2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemes;
23 import jalview.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.SequenceGroup;
27 import java.awt.event.ActionEvent;
28 import java.util.Hashtable;
29 import java.util.Vector;
32 * Helps generate the colors for RNA secondary structure. Future: add option to
33 * change colors based on covariation.
35 * @author Lauren Michelle Lui
38 public class RNAHelicesColourChooser
43 AlignmentViewPanel ap;
47 Hashtable oldgroupColours;
49 jalview.datamodel.AlignmentAnnotation currentAnnotation;
51 boolean adjusting = false;
53 public RNAHelicesColourChooser(AlignViewportI av,
54 final AlignmentViewPanel ap)
56 oldcs = av.getGlobalColourScheme();
57 if (av.getAlignment().getGroups() != null)
59 oldgroupColours = new Hashtable();
60 for (SequenceGroup sg : ap.getAlignment().getGroups())
64 oldgroupColours.put(sg, sg.cs);
71 if (oldcs instanceof RNAHelicesColour)
73 RNAHelicesColour rhc = (RNAHelicesColour) oldcs;
78 Vector list = new Vector();
80 for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
82 String label = av.getAlignment().getAlignmentAnnotation()[i].label;
83 if (!list.contains(label))
85 list.addElement(label);
89 list.addElement(label + "_" + (index++));
101 // Check if combobox is still adjusting
106 RNAHelicesColour rhc = null;
108 rhc = new RNAHelicesColour(av.getAlignment());
110 av.setGlobalColourScheme(rhc);
112 ap.paintAlignment(true);
117 av.setGlobalColourScheme(oldcs);
118 if (av.getAlignment().getGroups() != null)
120 for (SequenceGroup sg : ap.getAlignment().getGroups())
122 sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
127 public void annotations_actionPerformed(ActionEvent e)