--- /dev/null
+/*
+ VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
+ Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
+ electronic mail : Yann.Ponty@lri.fr
+ paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
+
+ This file is part of VARNA version 3.1.
+ VARNA version 3.1 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.
+
+ VARNA version 3.1 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 VARNA version 3.1.
+ If not, see http://www.gnu.org/licenses.
+ */
+package fr.orsay.lri.varna.applications;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.Collections;
+
+import javax.swing.BorderFactory;
+import javax.swing.DefaultComboBoxModel;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+import javax.swing.JTextPane;
+import javax.swing.border.BevelBorder;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.controlers.ControleurInterpolator;
+import fr.orsay.lri.varna.exceptions.ExceptionDrawingAlgorithm;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
+import fr.orsay.lri.varna.exceptions.ExceptionNAViewAlgorithm;
+import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
+import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.exceptions.MappingException;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.VARNAConfig.BP_STYLE;
+import fr.orsay.lri.varna.models.rna.Mapping;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModelBaseStyle;
+import fr.orsay.lri.varna.models.rna.RNA;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNABasesListener;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;;
+
+public class NussinovDemo extends JFrame implements InterfaceVARNAListener,InterfaceVARNABasesListener {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -790155708306987257L;
+
+ private static final String SEQUENCE_DUMMY = "AAAAAAAAAA";
+ private static final String SEQUENCE_A = "AGGCACGUCU";
+ private static final String SEQUENCE_B = "GAGUAGCCUC";
+ private static final String SEQUENCE_C = "GCAUAGCUGC";
+ private static final String SEQUENCE_INRIA = "GAGAAGUACUUGAAAUUGGCCUCCUC";
+
+
+ private static final String SEQUENCE_BIG = "AAAACAAAAACACCAUGGUGUUUUCACCCAAUUGGGUGAAAACAGAGAUCUCGAGAUCUCUGUUUUUGUUUU";
+
+ private static final String DEFAULT_STRUCTURE = "..........";
+ // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
+ // private static final String DEFAULT_STRUCTURE2 =
+ // "((((..(((....)))..))))";
+
+ private VARNAPanel _vpMaster;
+
+ private InfoPanel _infos = new InfoPanel();
+ private JPanel _tools = new JPanel();
+ private JPanel _input = new JPanel();
+
+ private JPanel _seqPanel = new JPanel();
+ private JPanel _structPanel = new JPanel();
+ private JLabel _actions = new JLabel();
+ private JLabel _struct = new JLabel(DEFAULT_STRUCTURE);
+ private JComboBox _seq1 = new JComboBox();
+ private JLabel _structLabel = new JLabel("Structure Secondaire");
+ private JLabel _seqLabel = new JLabel("Sequence d'ARN");
+ private JButton _goButton = new JButton("Repliement");
+ private JButton _switchButton = new JButton("Effacer");
+
+
+ private Color _backgroundColor = Color.white;
+
+ public static Font textFieldsFont = Font.decode("MonoSpaced-BOLD-16");
+ public static Font labelsFont = Font.decode("SansSerif-BOLD-20");
+ public static final int marginTools = 250;
+ public static String APP_TITLE = "Fête de la science 2015 - Inria AMIB - Repliement d'ARN";
+
+
+ public static ModelBaseStyle createStyle(String txt)
+ {
+ ModelBaseStyle result = new ModelBaseStyle();
+ try {
+ result.assignParameters(txt);
+ } catch (ExceptionModeleStyleBaseSyntaxError e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionParameterError e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return result;
+ }
+
+ public void applyTo(VARNAPanel vp, ModelBaseStyle mb, int[] indices)
+ {
+ for(int i=0;i<indices.length;i++)
+ {
+ ModeleBase m = vp.getRNA().getBaseAt(indices[i]);
+ m.setStyleBase(mb);
+ if (m.getElementStructure()!=-1)
+ {
+ vp.getRNA().getBaseAt(m.getElementStructure()).setStyleBase(mb);
+ }
+ }
+ vp.repaint();
+ }
+
+
+ public NussinovDemo() {
+ super();
+ try {
+ _vpMaster = new VARNAPanel(getSeq(), "");
+ } catch (ExceptionNonEqualLength e) {
+ _vpMaster.errorDialog(e);
+ }
+ _vpMaster.setPreferredSize(new Dimension(600, 600));
+ RNAPanelDemoInit();
+ }
+
+ public static void formatLabel(JLabel j)
+ {
+ j.setHorizontalTextPosition(JLabel.LEFT);
+ j.setPreferredSize(new Dimension(marginTools, 15));
+ j.setFont(labelsFont);
+ }
+
+ private void RNAPanelDemoInit() {
+
+
+
+ _seq1.setFont(textFieldsFont);
+ String[] seqs = {SEQUENCE_DUMMY,SEQUENCE_INRIA,SEQUENCE_A,SEQUENCE_B,SEQUENCE_C,SEQUENCE_BIG};
+ _seq1.setModel(new DefaultComboBoxModel(seqs));
+ _seq1.setEditable(true);
+
+
+ setBackground(_backgroundColor);
+ _vpMaster.setBackground(_backgroundColor);
+ _vpMaster.addVARNAListener(this);
+ _vpMaster.setFlatExteriorLoop(true);
+
+
+
+ formatLabel(_seqLabel);
+ formatLabel(_structLabel);
+
+ _goButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ showSolution();
+ onStructureRedrawn();
+ }
+ });
+
+ _switchButton.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ try {
+ RNA r = new RNA();
+ r.setRNA("", "");
+ _struct.setText("");
+ _vpMaster.setTitle("");
+ _vpMaster.showRNA(r);
+ onStructureRedrawn();
+ }
+ catch (ExceptionFileFormatOrSyntax e2) {
+ e2.printStackTrace();
+ } catch (ExceptionUnmatchedClosingParentheses e2) {
+ // TODO Auto-generated catch block
+ e2.printStackTrace();
+ }
+ _vpMaster.repaint();
+ }
+ });
+
+ _seqPanel.setLayout(new BorderLayout());
+ _seqPanel.add(_seqLabel, BorderLayout.WEST);
+ _seqPanel.add(_seq1, BorderLayout.CENTER);
+
+ _structLabel.setPreferredSize(new Dimension(marginTools, 15));
+ _structLabel.setHorizontalTextPosition(JLabel.LEFT);
+ _struct.setFont(textFieldsFont);
+ _structPanel.setLayout(new BorderLayout());
+ _structPanel.add(_structLabel, BorderLayout.WEST);
+ _structPanel.add(_struct, BorderLayout.CENTER);
+
+ _input.setLayout(new GridLayout(0, 1));
+ _input.add(_seqPanel);
+ _input.add(_structPanel);
+
+ JPanel goPanel = new JPanel();
+ goPanel.setLayout(new BorderLayout());
+
+ _infos.setFont(labelsFont);
+
+
+ _tools.setLayout(new BorderLayout());
+ _tools.add(_infos, BorderLayout.SOUTH);
+ _tools.add(_input, BorderLayout.CENTER);
+ _tools.add(_actions, BorderLayout.NORTH);
+ _tools.add(goPanel, BorderLayout.EAST);
+ _tools.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+
+ goPanel.add(_goButton, BorderLayout.CENTER);
+ goPanel.add(_switchButton, BorderLayout.SOUTH);
+
+ getContentPane().setLayout(new BorderLayout());
+ JPanel VARNAs = new JPanel();
+ VARNAs.setLayout(new GridLayout(1,2));
+ VARNAs.add(_vpMaster);
+ VARNAs.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED));
+ getContentPane().add(VARNAs, BorderLayout.CENTER);
+ getContentPane().add(_tools, BorderLayout.SOUTH);
+
+ setVisible(true);
+
+ _vpMaster.getVARNAUI().UIRadiate();
+ _vpMaster.setTitleFontSize(26f);
+ _vpMaster.setTitleFontStyle(Font.PLAIN);
+ _vpMaster.addVARNABasesListener(this);
+ _vpMaster.setBackground(Color.decode("#308099"));
+ _vpMaster.setModifiable(false);
+ _vpMaster.setTitle("Repliement cible");
+ _vpMaster.setBPStyle(BP_STYLE.SIMPLE);
+ _vpMaster.setBackboneColor(Color.white);
+ _vpMaster.setDefaultBPColor(Color.white);
+ _vpMaster.setBaseNumbersColor(Color.white);
+ _vpMaster.setBaseOutlineColor(Color.white);
+ _vpMaster.setTitleColor(Color.white);
+ _vpMaster.setTitleFontSize(26f);
+
+
+
+ this.setTitle(APP_TITLE);
+
+ showSolution();
+ onStructureRedrawn();
+ }
+
+ private synchronized void showSolution()
+ {
+ ArrayList<String> sols = getStructs();
+ _infos.setInfo(sols, count(getSeq()));
+ }
+
+
+
+
+ public String getSeq()
+ {
+ return (""+_seq1.getSelectedItem()).toUpperCase();
+ }
+
+
+ private boolean canBasePairAll(char a, char b)
+ {
+ return true;
+ }
+
+ private boolean canBasePairBasic(char a, char b)
+ {
+ if ((a=='G')&&(b=='C'))
+ return true;
+ if ((a=='C')&&(b=='G'))
+ return true;
+ if ((a=='U')&&(b=='A'))
+ return true;
+ if ((a=='A')&&(b=='U'))
+ return true;
+ if ((a=='G')&&(b=='U'))
+ return true;
+ if ((a=='U')&&(b=='G'))
+ return true;
+ return false;
+ }
+
+ private double basePairScoreBasic(char a, char b)
+ {
+ if ((a=='G')&&(b=='C'))
+ return 1.0;
+ if ((a=='C')&&(b=='G'))
+ return 1.0;
+ if ((a=='U')&&(b=='A'))
+ return 1.0;
+ if ((a=='A')&&(b=='U'))
+ return 1.0;
+ if ((a=='G')&&(b=='U'))
+ return 1.0;
+ if ((a=='U')&&(b=='G'))
+ return 1.0;
+ return Double.NEGATIVE_INFINITY;
+ }
+
+
+ private boolean canBasePairNussinov(char a, char b)
+ {
+ if ((a=='G')&&(b=='C'))
+ return true;
+ if ((a=='C')&&(b=='G'))
+ return true;
+ if ((a=='U')&&(b=='A'))
+ return true;
+ if ((a=='A')&&(b=='U'))
+ return true;
+ if ((a=='U')&&(b=='G'))
+ return true;
+ if ((a=='G')&&(b=='U'))
+ return true;
+ return false;
+ }
+
+ private double basePairScoreNussinov(char a, char b)
+ {
+ if ((a=='G')&&(b=='C'))
+ return 3.0;
+ if ((a=='C')&&(b=='G'))
+ return 3.0;
+ if ((a=='U')&&(b=='A'))
+ return 2.0;
+ if ((a=='A')&&(b=='U'))
+ return 2.0;
+ if ((a=='U')&&(b=='G'))
+ return 1.0;
+ if ((a=='G')&&(b=='U'))
+ return 1.0;
+ return Double.NEGATIVE_INFINITY;
+ }
+
+ private boolean canBasePairINRIA(char a, char b)
+ {
+ if ((a=='U')&&(b=='A'))
+ return true;
+ if ((a=='A')&&(b=='U'))
+ return true;
+ if ((a=='G')&&(b=='C'))
+ return true;
+ if ((a=='C')&&(b=='G'))
+ return true;
+
+ if ((a=='A')&&(b=='G'))
+ return true;
+ if ((a=='G')&&(b=='A'))
+ return true;
+ if ((a=='U')&&(b=='C'))
+ return true;
+ if ((a=='C')&&(b=='U'))
+ return true;
+ if ((a=='A')&&(b=='A'))
+ return true;
+ if ((a=='U')&&(b=='U'))
+ return true;
+
+ if ((a=='U')&&(b=='G'))
+ return true;
+ if ((a=='G')&&(b=='U'))
+ return true;
+ if ((a=='A')&&(b=='C'))
+ return true;
+ if ((a=='C')&&(b=='A'))
+ return true;
+ return false;
+ }
+
+ private double basePairScoreINRIA(char a, char b)
+ {
+ if ((a=='U')&&(b=='A'))
+ return 3;
+ if ((a=='A')&&(b=='U'))
+ return 3;
+ if ((a=='G')&&(b=='C'))
+ return 3;
+ if ((a=='C')&&(b=='G'))
+ return 3;
+
+ if ((a=='A')&&(b=='G'))
+ return 2;
+ if ((a=='G')&&(b=='A'))
+ return 2;
+ if ((a=='U')&&(b=='C'))
+ return 2;
+ if ((a=='C')&&(b=='U'))
+ return 2;
+ if ((a=='A')&&(b=='A'))
+ return 2;
+ if ((a=='U')&&(b=='U'))
+ return 2;
+
+ if ((a=='U')&&(b=='G'))
+ return 1;
+ if ((a=='G')&&(b=='U'))
+ return 1;
+ if ((a=='A')&&(b=='C'))
+ return 1;
+ if ((a=='C')&&(b=='A'))
+ return 1;
+ return Double.NEGATIVE_INFINITY;
+ }
+
+ private boolean canBasePair(char a, char b)
+ {
+ return canBasePairBasic(a,b);
+ //return canBasePairNussinov(a,b);
+ //return canBasePairINRIA(a,b);
+ }
+
+ private double basePairScore(char a, char b)
+ {
+ return basePairScoreBasic(a,b);
+ //return basePairScoreNussinov(a,b);
+ //return basePairScoreINRIA(a,b);
+ }
+
+ public double[][] fillMatrix(String seq)
+ {
+ int n = seq.length();
+ double[][] tab = new double[n][n];
+ for(int m=1;m<=n;m++)
+ {
+ for(int i=0;i<n-m+1;i++)
+ {
+ int j = i+m-1;
+ tab[i][j] = 0;
+ if (i<j)
+ {
+ tab[i][j] = Math.max(tab[i][j], tab[i+1][j]);
+ for (int k=i+1;k<=j;k++)
+ {
+ if (canBasePair(seq.charAt(i),seq.charAt(k)))
+ {
+ double fact1 = 0;
+ if (k>i+1)
+ {
+ fact1 = tab[i+1][k-1];
+ }
+ double fact2 = 0;
+ if (k<j)
+ {
+ fact2 = tab[k+1][j];
+ }
+ tab[i][j] = Math.max(tab[i][j],basePairScore(seq.charAt(i),seq.charAt(k))+fact1+fact2);
+ }
+ }
+ }
+ }
+ }
+ return tab;
+ }
+
+ public static ArrayList<Double> combine(double bonus, ArrayList<Double> part1, ArrayList<Double> part2)
+ {
+ ArrayList<Double> base = new ArrayList<Double>();
+ for(double d1: part1)
+ {
+ for(double d2: part2)
+ {
+ base.add(bonus+d1+d2);
+ }
+ }
+ return base;
+ }
+
+ public static ArrayList<Double> selectBests(ArrayList<Double> base)
+ {
+ ArrayList<Double> result = new ArrayList<Double>();
+ double best = Double.NEGATIVE_INFINITY;
+ for(double val: base)
+ {
+ best = Math.max(val, best);
+ }
+ for(double val: base)
+ {
+ if (val == best)
+ result.add(val);
+ }
+ return result;
+ }
+
+
+ private ArrayList<String> backtrack(double[][] tab, String seq)
+ {
+ return backtrack(tab,seq, 0, seq.length()-1);
+ }
+
+ private ArrayList<String> backtrack(double[][] tab, String seq, int i, int j)
+ {
+ ArrayList<String> result = new ArrayList<String>();
+ if (i<j)
+ {
+ ArrayList<Integer> indices = new ArrayList<Integer>();
+ indices.add(-1);
+ for (int k=i+1;k<=j;k++)
+ {
+ indices.add(k);
+ }
+ for (int k : indices)
+ {
+ if (k==-1)
+ {
+ if (tab[i][j] == tab[i+1][j])
+ {
+ for (String s:backtrack(tab, seq, i+1,j))
+ {
+ result.add("."+s);
+ }
+ }
+ }
+ else
+ {
+ if (canBasePair(seq.charAt(i),seq.charAt(k)))
+ {
+ double fact1 = 0;
+ if (k>i+1)
+ {
+ fact1 = tab[i+1][k-1];
+ }
+ double fact2 = 0;
+ if (k<j)
+ {
+ fact2 = tab[k+1][j];
+ }
+ if (tab[i][j]==basePairScore(seq.charAt(i),seq.charAt(k))+fact1+fact2)
+ {
+ for (String s1:backtrack(tab, seq, i+1,k-1))
+ {
+ for (String s2:backtrack(tab, seq, k+1,j))
+ {
+ result.add("("+s1+")"+s2);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ else if (i==j)
+ {
+ result.add(".");
+ }
+ else
+ {
+ result.add("");
+ }
+ return result;
+ }
+
+ public BigInteger count(String seq)
+ {
+ int n = seq.length();
+
+ BigInteger[][] tab = new BigInteger[n][n];
+ for(int m=1;m<=n;m++)
+ {
+ for(int i=0;i<n-m+1;i++)
+ {
+ int j = i+m-1;
+ tab[i][j] = BigInteger.ZERO;
+ if (i<j)
+ {
+ tab[i][j] = tab[i][j].add(tab[i+1][j]);
+ for (int k=i+1;k<=j;k++)
+ {
+ if (canBasePair(seq.charAt(i),seq.charAt(k)))
+ {
+ BigInteger fact1 = BigInteger.ONE;
+ if (k>i+1)
+ {
+ fact1 = tab[i+1][k-1];
+ }
+ BigInteger fact2 = BigInteger.ONE;
+ if (k<j)
+ {
+ fact2 = tab[k+1][j];
+ }
+ tab[i][j] = tab[i][j].add(fact1.multiply(fact2));
+ }
+ }
+ }
+ else
+ {
+ tab[i][j] = BigInteger.ONE;
+ }
+ }
+ }
+ return tab[0][n-1];
+ }
+
+ private String _cache = "";
+ ArrayList<String> _cacheStructs = new ArrayList<String>();
+
+ public ArrayList<String> getStructs() {
+ String seq = getSeq();
+ seq = seq.toUpperCase();
+ if (!_cache.equals(seq))
+ {
+ double[][] mfe = fillMatrix(seq);
+ _cacheStructs = backtrack(mfe,seq);
+ _cache = seq;
+ }
+ return _cacheStructs;
+ }
+
+ public VARNAPanel get_varnaPanel() {
+ return _vpMaster;
+ }
+
+ public void set_varnaPanel(VARNAPanel surface) {
+ _vpMaster = surface;
+ }
+
+
+ public JLabel get_info() {
+ return _actions;
+ }
+
+ public void set_info(JLabel _info) {
+ this._actions = _info;
+ }
+
+ public static void main(String[] args) {
+ NussinovDemo d = new NussinovDemo();
+ d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ d.pack();
+ d.setVisible(true);
+ }
+
+ public void onStructureRedrawn() {
+ _vpMaster.repaint();
+ }
+
+ public void onWarningEmitted(String s) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void onLoad(String path) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void onLoaded() {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void onUINewStructure(VARNAConfig v, RNA r) {
+ // TODO Auto-generated method stub
+
+ }
+
+ static final String[] _bases = {"A","C","G","U"};
+ static final String[] _basesComp = {"U","G","C","A"};
+
+ public void onBaseClicked(ModeleBase mb, MouseEvent e) {
+ }
+
+ public void onZoomLevelChanged() {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void onTranslationChanged() {
+ // TODO Auto-generated method stub
+
+ }
+ private class InfoPanel extends JPanel
+ {
+ ArrayList<String> _sols = new ArrayList<String>();
+ BigInteger _nbFolds = BigInteger.ZERO;
+ JTextArea _text = new JTextArea("");
+ JTextArea _subopts = new JTextArea("");
+ JPanel _suboptBrowser = new JPanel();
+ JPanel _suboptCount = new JPanel();
+ int _selectedIndex = 0;
+ JButton next = new JButton(">");
+ JButton previous = new JButton("<");
+
+ InfoPanel()
+ {
+ setLayout(new BorderLayout());
+ add(_suboptBrowser,BorderLayout.SOUTH);
+ add(_suboptCount,BorderLayout.NORTH);
+
+ next.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent arg0) {
+ if (_sols.size()>0)
+ {
+ setSelectedIndex((_selectedIndex+1)%_sols.size());
+ }
+ }
+ });
+
+ previous.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent arg0) {
+ if (_sols.size()>0)
+ {
+ setSelectedIndex((_selectedIndex+_sols.size()-1)%_sols.size());
+ }
+ }
+ });
+ next.setEnabled(false);
+ previous.setEnabled(false);
+
+
+ JLabel nbLab = new JLabel("#Repliements");
+ NussinovDemo.formatLabel(nbLab);
+
+ _suboptCount.setLayout(new BorderLayout());
+ _suboptCount.add(nbLab,BorderLayout.WEST);
+ _suboptCount.add(_text,BorderLayout.CENTER);
+
+ JLabel cooptlab = new JLabel("#Co-optimaux");
+ NussinovDemo.formatLabel(cooptlab);
+
+ JPanel commands = new JPanel();
+ commands.add(previous);
+ commands.add(next);
+
+ JPanel jp = new JPanel();
+ jp.setLayout(new BorderLayout());
+ jp.add(_subopts,BorderLayout.WEST);
+ jp.add(commands,BorderLayout.CENTER);
+
+ _suboptBrowser.setLayout(new BorderLayout());
+ _suboptBrowser.add(cooptlab,BorderLayout.WEST);
+ _suboptBrowser.add(jp,BorderLayout.CENTER);
+
+
+ }
+
+
+ public void setSelectedIndex(int i)
+ {
+ _selectedIndex = i;
+ RNA rfolded = new RNA();
+ try {
+ rfolded.setRNA(getSeq(), _sols.get(i));
+ rfolded.drawRNARadiate(_vpMaster.getConfig());
+ rfolded.setBaseNameColor(Color.white);
+ rfolded.setBaseOutlineColor(Color.white);
+ rfolded.setBaseNumbersColor(Color.white);
+ _vpMaster.setBaseNumbersColor(Color.white);
+ _vpMaster.setBaseOutlineColor(Color.white);
+ _vpMaster.setFillBases(false);
+ _vpMaster.setBaseNameColor(Color.white);
+ _vpMaster.showRNAInterpolated(rfolded);
+
+ } catch (ExceptionUnmatchedClosingParentheses e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ExceptionFileFormatOrSyntax e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ _struct.setText(_sols.get(i));
+ formatDescription();
+ }
+
+ public void setFont(Font f)
+ {
+ super.setFont(f);
+ if(_text!=null)
+ {
+ _text.setFont(f);
+ _text.setOpaque(false);
+ }
+ if(_subopts!=null)
+ {
+ _subopts.setFont(f);
+ _subopts.setOpaque(false);
+ }
+ }
+ public void setInfo(ArrayList<String> sols, BigInteger nbFolds)
+ {
+ _sols = sols;
+ _nbFolds = nbFolds;
+ formatDescription();
+ setSelectedIndex(0);
+ }
+
+ private void formatDescription()
+ {
+ _text.setText(""+_nbFolds);
+ _subopts.setText(""+_sols.size());
+ next.setEnabled(_sols.size()>1);
+ previous.setEnabled(_sols.size()>1);
+
+ }
+
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff