X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fviews%2FVueBases.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fviews%2FVueBases.java;h=0000000000000000000000000000000000000000;hb=d27359893c99db0e749a59d8a7ab73ea751da09e;hp=6f9d95a9afd4c0996ad25fc4a62c65ff4aee802d;hpb=9f55415c9f8005e9dcd8243453883ff853fd5b76;p=jalview.git diff --git a/src2/fr/orsay/lri/varna/views/VueBases.java b/src2/fr/orsay/lri/varna/views/VueBases.java deleted file mode 100644 index 6f9d95a..0000000 --- a/src2/fr/orsay/lri/varna/views/VueBases.java +++ /dev/null @@ -1,215 +0,0 @@ -/* - 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 data = new ArrayList(); - - private Hashtable revdata = new Hashtable(); - - 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 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; - } - -}