+++ /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.applications;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridLayout;
-import java.awt.Image;
-import java.awt.Point;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-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.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.AdjustmentEvent;
-import java.awt.event.AdjustmentListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.geom.Point2D.Double;
-import java.io.File;
-import java.text.DateFormat;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Date;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.DefaultListModel;
-import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
-import javax.swing.JButton;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollBar;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTextField;
-import javax.swing.ListModel;
-import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.DefaultHighlighter;
-
-import fr.orsay.lri.varna.VARNAPanel;
-import fr.orsay.lri.varna.components.ReorderableJList;
-import fr.orsay.lri.varna.components.ZoomWindow;
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.factories.RNAFactory;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener;
-import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
-import fr.orsay.lri.varna.models.BaseList;
-import fr.orsay.lri.varna.models.FullBackup;
-import fr.orsay.lri.varna.models.VARNAConfig;
-import fr.orsay.lri.varna.models.rna.Mapping;
-import fr.orsay.lri.varna.models.rna.ModeleBP;
-import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-public class VARNAGUI extends JFrame implements DropTargetListener, InterfaceVARNAListener, MouseListener, AdjustmentListener {
-
- /**
- *
- */
- private static final long serialVersionUID = -790155708306987257L;
-
- private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
-
- private static final String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
- private static final String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
- // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
- // private static final String DEFAULT_STRUCTURE2 =
- // "((((..(((....)))..))))";
-
- private VARNAPanel _vp;
-
- private JPanel _tools = new JPanel();
- private JPanel _input = new JPanel();
-
- private JPanel _seqPanel = new JPanel();
- private JPanel _strPanel = new JPanel();
- private JLabel _info = new JLabel();
-
- private JTextField _str = new JTextField(DEFAULT_STRUCTURE1);
- Object _hoverHighlightStr = null;
- ArrayList<Object> _selectionHighlightStr = new ArrayList<Object>();
-
- private JTextField _seq = new JTextField(DEFAULT_SEQUENCE);
- Object _hoverHighlightSeq = null;
- ArrayList<Object> _selectionHighlightSeq = new ArrayList<Object>();
-
-
- private ZoomWindow _zoomWindow;
- private JLabel _strLabel = new JLabel(" Str:");
- private JLabel _seqLabel = new JLabel(" Seq:");
- private JButton _createButton = new JButton("Create");
- private JButton _deleteButton = new JButton("Delete");
- private JButton _duplicateButton = new JButton("Snapshot");
-
- private JPanel _listPanel = new JPanel();
- private ReorderableJList _sideList = null;
-
-
- private static String errorOpt = "error";
- @SuppressWarnings("unused")
- private boolean _error;
-
- private Color _backgroundColor = Color.white;
-
- private JScrollBar _vert = new JScrollBar(JScrollBar.VERTICAL);
- private JScrollBar _horiz = new JScrollBar(JScrollBar.HORIZONTAL);
-
- private static int _nextID = 1;
- @SuppressWarnings("unused")
- private int _algoCode;
-
- private BackupHolder _rnaList;
-
-
- public VARNAGUI() {
- super("VARNA GUI");
- RNAPanelDemoInit();
- }
-
- private void RNAPanelDemoInit()
- {
- DefaultListModel dlm = new DefaultListModel();
-
-
- int marginTools = 40;
-
- DefaultListSelectionModel m = new DefaultListSelectionModel();
- m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- m.setLeadAnchorNotificationEnabled(false);
-
-
- _sideList = new ReorderableJList();
- _sideList.setModel(dlm);
- _sideList.addMouseListener(this);
- _sideList.setSelectionModel(m);
- _sideList.setPreferredSize(null);
-
- _sideList.addListSelectionListener( new ListSelectionListener(){
- public void valueChanged(ListSelectionEvent arg0) {
- //System.out.println(arg0);
- if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
- {
- FullBackup sel = (FullBackup) _sideList.getSelectedValue();
- _vp.setConfig(sel.config);
- showRNA(sel.rna);
- _seq.setText(sel.rna.getSeq());
- _str.setText(sel.rna.getStructDBN(true));
- }
- }
- });
-
- _rnaList = new BackupHolder(dlm,_sideList);
- RNA _RNA1 = new RNA("User defined 1");
- RNA _RNA2 = new RNA("User defined 2");
- try {
- _vp = new VARNAPanel("0",".");
- _zoomWindow = new ZoomWindow(_vp);
- _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
- _RNA1.drawRNARadiate(_vp.getConfig());
- _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
- _RNA2.drawRNARadiate(_vp.getConfig());
- } catch (ExceptionNonEqualLength e) {
- _vp.errorDialog(e);
- } catch (ExceptionUnmatchedClosingParentheses e2) {
- e2.printStackTrace();
- } catch (ExceptionFileFormatOrSyntax e3) {
- e3.printStackTrace();
- }
- _vp.setPreferredSize(new Dimension(400, 400));
- _rnaList.add(_vp.getConfig().clone(),_RNA2,generateDefaultName());
- _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
-
-
- JScrollPane listScroller = new JScrollPane(_sideList);//,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- listScroller.setPreferredSize(new Dimension(150, 0));
-
- setBackground(_backgroundColor);
- _vp.setBackground(_backgroundColor);
-
-
- Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
-
- _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
- _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
- _seq.setFont(textFieldsFont);
- _seq.setText(DEFAULT_SEQUENCE);
-
- _createButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- try {
- RNA nRNA = new RNA(generateDefaultName());
- nRNA.setRNA(_seq.getText(), _str.getText());
- nRNA.drawRNARadiate(_vp.getConfig());
- _rnaList.add(new VARNAConfig(),nRNA,true);
- } catch (ExceptionUnmatchedClosingParentheses e1) {
- JOptionPane.showMessageDialog(_vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
- } catch (ExceptionFileFormatOrSyntax e1) {
- JOptionPane.showMessageDialog(_vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
- }
- }
- });
-
-
- _seqPanel.setLayout(new BorderLayout());
- _seqPanel.add(_seqLabel, BorderLayout.WEST);
- _seqPanel.add(_seq, BorderLayout.CENTER);
-
- _strLabel.setPreferredSize(new Dimension(marginTools, 15));
- _strLabel.setHorizontalTextPosition(JLabel.LEFT);
- _str.setFont(textFieldsFont);
- _strPanel.setLayout(new BorderLayout());
- _strPanel.add(_strLabel, BorderLayout.WEST);
- _strPanel.add(_str, BorderLayout.CENTER);
-
- _input.setLayout(new GridLayout(2, 0));
- _input.add(_seqPanel);
- _input.add(_strPanel);
-
- JPanel goPanel = new JPanel();
- goPanel.setLayout(new BorderLayout());
-
- _tools.setLayout(new BorderLayout());
- _tools.add(_input, BorderLayout.CENTER);
- _tools.add(_info, BorderLayout.SOUTH);
- _tools.add(goPanel, BorderLayout.EAST);
-
- _deleteButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- _rnaList.removeSelected();
- }
- });
- // BH 2018 SwingJS can't clone, as it does not implement serialization
- if (/** @j2sNative false && */ true)
- _duplicateButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- _rnaList.add((VARNAConfig)_vp.getConfig().clone(),_vp.getRNA().clone(),_vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
- }});
-
- JPanel ops = new JPanel();
- ops.setLayout(new GridLayout(1,2));
- ops.add(_deleteButton);
- if (/** @j2sNative false && */ true)
- ops.add(_duplicateButton);
-
- JPanel opspanel = new JPanel(new BorderLayout());
- opspanel.add(ops,BorderLayout.NORTH);
- opspanel.add(_zoomWindow,BorderLayout.SOUTH);
-
- _zoomWindow.setPreferredSize(new Dimension(-1,200));
-
-
- JLabel j = new JLabel("Structure Manager",JLabel.CENTER);
- _listPanel.setLayout(new BorderLayout());
-
- _listPanel.add(opspanel,BorderLayout.SOUTH);
- _listPanel.add(j,BorderLayout.NORTH);
- _listPanel.add(listScroller,BorderLayout.CENTER);
-
- goPanel.add(_createButton, BorderLayout.CENTER);
-
- JPanel vpScroll = new JPanel();
- vpScroll.setLayout(new BorderLayout());
- _horiz.setVisible(false);
- _horiz.addAdjustmentListener(this);
- _vert.setVisible(false);
- _vert.addAdjustmentListener(this);
- vpScroll.add(_horiz,BorderLayout.SOUTH);
- vpScroll.add(_vert,BorderLayout.EAST);
- vpScroll.add(_vp,BorderLayout.CENTER);
- JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vpScroll);
- getContentPane().setLayout(new BorderLayout());
- getContentPane().add(split, BorderLayout.CENTER);
- getContentPane().add(_tools, BorderLayout.NORTH);
-
-
- setVisible(true);
- DropTarget dt = new DropTarget(_vp, this);
-
- _vp.addRNAListener(new InterfaceVARNARNAListener(){
- public void onSequenceModified(int index, String oldseq, String newseq) {
- //System.out.println("Sequence changed: Index:"+index+" ["+oldseq+"]=>["+newseq+"]");
- }
-
- public void onStructureModified(Set<ModeleBP> current,
- Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs) {
- String result = "";
- //System.out.println("Structure changed: ");
- for (ModeleBP s:addedBasePairs)
- { result +=s; }
- //System.out.println(" Added: "+result);
- result = "";
- for (ModeleBP s:removedBasePairs)
- { result +=s; }
- //System.out.println(" Removed: "+result);
- }
-
- public void onRNALayoutChanged(Hashtable<Integer, Double> previousPositions) {
- //System.out.print("Layout changed, bases#: ");
- String result = "";
- for (Integer s:previousPositions.keySet())
- { result +=s+" "; }
- //System.out.println(result);
- }
-
- });
-
- _vp.addSelectionListener(new InterfaceVARNASelectionListener(){
-
- public void onHoverChanged(ModeleBase oldbase, ModeleBase newBase) {
- if (_hoverHighlightSeq!=null)
- {
- _seq.getHighlighter().removeHighlight(_hoverHighlightSeq);
- _hoverHighlightSeq = null;
- }
- if (_hoverHighlightStr!=null)
- {
- _str.getHighlighter().removeHighlight(_hoverHighlightStr);
- _hoverHighlightStr = null;
- }
- if (newBase!=null)
- {
- try {
- int i = newBase.getIndex();
- int[] shifts = _vp.getRNA().getStrandShifts();
- _hoverHighlightSeq = _seq.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
- _hoverHighlightStr = _str.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
- } catch (BadLocationException e) {
- e.printStackTrace();
- }
- }
- }
-
- public void onSelectionChanged(BaseList selection,
- BaseList addedBases, BaseList removedBases) {
- for(Object tag: _selectionHighlightSeq)
- {
- _seq.getHighlighter().removeHighlight(tag);
- }
- _selectionHighlightSeq.clear();
- for(Object tag: _selectionHighlightStr)
- {
- _str.getHighlighter().removeHighlight(tag);
- }
- _selectionHighlightStr.clear();
- int[] shifts = _vp.getRNA().getStrandShifts();
- for (ModeleBase m: selection.getBases())
- {
- try {
- int i = m.getIndex();
- _selectionHighlightSeq.add(_seq.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) ));
- _selectionHighlightStr.add(_str.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) ));
- } catch (BadLocationException e) {
- e.printStackTrace();
- }
- }
- }
-
- });
-
- _vp.addVARNAListener(this);
-
- new Thread(_zoomWindow).start();
- }
-
- protected void showRNA(RNA rna) {
- _vp.showRNAInterpolated(rna);
- _zoomWindow.repaint();
- }
-
-
- public void addRNA(RNA r, VARNAConfig cfg)
- {
- _rnaList.add(cfg,r);
- }
-
- public static String generateDefaultName()
- {
- return "User file #"+_nextID++;
- }
-
- public RNA getRNA() {
- return (RNA)_sideList.getSelectedValue();
- }
-
-
-
- public String[][] getParameterInfo() {
- String[][] info = {
- // Parameter Name Kind of Value Description,
- { "sequenceDBN", "String", "A raw RNA sequence" },
- { "structureDBN", "String",
- "An RNA structure in dot bracket notation (DBN)" },
- { errorOpt, "boolean", "To show errors" }, };
- return info;
- }
-
- public void init() {
- _vp.setBackground(_backgroundColor);
- _error = true;
- }
-
- @SuppressWarnings("unused")
- private Color getSafeColor(String col, Color def) {
- Color result;
- try {
- result = Color.decode(col);
- } catch (Exception e) {
- try {
- result = Color.getColor(col, def);
- } catch (Exception e2) {
- return def;
- }
- }
- return result;
- }
-
- public VARNAPanel get_varnaPanel() {
- return _vp;
- }
-
- public void set_varnaPanel(VARNAPanel surface) {
- _vp = surface;
- }
-
-
- public JTextField get_seq() {
- return _seq;
- }
-
- public void set_seq(JTextField _seq) {
- this._seq = _seq;
- }
-
- public JLabel get_info() {
- return _info;
- }
-
- public void set_info(JLabel _info) {
- this._info = _info;
- }
-
- public static void main(String[] args) {
- List<Image> icons = new ArrayList<Image>();
- //JOptionPane.showMessageDialog(null, ""+Toolkit.getDefaultToolkit().getImage("./VARNA16x16.png"), "Check", JOptionPane.INFORMATION_MESSAGE);
- icons.add(Toolkit.getDefaultToolkit().getImage("./VARNA16x16.png"));
- icons.add(Toolkit.getDefaultToolkit().getImage("./VARNA32x32.png"));
- icons.add(Toolkit.getDefaultToolkit().getImage("./VARNA64x64.png"));
- VARNAGUI d = new VARNAGUI();
- d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- d.pack();
- d.setIconImages(icons);
- d.setVisible(true);
- }
-
-
- public void dragEnter(DropTargetDragEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- public void dragExit(DropTargetEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- public void dragOver(DropTargetDragEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- 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);
- Object ob = tr.getTransferData(flavors[i]);
- if (ob instanceof List)
- {
- List list = (List) ob;
- 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)
- {
- String path = o.toString();
- VARNAPanel vp = (VARNAPanel) c;
- try{
- FullBackup bck = VARNAPanel.importSession((File) o); // BH SwingJS
- _rnaList.add(bck.config, bck.rna,bck.name,true);
- }
- catch (ExceptionLoadingFailed e3)
- {
- ArrayList<RNA> rnas = RNAFactory.loadSecStr((File) o); // BH SwingJS
- if (rnas.isEmpty())
- {
- throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from that source.");
- }
-
- dtde.dropComplete(true);
- _vp.getVARNAUI().UIChooseRNAs(rnas);
- return;
- /*
- for(RNA r: rnas)
- {
- r.drawRNA(vp.getConfig());
- String name = r.getName();
- if (name.equals(""))
- {
- name = path.substring(path.lastIndexOf(File.separatorChar)+1);
- }
- if (rnas.size()>1)
- {
- name += " - Molecule# "+id++;
- }
- _rnaList.add(vp.getConfig().clone(),r,name,true);
- }*/
- }
- }
- }
- }
- }
- // If we made it this far, everything worked.
- dtde.dropComplete(true);
- return;
- }
- }
- // Hmm, the user must not have dropped a file list
- dtde.rejectDrop();
- } catch (Exception e) {
- e.printStackTrace();
- dtde.rejectDrop();
- }
-
- }
-
- public void dropActionChanged(DropTargetDragEvent arg0) {
- }
-
- private class BackupHolder{
- private DefaultListModel _rnaList;
- private ArrayList<RNA> _rnas = new ArrayList<RNA>();
- JList _l;
-
- public BackupHolder(DefaultListModel rnaList, JList l)
- {
- _rnaList = rnaList;
- _l = l;
- }
-
- public void add(VARNAConfig c, RNA r)
- {
- add(c, r, r.getName(),false);
- }
-
- public void add(VARNAConfig c, RNA r,boolean select)
- {
- add(c, r, r.getName(),select);
- }
-
- public void add(VARNAConfig c, RNA r, String name)
- {
- add(c, r, name,false);
- }
- public void add(VARNAConfig c, RNA r, String name, boolean select)
- {
- if (!_rnas.contains(r))
- {
- if (select){
- _l.removeSelectionInterval(0, _rnaList.size());
- }
- if (name.equals(""))
- {
- name = generateDefaultName();
- }
- FullBackup bck = new FullBackup(c,r,name);
- _rnas.add(0, r);
- _rnaList.add(0,bck);
- _l.doLayout();
- if (select){
- _l.setSelectedIndex(0);
- }
- }
- }
-
- public void remove(int i)
- {
- _rnas.remove(i);
- _rnaList.remove(i);
-
- }
- public DefaultListModel getModel()
- {
- return _rnaList;
- }
- public boolean contains(RNA r)
- {
- return _rnas.contains(r);
- }
- /*public int getSize()
- {
- return _rnaList.getSize();
- }*/
- public FullBackup getElementAt(int i)
- {
- return (FullBackup) _rnaList.getElementAt(i);
- }
-
- public void removeSelected()
- {
- int i = _l.getSelectedIndex();
- if (i!=-1)
- {
- if (_rnaList.getSize()==1)
- {
- RNA r = new RNA();
- try {
- r.setRNA(" ", ".");
- } catch (ExceptionUnmatchedClosingParentheses e1) {
- } catch (ExceptionFileFormatOrSyntax e1) {
- }
- showRNA(r);
- }
- else
- {
- int newi = i+1;
- if (newi==_rnaList.getSize())
- {
- newi = _rnaList.getSize()-2;
- }
- FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
- _l.setSelectedValue(bck,true);
- }
- _rnaList.remove(i);
- }
-
- }
- }
-
- public void onStructureRedrawn() {
- // TODO Auto-generated method stub
-
- }
-
- public void onUINewStructure(VARNAConfig v, RNA r) {
- _rnaList.add(v, r,r.getName(),true);
- onZoomLevelChanged();
- }
-
- public void onWarningEmitted(String s) {
- // TODO Auto-generated method stub
-
- }
-
- public void mouseClicked(MouseEvent e) {
- if(e.getClickCount() == 2){
- int index = _sideList.locationToIndex(e.getPoint());
- ListModel dlm = _sideList.getModel();
- FullBackup item = (FullBackup) dlm.getElementAt(index);;
- _sideList.ensureIndexIsVisible(index);
- Object newName = JOptionPane.showInputDialog(
- this,
- "Specify a new name for this RNA",
- "Rename RNA",
- JOptionPane.QUESTION_MESSAGE,
- (Icon)null,
- null,
- item.toString());
- if (newName!=null)
- {
- item.name = newName.toString();
- this._sideList.repaint();
- }
- }
- }
-
- public void mouseEntered(MouseEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- public void mouseExited(MouseEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- public void mousePressed(MouseEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- public void mouseReleased(MouseEvent arg0) {
- // TODO Auto-generated method stub
-
- }
-
- public void onZoomLevelChanged() {
- if (_vp.getZoom()>1.02)
- {
- Rectangle r = _vp.getZoomedInTranslationBox();
- _horiz.setMinimum(r.x);
- _horiz.setMaximum(r.x+r.width+_vp.getWidth());
- _horiz.getModel().setExtent(_vp.getWidth());
- _horiz.getModel().setValue(_vp.getTranslation().x);
- _horiz.doLayout();
- _horiz.setVisible(true);
-
- _vert.setMinimum(r.y);
- _vert.setMaximum(r.y+r.height+_vp.getHeight());
- _vert.getModel().setExtent(_vp.getHeight());
- _vert.getModel().setValue(_vp.getTranslation().y);
- _vert.doLayout();
- _vert.setVisible(true);
- }
- else
- {
- _horiz.setVisible(false);
- _vert.setVisible(false);
- }
- }
-
- public void onTranslationChanged() {
- if (_vp.getZoom()>1.02)
- {
- int nx = _horiz.getMaximum()-(_vp.getTranslation().x-_horiz.getMinimum())-_vp.getWidth();
- int ny = _vert.getMaximum()-(_vp.getTranslation().y-_vert.getMinimum())-_vp.getHeight();
- _horiz.getModel().setValue(nx);
- _horiz.doLayout();
- _vert.getModel().setValue(ny);
- _vert.doLayout();
- }
- }
-
- public void adjustmentValueChanged(AdjustmentEvent arg0) {
- if (arg0.getSource()==_horiz)
- {
- _vp.setTranslation(new Point(_horiz.getMaximum()-(arg0.getValue()-_horiz.getMinimum())-_vp.getWidth(),_vp.getTranslation().y));
- _vp.repaint();
- }
- else if (arg0.getSource()==_vert)
- {
- _vp.setTranslation(new Point(_vp.getTranslation().x,_vert.getMaximum()-(arg0.getValue()-_vert.getMinimum())-_vp.getHeight()));
- _vp.repaint();
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff