X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3de7c3c81e77349f71843ab2c85678a6432024df;hb=954039bbfbde3648ac4c795277e788e49be5181b;hp=d91fa7050566c4bfd6e783051f1a36fe7db6547f;hpb=88f7d0a53dc11d3b23148fe0866b502b4b53b0e9;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index d91fa70..3de7c3c 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -31,8 +31,8 @@ import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -47,7 +47,6 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -56,6 +55,7 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -1446,13 +1446,21 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   {
     if (sequence != null)
     {
-      ColumnSelection cs = ap.av.getColumnSelection();
-      if (cs == null)
+      /* ColumnSelection cs = ap.av.getColumnSelection();
+       if (cs == null)
+       {
+         cs = new ColumnSelection();
+       }
+       cs.hideInsertionsFor(sequence);
+       ap.av.setColumnSelection(cs);*/
+
+      HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+      if (hidden == null)
       {
-        cs = new ColumnSelection();
+        hidden = new HiddenColumns();
       }
-      cs.hideInsertionsFor(sequence);
-      ap.av.setColumnSelection(cs);
+      hidden.hideInsertionsFor(sequence);
+      ap.av.getAlignment().setHiddenColumns(hidden);
     }
     refresh();
   }
@@ -1881,28 +1889,25 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    int rsize = 0, gSize = sg.getSize();
-    SequenceI[] rseqs, seqs = new SequenceI[gSize];
-    SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
 
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    int gSize = sg.getSize();
     for (int i = 0; i < gSize; i++)
     {
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
       int end = sg.findEndRes(sg.getSequenceAt(i));
       if (start <= end)
       {
-        seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
-        features[rsize] = new SequenceFeature(null, null, null, start, end,
-                "Jalview");
-        rsize++;
+        seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+        features.add(new SequenceFeature(null, null, null, start, end, null));
       }
     }
-    rseqs = new SequenceI[rsize];
-    tfeatures = new SequenceFeature[rsize];
-    System.arraycopy(seqs, 0, rseqs, 0, rsize);
-    System.arraycopy(features, 0, tfeatures, 0, rsize);
-    features = tfeatures;
-    seqs = rseqs;
+
     if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
@@ -1984,28 +1989,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   public void changeColour_actionPerformed(String colourSchemeName)
   {
     SequenceGroup sg = getGroup();
-    if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
-    {
-      /*
-       * open a panel to load or configure a user-defined colour scheme
-       */
-      new UserDefinedColours(ap, sg);
-    }
-    else
+    /*
+     * switch to the chosen colour scheme (or null for None)
+     */
+    ColourSchemeI colourScheme = ColourSchemes.getInstance()
+            .getColourScheme(colourSchemeName, sg,
+                    ap.av.getHiddenRepSequences());
+    sg.setColourScheme(colourScheme);
+    if (colourScheme instanceof Blosum62ColourScheme
+            || colourScheme instanceof PIDColourScheme)
     {
-      /*
-       * switch to the chosen colour scheme (or null for None)
-       */
-      ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
-              colourSchemeName, sg, ap.av.getHiddenRepSequences());
-      sg.setColourScheme(colourScheme);
-      if (colourScheme instanceof Blosum62ColourScheme
-              || colourScheme instanceof PIDColourScheme)
-      {
-        sg.cs.setConsensus(AAFrequency.calculate(
-                sg.getSequences(ap.av.getHiddenRepSequences()),
-                sg.getStartRes(), sg.getEndRes() + 1));
-      }
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.getHiddenRepSequences()),
+              sg.getStartRes(), sg.getEndRes() + 1));
     }
 
     refresh();