JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4e625e1..d4300e4 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -70,13 +70,16 @@ import javax.swing.ToolTipManager;
 public class AnnotationLabels extends JPanel implements MouseListener,
         MouseMotionListener, ActionListener
 {
-  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+  private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
+          .compile("<");
 
-  String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
+  String TOGGLE_LABELSCALE = MessageManager
+          .getString("label.scale_label_to_column");
 
   String ADDNEW = MessageManager.getString("label.add_new_row");
 
-  String EDITNAME = MessageManager.getString("label.edit_label_description");
+  String EDITNAME = MessageManager
+          .getString("label.edit_label_description");
 
   String HIDE = MessageManager.getString("label.hide_row");
 
@@ -86,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
 
-  String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+  String COPYCONS_SEQ = MessageManager
+          .getString("label.copy_consensus_sequence");
 
   boolean resizePanel = false;
 
@@ -253,8 +257,7 @@ 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))
     {
@@ -547,9 +550,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           }
           else
           {
-            ap.getSeqPanel().ap.getIdPanel()
-                    .highlightSearchResults(aa[selectedRow].groupRef
-                            .getSequences(null));
+            ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
+                    aa[selectedRow].groupRef.getSequences(null));
           }
           return;
         }
@@ -557,36 +559,45 @@ 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)
           {
             ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
             SequenceGroup sg = ap.av.getSelectionGroup();
-            if (sg!=null)
+            if (sg != null)
             {
-              // we make a copy rather than edit the current selection if no modifiers pressed
+              // we make a copy rather than edit the current selection if no
+              // modifiers pressed
               // see Enhancement JAL-1557
               if (!(evt.isControlDown() || evt.isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
                 sg.addSequence(aa[selectedRow].sequenceRef, false);
-              } else {
+              }
+              else
+              {
                 if (evt.isControlDown())
                 {
                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
-                } else {
-                  // notionally, we should also add intermediate sequences from last added sequence ?
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
                   sg.addSequence(aa[selectedRow].sequenceRef, true);
                 }
               }
-            } else {
+            }
+            else
+            {
               sg = new SequenceGroup();
               sg.setStartRes(0);
-              sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+              sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
@@ -632,7 +643,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       {
         final String label = aa[selectedRow].label;
         JMenuItem hideType = new JMenuItem();
-        String text = MessageManager.getString("label.hide_all") + " " + label;
+        String text = MessageManager.getString("label.hide_all") + " "
+                + label;
         hideType.setText(text);
         hideType.addActionListener(new ActionListener()
         {
@@ -692,7 +704,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                        MessageManager.getString("label.ignore_gaps_consensus"),
+                MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                         .getIgnoreGapsConsensus() : ap.av
                         .isIgnoreGapsConsensus());
@@ -705,7 +717,8 @@ 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
             {
@@ -718,7 +731,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_group_histogram"),
+                  MessageManager.getString("label.show_group_histogram"),
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
@@ -737,7 +750,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_group_logo"),
+                  MessageManager.getString("label.show_group_logo"),
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
@@ -756,7 +769,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprofl);
           final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.normalise_group_logo"),
+                  MessageManager.getString("label.normalise_group_logo"),
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
@@ -781,7 +794,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         else
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                  MessageManager.getString("label.show_histogram"),
+                  av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -800,7 +814,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                  MessageManager.getString("label.show_logo"),
+                  av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -819,7 +834,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprof);
           final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                          MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                  MessageManager.getString("label.normalise_logo"),
+                  av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -855,11 +871,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
-    SequenceI[] seqs = new SequenceI[]
-    { sq };
+    SequenceI[] seqs = new SequenceI[] { sq };
     String[] omitHidden = null;
-    SequenceI[] dseqs = new SequenceI[]
-    { sq.getDatasetSequence() };
+    SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
     if (dseqs[0] == null)
     {
       dseqs[0] = new Sequence(sq);
@@ -875,8 +889,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               sq.getLength(), seqs);
     }
 
-    int[] alignmentStartEnd = new int[]
-    { 0, ds.getWidth() - 1 };
+    int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
     List<int[]> hiddenCols = av.getColumnSelection().getHiddenColumns();
     if (hiddenCols != null)
     {
@@ -895,13 +908,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       hiddenColumns = new ArrayList<int[]>();
       for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        hiddenColumns.add(new int[]
-        { region[0], region[1] });
+        hiddenColumns.add(new int[] { region[0], region[1] });
       }
     }
 
-    Desktop.jalviewClipboard = new Object[]
-    { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+    Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
+                                                        // of a consensus
+                                                        // sequence ? need to
+                                                        // flag
         // sequence as special.
         hiddenColumns };
   }
@@ -990,8 +1004,8 @@ 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];