X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=5a09a34d2e4802223dfacb6bb96bd5d6ccf6e866;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=25b65b339152cccee91ddd0d62eb2c66750d6b04;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 25b65b3..5a09a34 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,29 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.util.*;
-import java.awt.event.*;
-
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+
+import java.awt.event.ActionEvent;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* Helps generate the colors for RNA secondary structure. Future: add option to
@@ -78,9 +81,13 @@ public class RNAHelicesColourChooser
{
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
if (!list.contains(label))
+ {
list.addElement(label);
+ }
else
+ {
list.addElement(label + "_" + (index++));
+ }
}
adjusting = false;
@@ -96,30 +103,13 @@ public class RNAHelicesColourChooser
{
return;
}
-
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
RNAHelicesColour rhc = null;
- rhc = new RNAHelicesColour(currentAnnotation);
+ rhc = new RNAHelicesColour(av.getAlignment());
av.setGlobalColourScheme(rhc);
- if (av.getAlignment().getGroups() != null)
- {
- for (SequenceGroup sg : ap.getAlignment().getGroups())
- {
- if (sg.cs == null)
- {
- continue;
- }
-
- sg.cs = new RNAHelicesColour(currentAnnotation);
-
- }
- }
-
- ap.paintAlignment(false);
+ ap.paintAlignment(true);
}
void reset()