X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=d6b514e7e393fe331cf5dc15f943eb4508cf2ed9;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=e575b91dc058277b63fce6e632ade28bfad0ab1a;hpb=44f6e9fd1e6df7c78950ef2c778e86add4ec498e;p=jalview.git
diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index e575b91..d6b514e 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,25 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.gui;
+package jalview.schemes;
import java.util.*;
import java.awt.event.*;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.*;
import jalview.schemes.*;
@@ -33,9 +38,9 @@ import jalview.schemes.*;
public class RNAHelicesColourChooser
{
- AlignViewport av;
+ AlignViewportI av;
- AlignmentPanel ap;
+ AlignmentViewPanel ap;
ColourSchemeI oldcs;
@@ -45,17 +50,15 @@ public class RNAHelicesColourChooser
boolean adjusting = false;
- public RNAHelicesColourChooser(AlignViewport av, final AlignmentPanel ap)
+ public RNAHelicesColourChooser(AlignViewportI av,
+ final AlignmentViewPanel ap)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
if (sg.cs != null)
{
oldgroupColours.put(sg, sg.cs);
@@ -96,29 +99,22 @@ 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)
{
- Vector allGroups = ap.av.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
-
if (sg.cs == null)
{
continue;
}
- sg.cs = new RNAHelicesColour(currentAnnotation);
+ sg.cs = new RNAHelicesColour(sg);
}
}
@@ -131,11 +127,8 @@ public class RNAHelicesColourChooser
av.setGlobalColourScheme(oldcs);
if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg : ap.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
}