X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2FVARNA.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2FVARNA.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=1f98d50ca1574792381d9ce44b7c964732410ff2;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/srcjar/fr/orsay/lri/varna/VARNA.java b/srcjar/fr/orsay/lri/varna/VARNA.java deleted file mode 100644 index 1f98d50..0000000 --- a/srcjar/fr/orsay/lri/varna/VARNA.java +++ /dev/null @@ -1,260 +0,0 @@ -package fr.orsay.lri.varna; -/* - 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. - */ -import java.awt.Component; -import java.awt.GridLayout; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTarget; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.io.File; -import java.io.FileReader; -import java.io.IOException; -import java.util.ArrayList; -import java.util.List; - -import javax.swing.JApplet; -import javax.swing.JOptionPane; - -import fr.orsay.lri.varna.controlers.ControleurScriptParser; -import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; -import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; -import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError; -import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength; -import fr.orsay.lri.varna.exceptions.ExceptionParameterError; -import fr.orsay.lri.varna.interfaces.InterfaceParameterLoader; -import fr.orsay.lri.varna.models.VARNAConfigLoader; -import fr.orsay.lri.varna.models.rna.RNA; - - -// @j2s issues -- see README_SWINGJS.txt - -public class VARNA extends JApplet implements InterfaceParameterLoader,DropTargetListener { - ArrayList _vpl = null; - static{ - /** - * - * @j2sNative - * - * - * if (!thisApplet.__Info.sequenceDBN) { - * thisApplet.__Info.sequenceDBN = "GGGGCCAAUAUGGCCAUCC"; - * thisApplet.__Info.structureDBN = "((((((.....))))..))"; - * thisApplet.__Info.title = "Hello RNA world, from SwingJS!";//prompt("Title?","Hello RNA world!"); - * } - * - * - * - */ - } - - -// private static final_long serialVersionUID = -2598221520127067670L; - - public VARNA() { - super(); - } - - public void init() { - try { - VARNAConfigLoader VARNAcfg = new VARNAConfigLoader(this); - - try { - _vpl = VARNAcfg.createVARNAPanels(); - for (int i=0;i<_vpl.size();i++) - { - new DropTarget(_vpl.get(i), this); - } - } catch (IOException e) { - JOptionPane.showMessageDialog(this, e.getMessage(), - "VARNA Error", JOptionPane.ERROR_MESSAGE); - } catch (ExceptionFileFormatOrSyntax e) { - JOptionPane.showMessageDialog(this, e.getMessage(), - "VARNA Error", JOptionPane.ERROR_MESSAGE); - } catch (ExceptionLoadingFailed e) { - JOptionPane.showMessageDialog(this, e.getMessage(), - "VARNA Error", JOptionPane.ERROR_MESSAGE); - } - setLayout(new GridLayout(VARNAcfg.getNbColumns(), VARNAcfg - .getNbRows())); - for (int i = 0; i < _vpl.size(); i++) { - getContentPane().add(_vpl.get(i)); - } - } catch (ExceptionParameterError e) { - VARNAPanel.errorDialogStatic(e, this); - } catch (ExceptionModeleStyleBaseSyntaxError e) { - VARNAPanel.errorDialogStatic(e, this); - } catch (ExceptionNonEqualLength e) { - VARNAPanel.errorDialogStatic(e, this); - } - - } - - public void start() { - //setVisible(true); - //repaint(); - //getContentPane().setVisible(true); - //getContentPane().repaint(); - } - - public void update() { - System.out.println("update"); - } - - public String getParameterValue(String key, String def) { - if (getParameter(key) == null) { - return def; - } else { - return getParameter(key); - } - } - - public String[][] getParameterInfo() { - return VARNAConfigLoader.getParameterInfo(); - } - - public ArrayList getPanels() - { - return _vpl; - } - - public String getSelection() - { - return getSelection(0); - } - - public String getSelection(int panel) - { - String result = "["; - VARNAPanel v = _vpl.get(panel); - List l = v.getSelectionIndices(); - for(int i=0;i0) - {result += ",";} - result += n; - - } - result += "]"; - return result; - } - - public void runScript(String script) - { - if (_vpl.size()>0) - { - VARNAPanel _vp = _vpl.get(0); - try { - ControleurScriptParser.executeScript(_vp, script); - } catch (Exception e) { - e.printStackTrace(); - } - } - } - - - public void setRNA(String seq, String str) - { - if (_vpl.size()>0) - { - try { - _vpl.get(0).drawRNA(seq, str); - } catch (ExceptionNonEqualLength e) { - e.printStackTrace(); - } - } - } - - public void setSmoothedRNA(String seq, String str) - { - if (_vpl.size()>0) - { - try { - - _vpl.get(0).drawRNAInterpolated(seq, str); - _vpl.get(0).repaint(); - } catch (ExceptionNonEqualLength e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - } - } - - public void dragEnter(DropTargetDragEvent arg0) { - } - - public void dragExit(DropTargetEvent arg0) { - } - - public void dragOver(DropTargetDragEvent arg0) { - } - - public void drop(DropTargetDropEvent dtde) - { - try - { - Transferable tr = dtde.getTransferable(); - DataFlavor[] flavors = tr.getTransferDataFlavors(); - for (int i = 0; i < flavors.length; i++) - { - if (flavors[i].isFlavorJavaFileListType()) - { - dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - List list = (List) tr.getTransferData(flavors[i]); - for (int j = 0; j < list.size(); j++) - { - Object o = list.get(j); - if (dtde.getSource() instanceof DropTarget) - { - DropTarget dt = (DropTarget) dtde.getSource(); - Component c = dt.getComponent(); - if (c instanceof VARNAPanel) - { - VARNAPanel vp = (VARNAPanel) c; - // BH -- in JavaScript, the File object has a .bytes - // property that we need to maintain. - //String path = o.toString(); - vp.loadFile((File) o,true); - //vp.repaint(); BH unnecessary - } - } - } - dtde.dropComplete(true); - return; - } - } - dtde.rejectDrop(); - } - catch (Exception e) - { - e.printStackTrace(); - dtde.rejectDrop(); - } - } - - public void dropActionChanged(DropTargetDragEvent arg0) { - } - - -} -