--- /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.views;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.filechooser.FileFilter;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.components.AnnotationTableModel;
+import fr.orsay.lri.varna.controlers.ControleurTableAnnotations;
+import fr.orsay.lri.varna.models.annotations.TextAnnotation;
+import fr.orsay.lri.varna.models.rna.ModeleColorMap;
+
+/**
+ * a view for all annoted texts on the VARNAPanel
+ *
+ * @author Darty@lri.fr
+ *
+ */
+public class VueListeAnnotations extends JPanel {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * if this view is for removing annoted texts
+ */
+ public static final int REMOVE = 0;
+ /**
+ * if this view is for editing annoted texts
+ */
+ public static final int EDIT = 1;
+
+ private VARNAPanel _vp;
+ private ArrayList<Object> data;
+ private JTable table;
+ private int type;
+ private AnnotationTableModel specialTableModel;
+ // BH SwingJS - this is never used in JavaScript
+ private static JFileChooser fc = new JFileChooser(){
+ public void approveSelection(){
+ File f = getSelectedFile();
+ if(f.exists() && getDialogType() == SAVE_DIALOG){
+ int result = JOptionPane.showConfirmDialog(this,"The file exists, overwrite?","Existing file",JOptionPane.YES_NO_OPTION);
+ switch(result){
+ case JOptionPane.YES_OPTION:
+ super.approveSelection();
+ return;
+ case JOptionPane.NO_OPTION:
+ return;
+ case JOptionPane.CLOSED_OPTION:
+ return;
+ case JOptionPane.CANCEL_OPTION:
+ cancelSelection();
+ return;
+ }
+ }
+ super.approveSelection();
+ }
+ };
+
+
+ /**
+ * creates the view
+ *
+ * @param vp
+ * @param type
+ * (REMOVE or EDIT)
+ */
+ public VueListeAnnotations(VARNAPanel vp, int type) {
+ super(new BorderLayout());
+ this.type = type;
+ _vp = vp;
+ data = new ArrayList<Object>();
+ data.addAll(_vp.getListeAnnotations());
+ data.addAll(_vp.getRNA().getHighlightRegion());
+ data.addAll(_vp.getRNA().getChemProbAnnotations());
+ createView();
+ }
+
+ private void createView() {
+ specialTableModel = new AnnotationTableModel(data);
+ table = new JTable(specialTableModel);
+ ControleurTableAnnotations ctrl = new ControleurTableAnnotations(table,
+ _vp, type);
+ table.addMouseListener(ctrl);
+ table.addMouseMotionListener(ctrl);
+ // table.setPreferredScrollableViewportSize(new Dimension(500, 100));
+ // TODO: Find equivalent in JRE 1.5
+ // table.setFillsViewportHeight(true);
+ // Create the scroll pane and add the table to it.
+ JScrollPane scrollPane = new JScrollPane(table);
+
+ add(scrollPane, BorderLayout.CENTER);
+
+ FileFilter CPAFiles = new FileFilter(){
+ public boolean accept(File f) {
+ return f.getName().toLowerCase().endsWith(".cpa") || f.isDirectory();
+ }
+
+ public String getDescription() {
+ return "Chemical Probing Annotations (*.cpa) Files";
+ }
+
+ };
+ fc.addChoosableFileFilter(CPAFiles);
+ fc.setFileFilter(CPAFiles);
+
+
+ JButton loadStyleButton = new JButton("Load");
+ loadStyleButton.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e) {
+ if (fc.showOpenDialog(VueListeAnnotations.this)==JFileChooser.APPROVE_OPTION)
+ {
+ File file = fc.getSelectedFile();
+ try {
+ BufferedReader br = new BufferedReader(new FileReader(file));
+ String s = br.readLine();
+ while(s != null)
+ {
+ if (s.startsWith(TextAnnotation.HEADER_TEXT))
+ s = br.readLine();
+ }
+ // TODO
+ } catch (FileNotFoundException e1) {
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+ }
+
+ });
+ JButton saveStyleButton = new JButton("Save");
+ saveStyleButton.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e) {
+ if (fc.showSaveDialog(VueListeAnnotations.this)==JFileChooser.APPROVE_OPTION)
+ {
+ try {
+ PrintWriter out = new PrintWriter(fc.getSelectedFile());
+ // TODO out.println(_gp.getColorMap().getParamEncoding());
+ out.close();
+ } catch (FileNotFoundException e1) {
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+ }
+
+ });
+ saveStyleButton.setAlignmentX(CENTER_ALIGNMENT);
+ loadStyleButton.setAlignmentX(CENTER_ALIGNMENT);
+
+ JPanel jp2 = new JPanel();
+ BoxLayout bl = new BoxLayout(jp2, BoxLayout.X_AXIS);
+ jp2.setLayout(bl);
+ jp2.setAlignmentX(CENTER_ALIGNMENT);
+ jp2.add(loadStyleButton);
+ jp2.add(Box.createRigidArea(new Dimension(5,0)));
+ jp2.add(saveStyleButton);
+ this.add(jp2,BorderLayout.SOUTH);
+
+
+
+ UIvueListeAnnotations();
+ }
+
+ /**
+ * Create the GUI and show it. For thread safety, this method should be
+ * invoked from the event-dispatching thread.
+ */
+ public void UIvueListeAnnotations() {
+ JComponent newContentPane = this;
+ newContentPane.setOpaque(true);
+ JOptionPane.showMessageDialog(_vp, newContentPane,
+ "Annotation edition", JOptionPane.PLAIN_MESSAGE);
+ }
+
+ public ArrayList<Object> getData() {
+ return data;
+ }
+
+ public void setData(ArrayList<Object> data) {
+ this.data = data;
+ }
+
+ public VARNAPanel get_vp() {
+ return _vp;
+ }
+
+ public JTable getTable() {
+ return table;
+ }
+
+ public void setTable(JTable table) {
+ this.table = table;
+ }
+
+ public AnnotationTableModel getSpecialTableModel() {
+ return specialTableModel;
+ }
+
+ public void setSpecialTableModel(AnnotationTableModel specialTableModel) {
+ this.specialTableModel = specialTableModel;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff