--- /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.Color;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.util.ArrayList;
+import java.util.Hashtable;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.event.TableModelEvent;
+import javax.swing.event.TableModelListener;
+
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.components.BaseSpecialColorEditor;
+import fr.orsay.lri.varna.components.BaseTableModel;
+import fr.orsay.lri.varna.components.ColorRenderer;
+import fr.orsay.lri.varna.models.BaseList;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
+
+public class VueBases extends JPanel {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * for bases by kind
+ */
+ public final static int KIND_MODE = 1;
+ /**
+ * for all bases
+ */
+ public final static int ALL_MODE = 2;
+ /**
+ * for base pairs by king
+ */
+ public final static int COUPLE_MODE = 3;
+
+ private int _mode;
+
+ private VARNAPanel _vp;
+
+ private ArrayList<BaseList> data = new ArrayList<BaseList>();
+
+ private Hashtable<String,BaseList> revdata = new Hashtable<String,BaseList>();
+
+ private JTable table;
+
+ private BaseTableModel specialTableModel;
+
+ public VueBases(VARNAPanel vp, int mode) {
+ super(new GridLayout(1, 0));
+ _vp = vp;
+ switch (mode) {
+ case (KIND_MODE):
+ _mode = KIND_MODE;
+ kindMode();
+ break;
+ case (ALL_MODE):
+ _mode = ALL_MODE;
+ allMode();
+ break;
+ case (COUPLE_MODE):
+ _mode = COUPLE_MODE;
+ coupleMode();
+ break;
+ default:
+ break;
+ }
+ }
+
+ private BaseList locateOrAddList(String caption)
+ {
+ if (!revdata.containsKey(caption))
+ {
+ BaseList mbl = new BaseList(caption);
+ revdata.put(caption,mbl);
+ data.add(mbl);
+ }
+ return revdata.get(caption);
+ }
+
+ private void coupleMode() {
+ String pairString;
+ for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) {
+
+ int j = _vp.getRNA().get_listeBases().get(i).getElementStructure();
+ if (j > i) {
+ String tmp1 = (_vp.getRNA().get_listeBases().get(i).getContent());
+ String tmp2 = (_vp.getRNA().get_listeBases().get(j).getContent());
+ pairString = tmp1 +"-"+ tmp2;
+ BaseList bl = locateOrAddList(pairString);
+ bl.addBase(_vp.getRNA().get_listeBases().get(i));
+ bl.addBase(_vp.getRNA().get_listeBases().get(j));
+ }
+ }
+ createView();
+ }
+
+ private void allMode() {
+ for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) {
+ ModeleBase mb = _vp.getRNA().get_listeBases().get(i);
+ BaseList bl = locateOrAddList(""+i);
+ bl.addBase(mb);
+ }
+ createView();
+ }
+
+ private void kindMode() {
+ for (int i = 0; i < _vp.getRNA().get_listeBases().size(); i++) {
+ ModeleBase mb = _vp.getRNA().get_listeBases().get(i);
+ String tmp1 = (mb.getContent());
+ BaseList bl = locateOrAddList(tmp1);
+ bl.addBase(mb);
+ }
+ createView();
+ }
+
+ private void createView() {
+ specialTableModel = new BaseTableModel(data);
+ table = new JTable(specialTableModel);
+ table.setPreferredScrollableViewportSize(new Dimension(500, 300));
+ // 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);
+
+ // Set up renderer and editor for the Favorite Color column.
+ table.setDefaultRenderer(Color.class, new ColorRenderer(true));
+ table.setDefaultEditor(Color.class, new BaseSpecialColorEditor(this));
+ specialTableModel.addTableModelListener(new TableModelListener(){
+
+ public void tableChanged(TableModelEvent e) {
+ _vp.repaint();
+ }
+
+ });
+
+ // Add the scroll pane to this panel.
+ add(scrollPane);
+
+ UIvueBases();
+ }
+
+ /**
+ * Create the GUI and show it. For thread safety, this method should be
+ * invoked from the event-dispatching thread.
+ */
+ public void UIvueBases() {
+ // Create and set up the content pane.
+ JComponent newContentPane = this;
+ newContentPane.setOpaque(true); // content panes must be opaque
+
+ JOptionPane.showMessageDialog(_vp, newContentPane,
+ "Base Colors Edition", JOptionPane.PLAIN_MESSAGE);
+
+ }
+
+ public int getMode() {
+ return _mode;
+ }
+
+ public BaseList getDataAt(int i) {
+ return data.get(i);
+ }
+
+
+ public ArrayList<BaseList> getData() {
+ return data;
+ }
+
+ public VARNAPanel get_vp() {
+ return _vp;
+ }
+
+ public JTable getTable() {
+ return table;
+ }
+
+ public void setTable(JTable table) {
+ this.table = table;
+ }
+
+ public BaseTableModel getSpecialTableModel() {
+ return specialTableModel;
+ }
+
+ public void setSpecialTableModel(BaseTableModel specialTableModel) {
+ this.specialTableModel = specialTableModel;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff