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JAL-2418 source formatting
[jalview.git] / src / jalview / gui / AnnotationLabels.java
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index e16867a..d07cae2 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -67,8 +67,8 @@ import javax.swing.ToolTipManager;
  * @author $author$
  * @version $Revision$
  */
-public class AnnotationLabels extends JPanel implements MouseListener,
-        MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel
+        implements MouseListener, MouseMotionListener, ActionListener
 {
   private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
           .compile("<");
@@ -267,7 +267,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
       new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[] { aa[selectedRow] });
+              new AlignmentAnnotation[]
+              { aa[selectedRow] });
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
@@ -439,9 +440,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         // av and sequencegroup need to implement same interface for
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
                 MessageManager.getString("label.ignore_gaps_consensus"),
-                (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
-                        .getIgnoreGapsConsensus() : ap.av
-                        .isIgnoreGapsConsensus());
+                (aa[selectedRow].groupRef != null)
+                        ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
+                        : ap.av.isIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
@@ -452,8 +453,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               // TODO: pass on reference to ap so the view can be updated.
               aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.getAnnotationPanel().paint(
-                      ap.getAnnotationPanel().getGraphics());
+              ap.getAnnotationPanel()
+                      .paint(ap.getAnnotationPanel().getGraphics());
             }
             else
             {
@@ -699,11 +700,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
       if ((d.height - dif) > 20)
       {
-        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-                d.height - dif));
+        ap.annotationScroller
+                .setPreferredSize(new Dimension(d.width, d.height - dif));
         d = ap.annotationSpaceFillerHolder.getPreferredSize();
-        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-                d.width, d.height - dif));
+        ap.annotationSpaceFillerHolder
+                .setPreferredSize(new Dimension(d.width, d.height - dif));
         ap.paintAlignment(true);
       }
 
@@ -728,8 +729,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     getSelectedRow(evt.getY() - getScrollOffset());
 
-    if (selectedRow > -1
-            && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+    if (selectedRow > -1 && ap.av.getAlignment()
+            .getAlignmentAnnotation().length > selectedRow)
     {
       AlignmentAnnotation aa = ap.av.getAlignment()
               .getAlignmentAnnotation()[selectedRow];
@@ -743,8 +744,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         // 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(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
@@ -818,17 +819,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             // process modifiers
             SequenceGroup sg = ap.av.getSelectionGroup();
-            if (sg == null
-                    || sg == aa[selectedRow].groupRef
-                    || !(jalview.util.Platform.isControlDown(evt) || evt
-                            .isShiftDown()))
+            if (sg == null || sg == aa[selectedRow].groupRef
+                    || !(jalview.util.Platform.isControlDown(evt)
+                            || evt.isShiftDown()))
             {
               if (jalview.util.Platform.isControlDown(evt)
                       || evt.isShiftDown())
               {
                 // clone a new selection group from the associated group
-                ap.av.setSelectionGroup(new SequenceGroup(
-                        aa[selectedRow].groupRef));
+                ap.av.setSelectionGroup(
+                        new SequenceGroup(aa[selectedRow].groupRef));
               }
               else
               {
@@ -870,10 +870,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
           if (evt.getClickCount() == 1)
           {
-            ap.getSeqPanel().ap
-                    .getIdPanel()
-                    .highlightSearchResults(
-                            Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+            ap.getSeqPanel().ap.getIdPanel()
+                    .highlightSearchResults(Arrays.asList(new SequenceI[]
+                    { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
@@ -884,8 +883,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // we make a copy rather than edit the current selection if no
               // modifiers pressed
               // see Enhancement JAL-1557
-              if (!(jalview.util.Platform.isControlDown(evt) || evt
-                      .isShiftDown()))
+              if (!(jalview.util.Platform.isControlDown(evt)
+                      || evt.isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
@@ -947,15 +946,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (av.hasHiddenColumns())
     {
       omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0,
-              sq.getLength(), seqs);
+              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
     if (av.hasHiddenColumns())
     {
       alignmentStartEnd = av.getAlignment().getHiddenColumns()
-            .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
+              .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
     }
 
     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
@@ -1065,8 +1063,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     int ofontH = fontHeight;
     int sOffset = 0;
     int visHeight = 0;
-    int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
-            .getAnnotationPanel().getVisibleVRange() : null;
+    int[] visr = (ap != null && ap.getAnnotationPanel() != null)
+            ? ap.getAnnotationPanel().getVisibleVRange()
+            : null;
     if (clip && visr != null)
     {
       sOffset = visr[0];
@@ -1109,8 +1108,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               if (debugRedraw)
               {
-                System.out.println("Scroll offset: " + sOffset
-                        + " after vis: " + i);
+                System.out.println(
+                        "Scroll offset: " + sOffset + " after vis: " + i);
               }
               after = true;
             }
@@ -1148,7 +1147,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           }
           if (groupSize * (fontHeight + 8) < aa[i].height)
           {
-            graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+            graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+                    / 2;
           }
           else
           {
@@ -1162,11 +1162,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             {
               fontHeight = -8 + (int) h;
               s = ((float) fontHeight) / (float) ofontH;
-              Font f = baseFont.deriveFont(AffineTransform
-                      .getScaleInstance(s, s));
+              Font f = baseFont
+                      .deriveFont(AffineTransform.getScaleInstance(s, s));
               g.setFont(f);
               fm = g.getFontMetrics();
-              graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+              graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+                      / 2;
             }
           }
           if (visible)
@@ -1183,8 +1184,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
                   g.setColor(aa[gg]._linecolour);
                   g.drawLine(x, y - graphExtras + 3,
-                          x + fm.stringWidth(aa[gg].label), y - graphExtras
-                                  + 3);
+                          x + fm.stringWidth(aa[gg].label),
+                          y - graphExtras + 3);
                 }
 
                 g.setColor(Color.black);