+++ /dev/null
-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<VARNAPanel> _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<VARNAPanel> getPanels()
- {
- return _vpl;
- }
-
- public String getSelection()
- {
- return getSelection(0);
- }
-
- public String getSelection(int panel)
- {
- String result = "[";
- VARNAPanel v = _vpl.get(panel);
- List<Integer> l = v.getSelectionIndices();
- for(int i=0;i<l.size();i++)
- {
- int n = l.get(i);
- if (i>0)
- {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) {
- }
-
-
-}
-
git://source.jalview.org / jalview.git / blobdiff