+++ /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