X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=5288fe4862f4bc090b3f6c2455a9758467ed711c;hb=6b71746c98f7c1118b474b0b920db3bd7b2a15c0;hp=f4b3903ca4125e2fcba4d5a92b4e75c91379c79f;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index f4b3903..5288fe4 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -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();