Merge branch 'develop' into releases/Release_2_10_2_Branch

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

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 3f7e523..2fb737a 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -52,8 +52,8 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Vector;
 
-public class AnnotationLabels extends Panel implements ActionListener,
-        MouseListener, MouseMotionListener
+public class AnnotationLabels extends Panel
+        implements ActionListener, MouseListener, MouseMotionListener
 {
   Image image;
 
@@ -201,8 +201,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
               ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
-              + " - " + aa[selectedRow].label, 500, 100);
+      jalview.bin.JalviewLite.addFrame(frame,
+              ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+              100);
       cap.setText(aa[selectedRow].toString());
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
@@ -230,8 +231,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
-    Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
-            + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+    Checkbox padGaps = new Checkbox(
+            "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
+            annotation.padGaps);
 
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "      Annotation Label",
@@ -320,8 +322,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
     if (resizePanel)
     {
-      Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
-              .getSize(), f = ap.seqPanelHolder.getSize();
+      Dimension d = ap.annotationPanelHolder.getSize(),
+              e = ap.annotationSpaceFillerHolder.getSize(),
+              f = ap.seqPanelHolder.getSize();
       int dif = evt.getY() - oldY;
 
       dif /= ap.av.getCharHeight();
@@ -331,16 +334,16 @@ public class AnnotationLabels extends Panel implements ActionListener,
       {
         ap.annotationPanel.setSize(d.width, d.height - dif);
         setSize(new Dimension(e.width, d.height - dif));
-        ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
-                d.height - dif));
-        ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
-                - dif));
+        ap.annotationSpaceFillerHolder
+                .setSize(new Dimension(e.width, d.height - dif));
+        ap.annotationPanelHolder
+                .setSize(new Dimension(d.width, d.height - dif));
         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
                 av.calcPanelHeight());
         f.height += dif;
         ap.seqPanelHolder.setPreferredSize(f);
-        ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
-                .getStartSeq());
+        ap.setScrollValues(av.getRanges().getStartRes(),
+                av.getRanges().getStartSeq());
         ap.validate();
         // ap.paintAlignment(true);
         ap.addNotify();
@@ -451,7 +454,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
             .getAlignmentAnnotation();
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
 
       PopupMenu popup = new PopupMenu(
@@ -525,9 +529,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
             popup.addSeparator();
             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
                     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.addItemListener(new ItemListener()
             {
@@ -631,10 +636,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowConsensusHistogram(chist.getState());
-                  ap.alignFrame.showConsensusHistogram.setState(chist
-                          .getState()); // TODO: implement
-                                        // ap.updateGUI()/alignFrame.updateGUI
-                                        // for applet
+                  ap.alignFrame.showConsensusHistogram
+                          .setState(chist.getState()); // TODO: implement
+                                                       // ap.updateGUI()/alignFrame.updateGUI
+                                                       // for applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
@@ -680,11 +685,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowSequenceLogo(true);
-                  ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
-                                                                              // implement
-                                                                              // ap.updateGUI()/alignFrame.updateGUI
-                                                                              // for
-                                                                              // applet
+                  ap.alignFrame.normSequenceLogo
+                          .setState(cprofn.getState()); // TODO:
+                                                        // implement
+                                                        // ap.updateGUI()/alignFrame.updateGUI
+                                                        // for
+                                                        // applet
                   av.setNormaliseSequenceLogo(cprofn.getState());
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
@@ -715,17 +721,16 @@ public class AnnotationLabels extends Panel implements ActionListener,
             ap.seqPanel.ap.idPanel.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
               {
@@ -757,9 +762,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
           }
           else
           {
-            ap.seqPanel.ap.idPanel
-                    .highlightSearchResults(aa[selectedRow].groupRef
-                            .getSequences(null));
+            ap.seqPanel.ap.idPanel.highlightSearchResults(
+                    aa[selectedRow].groupRef.getSequences(null));
           }
           return;
         }
@@ -768,8 +772,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
           if (evt.getClickCount() == 1)
           {
             ap.seqPanel.ap.idPanel
-                    .highlightSearchResults(Arrays
-                            .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+                    .highlightSearchResults(Arrays.asList(new SequenceI[]
+                    { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
@@ -780,8 +784,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
               // 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();
@@ -833,14 +837,13 @@ public class AnnotationLabels extends Panel implements ActionListener,
       return;
     }
     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
-            + sq.getStart() + "\t" + sq.getEnd() + "\t"
-            + sq.getSequenceAsString() + "\n");
+    jalview.appletgui.AlignFrame.copiedSequences
+            .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
+                    + "\t" + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
-              av.getAlignment().getHiddenColumns()
-                      .getHiddenColumnsCopy());
+              av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
     }
   }