X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FVARNAOnlineDemo.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FVARNAOnlineDemo.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=2d02ce782727ded60218001d447e9c1fc7e9cb25;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/srcjar/fr/orsay/lri/varna/applications/VARNAOnlineDemo.java b/srcjar/fr/orsay/lri/varna/applications/VARNAOnlineDemo.java deleted file mode 100644 index 2d02ce7..0000000 --- a/srcjar/fr/orsay/lri/varna/applications/VARNAOnlineDemo.java +++ /dev/null @@ -1,255 +0,0 @@ -/* - 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; - -/* - VARNA is a Java library for quick automated drawings RNA secondary structure - Copyright (C) 2007 Yann Ponty - - This program 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. - - This program 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 this program. If not, see . - */ - -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Dimension; -import java.awt.Font; -import java.awt.GridLayout; - -import javax.swing.JApplet; -import javax.swing.JLabel; -import javax.swing.JPanel; -import javax.swing.JTextField; - -import fr.orsay.lri.varna.VARNAPanel; -import fr.orsay.lri.varna.controlers.ControleurDemoTextField; -import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; -import fr.orsay.lri.varna.models.rna.RNA; - -/** - * An RNA 2d Panel demo applet - * - * @author Yann Ponty & Darty Kévin - * - */ - -public class VARNAOnlineDemo extends JApplet { - - /** - * - */ - private static final long serialVersionUID = -790155708306987257L; - - private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA"; - - private static final String DEFAULT_STRUCTURE = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...))))).."; - - private VARNAPanel _vp; - - private JPanel _tools = new JPanel(); - private JPanel _input = new JPanel(); - - private JPanel _seqPanel = new JPanel(); - private JPanel _structPanel = new JPanel(); - private JLabel _info = new JLabel(); - private JTextField _struct = new JTextField(); - private JTextField _seq = new JTextField(); - private JLabel _structLabel = new JLabel(" Str:"); - private JLabel _seqLabel = new JLabel(" Seq:"); - - private static String errorOpt = "error"; - private boolean _error; - - private Color _backgroundColor = Color.white; - - private int _algoCode; - - public VARNAOnlineDemo() { - super(); - try { - _vp = new VARNAPanel(_seq.getText(), _struct.getText()); - _vp.setErrorsOn(false); - } catch (ExceptionNonEqualLength e) { - _vp.errorDialog(e); - } - RNAPanelDemoInit(); - } - - private void RNAPanelDemoInit() { - int marginTools = 40; - - setBackground(_backgroundColor); - _vp.setBackground(_backgroundColor); - - try { - _vp.getRNA().setRNA(_seq.getText(), _struct.getText()); - _vp.setErrorsOn(false); - } catch (Exception e1) { - _vp.errorDialog(e1); - } - - Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12"); - - _seqLabel.setHorizontalTextPosition(JLabel.LEFT); - _seqLabel.setPreferredSize(new Dimension(marginTools, 15)); - _seq.setFont(textFieldsFont); - _seq.setText(_vp.getRNA().getSeq()); - - _seqPanel.setLayout(new BorderLayout()); - _seqPanel.add(_seqLabel, BorderLayout.WEST); - _seqPanel.add(_seq, BorderLayout.CENTER); - - _structLabel.setPreferredSize(new Dimension(marginTools, 15)); - _structLabel.setHorizontalTextPosition(JLabel.LEFT); - _struct.setFont(textFieldsFont); - _struct.setText(_vp.getRNA().getStructDBN()); - _structPanel.setLayout(new BorderLayout()); - _structPanel.add(_structLabel, BorderLayout.WEST); - _structPanel.add(_struct, BorderLayout.CENTER); - - ControleurDemoTextField controleurTextField = new ControleurDemoTextField(this); - _seq.addCaretListener(controleurTextField); - _struct.addCaretListener(controleurTextField); - - _input.setLayout(new GridLayout(3, 0)); - _input.add(_seqPanel); - _input.add(_structPanel); - - _tools.setLayout(new BorderLayout()); - _tools.add(_input, BorderLayout.CENTER); - _tools.add(_info, BorderLayout.SOUTH); - - getContentPane().setLayout(new BorderLayout()); - getContentPane().add(_vp, BorderLayout.CENTER); - getContentPane().add(_tools, BorderLayout.SOUTH); - - setVisible(true); - _vp.getVARNAUI().UIRadiate(); - } - - public String[][] getParameterInfo() { - String[][] info = { - // Parameter Name Kind of Value Description, - { "sequenceDBN", "String", "A raw RNA sequence" }, - { "structureDBN", "String", - "An RNA structure in dot bracket notation (DBN)" }, - { errorOpt, "boolean", "To show errors" }, }; - return info; - } - - public void init() { - retrieveParametersValues(); - _vp.setBackground(_backgroundColor); - _error = true; - } - - private Color getSafeColor(String col, Color def) { - Color result; - try { - result = Color.decode(col); - } catch (Exception e) { - try { - result = Color.getColor(col, def); - } catch (Exception e2) { - return def; - } - } - return result; - } - - private String getParameterValue(String key, String def) { - String tmp; - tmp = getParameter(key); - if (tmp == null) { - return def; - } else { - return tmp; - } - } - - private void retrieveParametersValues() { - _error = Boolean.parseBoolean(getParameterValue(errorOpt, "false")); - _vp.setErrorsOn(_error); - _backgroundColor = getSafeColor(getParameterValue("background", - _backgroundColor.toString()), _backgroundColor); - _vp.setBackground(_backgroundColor); - _seq.setText(getParameterValue("sequenceDBN", "")); - _struct.setText(getParameterValue("structureDBN", "")); - String _algo = getParameterValue("algorithm", "radiate"); - if (_algo.equals("circular")) - _algoCode = RNA.DRAW_MODE_CIRCULAR; - else if (_algo.equals("naview")) - _algoCode = RNA.DRAW_MODE_NAVIEW; - else if (_algo.equals("line")) - _algoCode = RNA.DRAW_MODE_LINEAR; - else - _algoCode = RNA.DRAW_MODE_RADIATE; - if (_seq.getText().equals("") && _struct.getText().equals("")) { - _seq.setText(DEFAULT_SEQUENCE); - _struct.setText(DEFAULT_STRUCTURE); - } - try { - _vp.drawRNA(_seq.getText(), _struct.getText(), _algoCode); - } catch (ExceptionNonEqualLength e) { - e.printStackTrace(); - } - - } - - public VARNAPanel get_varnaPanel() { - return _vp; - } - - public void set_varnaPanel(VARNAPanel surface) { - _vp = surface; - } - - public JTextField get_struct() { - return _struct; - } - - public void set_struct(JTextField _struct) { - this._struct = _struct; - } - - public JTextField get_seq() { - return _seq; - } - - public void set_seq(JTextField _seq) { - this._seq = _seq; - } - - public JLabel get_info() { - return _info; - } - - public void set_info(JLabel _info) { - this._info = _info; - } -}