apply jalview code style

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a98c1da..94d22ef 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.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.
@@ -30,6 +30,7 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
 import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.UrlLink;
 
 /**
@@ -395,7 +396,7 @@ public class PopupMenu extends JPopupMenu
       {
         conservationMenuItem.setSelected(true);
       }
-      displayNonconserved.setSelected(sg.getShowunconserved());
+      displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
@@ -451,9 +452,9 @@ public class PopupMenu extends JPopupMenu
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
-                  .getDBRef(), new String[]
-          { urlLink.getTarget() });
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+                  seq.getDBRef(), new String[]
+                  { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -654,8 +655,14 @@ public class PopupMenu extends JPopupMenu
       }
       // and try and make the groupURL!
 
-      Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
-              + System.currentTimeMillis(), false);
+      Object[] urlset = null;
+      try
+      {
+        urlset = urlLink.makeUrlStubs(ids, seqstr,
+                "FromJalview" + System.currentTimeMillis(), false);
+      } catch (UrlStringTooLongException e)
+      {
+      }
       if (urlset != null)
       {
         int type = urlLink.getGroupURLType() & 3;
@@ -752,7 +759,12 @@ public class PopupMenu extends JPopupMenu
 
           public void run()
           {
-            showLink(urlgenerator.constructFrom(urlstub));
+            try
+            {
+              showLink(urlgenerator.constructFrom(urlstub));
+            } catch (UrlStringTooLongException e)
+            {
+            }
           }
 
         }).start();
@@ -1139,7 +1151,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void showNonconserved_actionPerformed()
   {
-    getGroup().setShowunconserved(displayNonconserved.isSelected());
+    getGroup().setShowNonconserved(displayNonconserved.isSelected());
     refresh();
   }
 
@@ -1163,9 +1175,9 @@ public class PopupMenu extends JPopupMenu
   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();
   }
 
@@ -1281,9 +1293,9 @@ public class PopupMenu extends JPopupMenu
 
     if (abovePIDColour.isSelected())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg
-              .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
-              .getEndRes() + 1));
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
@@ -1335,9 +1347,9 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg
-            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
-            .getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(
+            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getEndRes() + 1));
     refresh();
   }
 
@@ -1353,9 +1365,9 @@ public class PopupMenu extends JPopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg
-            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
-            .getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(
+            sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+            sg.getEndRes() + 1));
 
     refresh();
   }
@@ -1389,9 +1401,9 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       Conservation c = new Conservation("Group",
-              ResidueProperties.propHash, 3, sg
-                      .getSequences(ap.av.hiddenRepSequences), sg
-                      .getStartRes(), sg.getEndRes() + 1);
+              ResidueProperties.propHash, 3,
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1);
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
@@ -1418,8 +1430,8 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    AnnotationColourGradient acg = new AnnotationColourGradient(sequence
-            .getAnnotation()[0], null,
+    AnnotationColourGradient acg = new AnnotationColourGradient(
+            sequence.getAnnotation()[0], null,
             AnnotationColourGradient.NO_THRESHOLD);
 
     acg.predefinedColours = true;
@@ -1438,9 +1450,10 @@ public class PopupMenu extends JPopupMenu
   {
 
     SequenceGroup sg = getGroup();
-    EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
-            .getDescription(), "       Group Name ", "Group Description ",
-            "Edit Group Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sg.getName(),
+            sg.getDescription(), "       Group Name ",
+            "Group Description ", "Edit Group Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1477,9 +1490,10 @@ public class PopupMenu extends JPopupMenu
    */
   void sequenceName_actionPerformed()
   {
-    EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
-            .getDescription(), "       Sequence Name ",
-            "Sequence Description ", "Edit Sequence Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+            sequence.getDescription(), "       Sequence Name ",
+            "Sequence Description ", "Edit Sequence Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1669,8 +1683,8 @@ public class PopupMenu extends JPopupMenu
         caseChange = ChangeCaseCommand.TO_LOWER;
       }
 
-      ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
-              .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
               caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
@@ -1685,8 +1699,8 @@ public class PopupMenu extends JPopupMenu
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap, "Alignment output - "
-            + e.getActionCommand(), 600, 500);
+    Desktop.addInternalFrame(cap,
+            "Alignment output - " + e.getActionCommand(), 600, 500);
 
     String[] omitHidden = null;
 
@@ -1698,7 +1712,8 @@ public class PopupMenu extends JPopupMenu
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    if (nala!=null) {
+    if (nala != null)
+    {
       for (int i = 0; i < nala.length; i++)
       {
         AlignmentAnnotation na = nala[i];
@@ -1868,17 +1883,18 @@ public class PopupMenu extends JPopupMenu
       if (sequence == null)
         sequence = (Sequence) sg.getSequenceAt(0);
 
-      EditNameDialog dialog = new EditNameDialog(sequence
-              .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
-              null, "Edit Sequence ", null, "Edit Sequence");
+      EditNameDialog dialog = new EditNameDialog(
+              sequence.getSequenceAsString(sg.getStartRes(),
+                      sg.getEndRes() + 1), null, "Edit Sequence ", null,
+              "Edit Sequence", ap.alignFrame);
 
       if (dialog.accept)
       {
         EditCommand editCommand = new EditCommand("Edit Sequences",
                 EditCommand.REPLACE, dialog.getName().replace(' ',
-                        ap.av.getGapCharacter()), sg
-                        .getSequencesAsArray(ap.av.hiddenRepSequences), sg
-                        .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+                        ap.av.getGapCharacter()),
+                sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+                sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
 
         ap.alignFrame.addHistoryItem(editCommand);