JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 30f2e7f..1d2feb2 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -181,7 +181,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
           MessageManager.getString("label.sequence_details"));
 
   MenuItem makeReferenceSeq = new MenuItem();
-  
+
   SequenceI seq;
 
   MenuItem revealAll = new MenuItem();
@@ -231,8 +231,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (sg != null && sg.getSize() > 0)
     {
       editGroupName.setLabel(MessageManager.formatMessage(
-              "label.name_param", new Object[]
-              { sg.getName() }));
+              "label.name_param", new Object[] { sg.getName() }));
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
@@ -275,8 +274,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[]
-                  { target });
+                  seq.getDBRef(), new String[] { target });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -390,8 +388,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
                 .getString("action.set_as_reference")); // );
       }
       repGroup.setLabel(MessageManager.formatMessage(
-              "label.represent_group_with", new Object[]
-              { seq.getName() }));
+              "label.represent_group_with", new Object[] { seq.getName() }));
     }
     else
     {
@@ -720,7 +717,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
         if (dialog.accept)
         {
-          EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+          EditCommand editCommand = new EditCommand(
+                  MessageManager.getString("label.edit_sequences"),
                   Action.REPLACE, dialog.getName().replace(' ',
                           ap.av.getGapCharacter()),
                   sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
@@ -807,7 +805,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
               features, true, ap))
       {
         ap.alignFrame.sequenceFeatures.setState(true);
-        ap.av.setShowSequenceFeatures(true);;
+        ap.av.setShowSequenceFeatures(true);
+        ;
         ap.highlightSearchResults(null);
       }
     }
@@ -825,8 +824,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-            "label.selection_output_command", new Object[]
-            { e.getActionCommand() }), 600, 500);
+            "label.selection_output_command",
+            new Object[] { e.getActionCommand() }), 600, 500);
     // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
@@ -843,8 +842,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   protected void showSequenceDetails()
   {
-    createSequenceDetailsReport(new SequenceI[]
-    { seq });
+    createSequenceDetailsReport(new SequenceI[] { seq });
   }
 
   public void createSequenceDetailsReport(SequenceI[] sequences)
@@ -856,17 +854,16 @@ public class APopupMenu extends java.awt.PopupMenu implements
     for (SequenceI seq : sequences)
     {
       contents.append(MessageManager.formatMessage(
-              "label.annotation_for_displayid", new Object[]
-              { seq.getDisplayId(true) }));
-      new SequenceAnnotationReport(null)
-              .createSequenceAnnotationReport(
-                      contents,
-                      seq,
-                      true,
-                      true,
-                      false,
-                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
-                              : null);
+              "label.annotation_for_displayid",
+              new Object[] { seq.getDisplayId(true) }));
+      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+              contents,
+              seq,
+              true,
+              true,
+              false,
+              (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+                      .getMinMax() : null);
       contents.append("</p>");
     }
     Frame frame = new Frame();
@@ -875,8 +872,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
                     : "Selection"), 600, 500);
     cap.setText(MessageManager.formatMessage("label.html_content",
-            new Object[]
-            { contents.toString() }));
+            new Object[] { contents.toString() }));
   }
 
   void editName()
@@ -902,13 +898,13 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
       if (ap.av.applet.jmolAvailable)
       {
-        new jalview.appletgui.AppletJmol(entry, new SequenceI[]
-        { seq }, null, ap, AppletFormatAdapter.URL);
+        new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+                null, ap, AppletFormatAdapter.URL);
       }
       else
       {
-        new MCview.AppletPDBViewer(entry, new SequenceI[]
-        { seq }, null, ap, AppletFormatAdapter.URL);
+        new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+                ap, AppletFormatAdapter.URL);
       }
 
     }
@@ -920,8 +916,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
-              "label.paste_pdb_file_for_sequence", new Object[]
-              { seq.getName() }), 400, 300);
+              "label.paste_pdb_file_for_sequence",
+              new Object[] { seq.getName() }), 400, 300);
     }
   }
 
@@ -964,8 +960,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
     hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
     repGroup.setLabel(MessageManager.formatMessage(
-            "label.represent_group_with", new Object[]
-            { "" }));
+            "label.represent_group_with", new Object[] { "" }));
     revealAll.setLabel(MessageManager.getString("action.reveal_all"));
     revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
     menu1.setLabel(MessageManager.getString("label.group") + ":");
@@ -1005,32 +1000,39 @@ public class APopupMenu extends java.awt.PopupMenu implements
     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(this);
 
-    clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
+    clustalColour.setLabel(MessageManager
+            .getString("label.clustalx_colours"));
     clustalColour.addActionListener(this);
     zappoColour.setLabel(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(this);
     taylorColour.setLabel(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(this);
-    hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
+    hydrophobicityColour.setLabel(MessageManager
+            .getString("label.hydrophobicity"));
     hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour
+            .setLabel(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(this);
-    strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
+    strandColour.setLabel(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(this);
     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(this);
     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(this);
-    abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
+    abovePIDColour.setLabel(MessageManager
+            .getString("label.above_identity_percentage"));
 
-    userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
+    userDefinedColour.setLabel(MessageManager
+            .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(MessageManager
             .getString("label.percentage_identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62");
     BLOSUM62Colour.addActionListener(this);
-    conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
+    conservationMenuItem.setLabel(MessageManager
+            .getString("label.conservation"));
 
     editMenu.add(copy);
     copy.addActionListener(this);
@@ -1259,6 +1261,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     getGroup().setDisplayText(showText.getState());
     refresh();
   }
+
   public void makeReferenceSeq_actionPerformed()
   {
     if (!ap.av.getAlignment().hasSeqrep())
@@ -1299,8 +1302,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     SequenceGroup sg = ap.av.getSelectionGroup();
     if (sg == null || sg.getSize() < 1)
     {
-      ap.av.hideSequence(new SequenceI[]
-      { seq });
+      ap.av.hideSequence(new SequenceI[] { seq });
       return;
     }
 
@@ -1348,17 +1350,17 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     showMenu.removeAll();
     hideMenu.removeAll();
-  
+
     final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);
     showMenu.addSeparator();
     hideMenu.addSeparator();
-  
+
     final AlignmentAnnotation[] annotations = ap.getAlignment()
             .getAlignmentAnnotation();
-  
+
     /*
      * Find shown/hidden annotations types, distinguished by source (calcId),
      * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
@@ -1367,28 +1369,26 @@ public class APopupMenu extends java.awt.PopupMenu implements
      */
     Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
     Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
-    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
-            hiddenTypes,
-            AlignmentAnnotationUtils.asList(annotations),
-            forSequences);
-  
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(annotations), forSequences);
+
     for (String calcId : hiddenTypes.keySet())
     {
       for (List<String> type : hiddenTypes.get(calcId))
       {
-        addAnnotationTypeToShowHide(showMenu, forSequences,
-                calcId, type, false, true);
+        addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+                false, true);
       }
     }
     // grey out 'show annotations' if none are hidden
     showMenu.setEnabled(!hiddenTypes.isEmpty());
-  
+
     for (String calcId : shownTypes.keySet())
     {
       for (List<String> type : shownTypes.get(calcId))
       {
-        addAnnotationTypeToShowHide(hideMenu, forSequences,
-                calcId, type, false, false);
+        addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+                false, false);
       }
     }
     // grey out 'hide annotations' if none are shown
@@ -1425,8 +1425,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
-                forSequences, allTypes, actionIsShow);
+        AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+                types, forSequences, allTypes, actionIsShow);
         refresh();
       }
     });