src/jalview/gui/AppVarna.java

   1 /*
   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
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  10  *
  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.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21 import java.awt.*;
  22 import javax.swing.*;
  23 import javax.swing.event.*;
  24
  25 import java.awt.event.*;
  26 import java.io.*;
  27
  28 import jalview.api.SequenceStructureBinding;
  29 import jalview.bin.Cache;
  30 import jalview.datamodel.*;
  31 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  32 import jalview.structure.*;
  33 import jalview.io.*;
  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;
  44
  45
  46 public class AppVarna extends JInternalFrame implements InterfaceVARNAListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
  47
  48 {
  49   AppVarnaBinding vab;
  50
  51   VARNAPanel varnaPanel;
  52
  53   public String name;
  54
  55   /*public AppVarna(){
  56           vab = new AppVarnaBinding();
  57           initVarna();
  58   }*/
  59
  60   public AppVarna(String seq,String struc,String name){
  61           ArrayList<RNA> rnaList = new ArrayList<RNA>();
  62           RNA rna1 = new RNA(name);
  63           try {
  64                   rna1.setRNA(seq,struc);
  65           } catch (ExceptionUnmatchedClosingParentheses e2) {
  66                 e2.printStackTrace();
  67           } catch (ExceptionFileFormatOrSyntax e3) {
  68                 e3.printStackTrace();
  69           }
  70           rnaList.add(trimRNA(rna1));
  71           rnaList.add(rna1);
  72           rna1.setName("consenus_"+rna1.getName());
  73
  74
  75           vab = new AppVarnaBinding(rnaList);
  76           //vab = new AppVarnaBinding(seq,struc);
  77           //System.out.println("Hallo: "+name);
  78           this.name=name;
  79           initVarna();
  80   }
  81
  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);
  92           this.pack();
  93           showPanel(true);
  94   }
  95
  96   public RNA trimRNA(RNA rna){
  97           RNA rnaTrim = new RNA("trim_"+rna.getName());
  98           try {
  99                   rnaTrim.setRNA(rna.getSeq(),rna.getStructDBN());
 100           } catch (ExceptionUnmatchedClosingParentheses e2) {
 101                 e2.printStackTrace();
 102           } catch (ExceptionFileFormatOrSyntax e3) {
 103                 e3.printStackTrace();
 104           }
 105
 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);
 114
 115                                   struc.replace(m, m+1, "*");
 116                                   struc.replace(l, l+1, "*");
 117                           }else{
 118                                   struc.replace(i, i+1, "*");
 119                           }
 120                   }
 121           }
 122
 123           String newSeq=rnaTrim.getSeq().replace("-", "");
 124           rnaTrim.getSeq().replace(".", "");
 125           String newStruc=struc.toString().replace("*", "");
 126
 127           try {
 128                 rnaTrim.setRNA(newSeq,newStruc);
 129           } catch (ExceptionUnmatchedClosingParentheses e) {
 130                 // TODO Auto-generated catch block
 131                 e.printStackTrace();
 132           } catch (ExceptionFileFormatOrSyntax e) {
 133                 // TODO Auto-generated catch block
 134                 e.printStackTrace();
 135           }
 136
 137           return rnaTrim;
 138   }
 139
 140   public void showPanel(boolean show){
 141           this.setVisible(show);
 142   }
 143
 144   private boolean _started = false;
 145
 146   public void run(){
 147           _started = true;
 148
 149           try
 150       {
 151         initVarna();
 152       } catch (OutOfMemoryError oomerror)
 153       {
 154         new OOMWarning("When trying to open the Varna viewer!", oomerror);
 155       } catch (Exception ex)
 156       {
 157         Cache.log.error("Couldn't open Varna viewer!", ex);
 158       }
 159   }
 160
 161 @Override
 162 public void onLayoutChanged() {
 163         // TODO Auto-generated method stub
 164
 165 }
 166
 167 @Override
 168 public void onUINewStructure(VARNAConfig v, RNA r) {
 169         //TODO _rnaList.add(v, r,"",true);
 170         // TODO Auto-generated method stub
 171
 172 }
 173
 174 @Override
 175 public void onWarningEmitted(String s) {
 176         // TODO Auto-generated method stub
 177
 178 }
 179
 180
 181 }