apply jalview code style

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 4d58689..5288fe4 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.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.
@@ -151,7 +151,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
-      displayNonconserved.setState(sg.getShowunconserved());
+      displayNonconserved.setState(sg.getShowNonconserved());
       if (!ap.av.alignment.getGroups().contains(sg))
       {
         groupMenu.remove(unGroupMenuItem);
@@ -184,9 +184,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
-                  .getDBRef(), new String[]
-          { target });
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+                  seq.getDBRef(), new String[]
+                  { target });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -492,8 +492,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
         {
           EditCommand editCommand = new EditCommand("Edit Sequences",
                   EditCommand.REPLACE, dialog.getName().replace(' ',
-                          ap.av.getGapCharacter()), sg
-                          .getSequencesAsArray(ap.av.hiddenRepSequences),
+                          ap.av.getGapCharacter()),
+                  sg.getSequencesAsArray(ap.av.hiddenRepSequences),
                   sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
 
           ap.alignFrame.addHistoryItem(editCommand);
@@ -630,19 +630,20 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Selection output - "
-            + e.getActionCommand(), 600, 500);
+    jalview.bin.JalviewLite.addFrame(frame,
+            "Selection output - " + e.getActionCommand(), 600, 500);
 
-    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e
-            .getActionCommand(), new Alignment(ap.av
-            .getSelectionAsNewSequence()), ap.av.showJVSuffix));
+    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+            e.getActionCommand(),
+            new Alignment(ap.av.getSelectionAsNewSequence()),
+            ap.av.showJVSuffix));
 
   }
 
   void editName()
   {
-    EditNameDialog dialog = new EditNameDialog(seq.getName(), seq
-            .getDescription(), "       Sequence Name",
+    EditNameDialog dialog = new EditNameDialog(seq.getName(),
+            seq.getDescription(), "       Sequence Name",
             "Sequence Description", ap.alignFrame,
             "Edit Sequence Name / Description", 500, 100, true);
 
@@ -805,9 +806,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg
-            .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
-            .getWidth());
+    sg.cs = new ClustalxColourScheme(
+            sg.getSequences(ap.av.hiddenRepSequences),
+            ap.av.alignment.getWidth());
     refresh();
   }
 
@@ -869,9 +870,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg
-              .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
-              .getWidth()));
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.hiddenRepSequences), 0,
+              ap.av.alignment.getWidth()));
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
@@ -899,9 +900,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg
-            .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
-            .getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(
+            sg.getSequences(ap.av.hiddenRepSequences), 0,
+            ap.av.alignment.getWidth()));
     refresh();
   }
 
@@ -911,9 +912,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg
-            .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
-            .getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(
+            sg.getSequences(ap.av.hiddenRepSequences), 0,
+            ap.av.alignment.getWidth()));
 
     refresh();
   }
@@ -936,8 +937,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
 
       Conservation c = new Conservation("Group",
-              ResidueProperties.propHash, 3, sg
-                      .getSequences(ap.av.hiddenRepSequences), 0,
+              ResidueProperties.propHash, 3,
+              sg.getSequences(ap.av.hiddenRepSequences), 0,
               ap.av.alignment.getWidth());
 
       c.calculate();
@@ -992,7 +993,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   public void showNonconserved_itemStateChanged()
   {
-    getGroup().setShowunconserved(this.displayNonconserved.getState());
+    getGroup().setShowNonconserved(this.displayNonconserved.getState());
     refresh();
   }