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.ModeleBaseNucleotide;
42 import fr.orsay.lri.varna.models.rna.ModeleStyleBP;
43 import fr.orsay.lri.varna.models.rna.RNA;
46 public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
51 VARNAPanel varnaPanel;
56 vab = new AppVarnaBinding();
60 public AppVarna(String seq,String struc,String name){
61 ArrayList<RNA> rnaList = new ArrayList<RNA>();
62 RNA rna1 = new RNA(name);
64 rna1.setRNA(seq,struc);
65 } catch (ExceptionUnmatchedClosingParentheses e2) {
67 } catch (ExceptionFileFormatOrSyntax e3) {
70 rnaList.add(trimRNA(rna1));
72 rna1.setName("consenus_"+rna1.getName());
75 vab = new AppVarnaBinding(rnaList);
76 //vab = new AppVarnaBinding(seq,struc);
77 //System.out.println("Hallo: "+name);
82 public void initVarna(){
83 //vab.setFinishedInit(false);
84 varnaPanel=vab.get_varnaPanel();
85 setBackground(Color.white);
86 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
87 getContentPane().setLayout(new BorderLayout());
88 getContentPane().add(split, BorderLayout.CENTER);
89 getContentPane().add(vab.getTools(), BorderLayout.NORTH);
90 varnaPanel.addVARNAListener(this);
91 jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
96 public RNA trimRNA(RNA rna){
97 RNA rnaTrim = new RNA("trim_"+rna.getName());
99 rnaTrim.setRNA(rna.getSeq(),rna.getStructDBN());
100 } catch (ExceptionUnmatchedClosingParentheses e2) {
101 e2.printStackTrace();
102 } catch (ExceptionFileFormatOrSyntax e3) {
103 e3.printStackTrace();
106 StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
107 StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
108 for(int i=0;i<rnaTrim.getSeq().length();i++){
109 if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
110 if(!rnaTrim.findPair(i).isEmpty()){
111 System.out.println(rnaTrim.findPair(i));
112 int m=rnaTrim.findPair(i).get(1);
113 int l=rnaTrim.findPair(i).get(0);
115 struc.replace(m, m+1, "*");
116 struc.replace(l, l+1, "*");
118 struc.replace(i, i+1, "*");
123 String newSeq=rnaTrim.getSeq().replace("-", "");
124 rnaTrim.getSeq().replace(".", "");
125 String newStruc=struc.toString().replace("*", "");
128 rnaTrim.setRNA(newSeq,newStruc);
129 } catch (ExceptionUnmatchedClosingParentheses e) {
130 // TODO Auto-generated catch block
132 } catch (ExceptionFileFormatOrSyntax e) {
133 // TODO Auto-generated catch block
140 public void showPanel(boolean show){
141 this.setVisible(show);
144 private boolean _started = false;
152 } catch (OutOfMemoryError oomerror)
154 new OOMWarning("When trying to open the Varna viewer!", oomerror);
155 } catch (Exception ex)
157 Cache.log.error("Couldn't open Varna viewer!", ex);
162 public void onLayoutChanged() {
163 // TODO Auto-generated method stub
168 public void onUINewStructure(VARNAConfig v, RNA r) {
169 //TODO _rnaList.add(v, r,"",true);
170 // TODO Auto-generated method stub
175 public void onWarningEmitted(String s) {
176 // TODO Auto-generated method stub