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
       ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
@@ -429,7 +444,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
-      if (selectedRow < aa.length)
+      if (selectedRow > -1 && selectedRow < aa.length)
       {
         if (aa[selectedRow].groupRef != null)
         {
@@ -438,8 +453,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // todo: make the ap scroll to the selection
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
             ap.av.setSelectionGroup(// new SequenceGroup(
-                    aa[selectedRow].groupRef); // );
+            aa[selectedRow].groupRef); // );
+            ap.av.sendSelection();
             ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
           }
           else
           {
@@ -463,6 +480,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             SequenceGroup sg = new SequenceGroup();
             sg.addSequence(aa[selectedRow].sequenceRef, false);
             ap.av.setSelectionGroup(sg);
+            ap.av.sendSelection();
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
           }
@@ -478,17 +496,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     JPopupMenu pop = new JPopupMenu("Annotations");
     JMenuItem item = new JMenuItem(ADDNEW);
     item.addActionListener(this);
-
-    if ((aa == null) || (aa.length == 0))
+    pop.add(item);
+    if (selectedRow < 0)
     {
-      item = new JMenuItem(SHOWALL);
-      item.addActionListener(this);
-      pop.add(item);
+      if (hasHiddenRows)
+      { // let the user make everything visible again
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+      }
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
-
-    pop.add(item);
     item = new JMenuItem(EDITNAME);
     item.addActionListener(this);
     pop.add(item);
@@ -498,9 +517,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     item = new JMenuItem(DELETE);
     item.addActionListener(this);
     pop.add(item);
-    item = new JMenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
+    if (hasHiddenRows)
+    {
+      item = new JMenuItem(SHOWALL);
+      item.addActionListener(this);
+      pop.add(item);
+    }
     item = new JMenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
     pop.add(item);
@@ -528,8 +550,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
                 "Ignore Gaps In Consensus",
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
-                        .getIgnoreGapsConsensus()
-                        : ap.av.getIgnoreGapsConsensus());
+                        .getIgnoreGapsConsensus() : ap.av
+                        .getIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
@@ -552,8 +574,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  "Show Group Histogram", aa[selectedRow].groupRef
-                          .isShowConsensusHistogram());
+                  "Show Group Histogram",
+                  aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -570,10 +592,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             }
           });
           pop.add(chist);
-          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                  "Show Group Logo", aa[selectedRow].groupRef
-                          .isShowSequenceLogo());
-          cprof.addActionListener(new ActionListener()
+          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+                  "Show Group Logo",
+                  aa[selectedRow].groupRef.isShowSequenceLogo());
+          cprofl.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
             {
@@ -583,12 +605,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // view
               // can be
               // updated.
-              aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+              aaa.groupRef.setshowSequenceLogo(cprofl.getState());
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
           });
-          pop.add(cprof);
+          pop.add(cprofl);
         }
         else
         {
@@ -668,8 +690,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
             omitHidden);
 
-    Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
-            new StringSelection(output), Desktop.instance);
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+            .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
     if (av.hasHiddenColumns)
@@ -750,12 +772,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (aa != null)
     {
+      hasHiddenRows = false;
       for (int i = 0; i < aa.length; i++)
       {
         g.setColor(Color.black);
 
         if (!aa[i].visible)
         {
+          hasHiddenRows = true;
           continue;
         }
 
@@ -800,8 +824,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                 g.setColor(aa[gg].annotations[0].colour);
               }
 
-              g.drawLine(x, y - graphExtras - 3, x
-                      + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+              g.drawLine(x, y - graphExtras - 3,
+                      x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
 
               g.setColor(Color.black);
               graphExtras += fontHeight + 8;
@@ -822,9 +846,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
-      g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
-              .getY()
-              - scrollOffset);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+              dragEvent.getY() - scrollOffset);
     }
 
     if ((aa == null) || (aa.length < 1))