2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import javax.swing.event.*;
25 import java.awt.event.*;
28 import jalview.api.SequenceStructureBinding;
29 import jalview.bin.Cache;
30 import jalview.datamodel.*;
31 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
32 import jalview.structure.*;
34 import jalview.schemes.*;
35 import fr.orsay.lri.varna.VARNAPanel;
36 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
37 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
38 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
39 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
40 import fr.orsay.lri.varna.models.VARNAConfig;
41 import fr.orsay.lri.varna.models.rna.RNA;
44 public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
49 VARNAPanel varnaPanel;
54 vab = new AppVarnaBinding();
58 public AppVarna(String seq,String struc,String name){
59 ArrayList<RNA> rnaList = new ArrayList<RNA>();
60 RNA rna1 = new RNA(name);
62 rna1.setRNA(seq,struc);
63 } catch (ExceptionUnmatchedClosingParentheses e2) {
65 } catch (ExceptionFileFormatOrSyntax e3) {
70 vab = new AppVarnaBinding(rnaList);
71 //vab = new AppVarnaBinding(seq,struc);
76 public void initVarna(){
77 //TODO: Why is it not possible to include varnaPanel in the AppVarna-Jframe?
78 //vab.setFinishedInit(false);
79 varnaPanel=vab.get_varnaPanel();
80 setBackground(Color.white);
81 getContentPane().setLayout(new BorderLayout());
82 getContentPane().add(varnaPanel, BorderLayout.CENTER);
84 varnaPanel.addVARNAListener(this);
85 jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
87 this.setVisible(true);
91 public void showPanel(boolean show){
92 varnaPanel.setVisible(show);
95 private boolean _started = false;
103 } catch (OutOfMemoryError oomerror)
105 new OOMWarning("When trying to open the Varna viewer!", oomerror);
106 } catch (Exception ex)
108 Cache.log.error("Couldn't open Varna viewer!", ex);
113 public void onLayoutChanged() {
114 // TODO Auto-generated method stub
119 public void onUINewStructure(VARNAConfig v, RNA r) {
120 //TODO _rnaList.add(v, r,"",true);
121 // TODO Auto-generated method stub
126 public void onWarningEmitted(String s) {
127 // TODO Auto-generated method stub