/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.Container;
+import jalview.util.MessageManager;
+
+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.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.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
-import java.util.BitSet;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import javax.swing.DefaultListModel;
+import javax.swing.DefaultListSelectionModel;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JList;
import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListModel;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureSelectionManager;
-
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.components.ReorderableJList;
+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.interfaces.InterfaceVARNAListener;
+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.RNA;
-public class AppVarnaBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
+ implements DropTargetListener, InterfaceVARNAListener,
+ MouseListener
{
/**
+ *
+ */
+ // private static final long serialVersionUID = -790155708306987257L;
+
+ private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
+
+ private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
+
+ private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
+
+ public VARNAPanel vp;
+
+ protected 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();
+
+ private JTextField _seq = new JTextField();
+
+ private JLabel _strLabel = new JLabel(
+ MessageManager.getString("label.str"));
+
+ private JLabel _seqLabel = new JLabel(
+ MessageManager.getString("label.seq"));
+
+ private JButton _createButton = new JButton(
+ MessageManager.getString("action.create"));
+
+ private JButton _updateButton = new JButton(
+ MessageManager.getString("action.update"));
+
+ private JButton _deleteButton = new JButton(
+ MessageManager.getString("action.delete"));
+
+ private JButton _duplicateButton = new JButton(
+ MessageManager.getString("action.snapshot"));
+
+ protected JPanel _listPanel = new JPanel();
+
+ private ReorderableJList _sideList = null;
+
+ private static String errorOpt = "error";
+
+ @SuppressWarnings("unused")
+ private boolean _error;
+
+ private Color _backgroundColor = Color.white;
+
+ private static int _nextID = 1;
+
+ @SuppressWarnings("unused")
+ private int _algoCode;
+
+ private BackupHolder _rnaList;
+
+ /*
+ * public AppVarnaBinding() { //super("VARNA in Jalview");
+ * //this.set_seq("ATGC"); //this.set_str(".()."); //RNAPanelDemoInit();
*
+ * //initVarna("ATGCATGATATATATATAT","....((((...))))....");
+ * initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1); }
*/
- private AppJmol appJmolWindow;
- public AppVarnaBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ public AppVarnaBinding(String seq, String struc)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
- appJmolWindow = appJmol;
+ // super("VARNA in Jalview");
+ initVarna(seq, struc);
+
}
- FeatureRenderer fr = null;
+ public AppVarnaBinding(ArrayList<RNA> rnaList)
+ {
- @Override
- public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ // super("VARNA in Jalview");
+ initVarnaEdit(rnaList);
+ }
+
+ private void initVarna(String seq, String str)
{
- AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+
+ DefaultListModel dlm = new DefaultListModel();
+
+ 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(new Dimension(100, 0));
+ _sideList.addListSelectionListener(new ListSelectionListener()
{
- if (fr == null)
+ public void valueChanged(ListSelectionEvent arg0)
{
- fr = new FeatureRenderer(ap);
+ if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
+ {
+ FullBackup sel = (FullBackup) _sideList.getSelectedValue();
+ Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
+ .getSize(), sel.rna.getSize());
+ vp.showRNAInterpolated(sel.rna, sel.config, map);
+ _seq.setText(sel.rna.getSeq());
+ _str.setText(sel.rna.getStructDBN());
+ }
}
+ });
+
+ _rnaList = new BackupHolder(dlm, _sideList);
+ RNA _RNA1 = new RNA("User defined 1");
+
+ try
+ {
- fr.transferSettings(ap.
- seqPanel.seqCanvas.getFeatureRenderer());
+ vp = new VARNAPanel("0", ".");
+ _RNA1.setRNA(seq, str);
+ _RNA1.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(), _RNA1, generateDefaultName(), true);
- return fr;
- }
+ // TODO setBackground(_backgroundColor);
+ vp.setBackground(_backgroundColor);
- @Override
- public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
- {
- return new SequenceRenderer(((AlignmentPanel)alignment).av);
+ // TODO getContentPane().setLayout(new BorderLayout());
+ // TODO getContentPane().add(vp, BorderLayout.CENTER);
+
+ // setVisible(true);
+ vp.addVARNAListener(this);
}
- public void sendConsoleEcho(String strEcho)
+ private void initVarnaEdit(ArrayList<RNA> rnaInList)
{
- if (console != null)
+
+ 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(new Dimension(100, 0));
+ _sideList.addListSelectionListener(new ListSelectionListener()
+ {
+ public void valueChanged(ListSelectionEvent arg0)
+ {
+ // System.out.println(arg0);
+ if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
+ {
+ FullBackup sel = (FullBackup) _sideList.getSelectedValue();
+ Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
+ .getSize(), sel.rna.getSize());
+ // vp.showRNAInterpolated(sel.rna, sel.config, map);
+ vp.showRNA(sel.rna, sel.config);
+ // _seq.setText(sel.rna.getSeq());
+ _str.setText(sel.rna.getStructDBN());
+ }
+ }
+ });
+ _rnaList = new BackupHolder(dlm, _sideList);
+
+ try
+ {
+
+ vp = new VARNAPanel("0", ".");
+ for (int i = 0; i < rnaInList.size(); i++)
+ {
+ rnaInList.get(i).drawRNARadiate(vp.getConfig());
+
+ }
+ } catch (ExceptionNonEqualLength e)
{
- console.sendConsoleEcho(strEcho);
+ vp.errorDialog(e);
}
+ vp.setPreferredSize(new Dimension(400, 400));
+ for (int i = 0; i < rnaInList.size(); i++)
+ {
+ if (i < rnaInList.size() - 1)
+ {
+ _rnaList.add(vp.getConfig().clone(), rnaInList.get(i), rnaInList
+ .get(i).getName());
+ }
+ else
+ {
+ _rnaList.add(vp.getConfig().clone(), rnaInList.get(i), rnaInList
+ .get(i).getName(), true);
+ }
+ }
+
+ /*
+ * _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
+ * _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
+ */
+
+ JScrollPane listScroller = new JScrollPane(_sideList);
+ listScroller.setPreferredSize(new Dimension(150, 0));
+
+ 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(rnaInList.get(0).getSeq());
+
+ _updateButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ FullBackup sel = (FullBackup) _sideList.getSelectedValue();
+ sel.rna.setSequence("A");
+ }
+ });
+
+ // _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(1, 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(); } });
+ * _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); }});
+ */
+ goPanel.add(_updateButton, BorderLayout.CENTER);
+
+ JPanel ops = new JPanel();
+ ops.setLayout(new GridLayout(1, 2));
+ ops.add(_deleteButton);
+ ops.add(_duplicateButton);
+
+ JLabel j = new JLabel(
+ MessageManager.getString("label.structures_manager"),
+ JLabel.CENTER);
+ _listPanel.setLayout(new BorderLayout());
+
+ // _listPanel.add(ops, BorderLayout.SOUTH);
+ _listPanel.add(j, BorderLayout.NORTH);
+ _listPanel.add(listScroller, BorderLayout.CENTER);
+
+ // JSplitPane split = new
+ // JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
+ /**
+ * TODO getContentPane().setLayout(new BorderLayout());
+ * getContentPane().add(split, BorderLayout.CENTER);
+ * getContentPane().add(_tools, BorderLayout.NORTH);
+ */
+
+ // TODO setVisible(true);
+ DropTarget dt = new DropTarget(vp, this);
+
+ vp.addVARNAListener(this);
+ }
+
+ public JPanel getTools()
+ {
+ return _tools;
}
- public void sendConsoleMessage(String strStatus)
+ public JPanel getListPanel()
+ {
+ return _listPanel;
+ }
+
+ /**
+ * TODO: Is it effective to transfer the whole RNA?
+ *
+ * @return Currently selected RNA
+ */
+ public RNA getSelectedRNA()
+ {
+ return _rnaList.getElementAt(_sideList.getSelectedIndex()).rna;
+ }
+
+ /**
+ * Substitute currently selected RNA with the edited one
+ *
+ * @param rnaEdit
+ */
+ public void updateSelectedRNA(RNA rnaEdit)
{
- if (console != null && strStatus != null)
- // && !strStatus.equals("Script completed"))
- // should we squash the script completed string ?
+ vp.repaint();
+ vp.showRNA(rnaEdit);
+ }
+
+ /*
+ * 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(new Dimension(100, 0));
+ * _sideList.addListSelectionListener( new ListSelectionListener(){ public
+ * void valueChanged(ListSelectionEvent arg0) { //System.out.println(arg0); if
+ * (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting()) { FullBackup
+ * sel = (FullBackup) _sideList.getSelectedValue(); Mapping map =
+ * Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
+ * vp.showRNAInterpolated(sel.rna,sel.config,map);
+ * _seq.setText(sel.rna.getSeq()); _str.setText(sel.rna.getStructDBN()); } }
+ * });
+ *
+ * _rnaList = new BackupHolder(dlm,_sideList); RNA _RNA1 = new
+ * RNA("User defined 1"); RNA _RNA2 = new RNA("User defined 2"); try { vp =
+ * new VARNAPanel("0","."); _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);
+ * 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(); } });
+ * _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); ops.add(_duplicateButton);
+ *
+ * JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
+ * _listPanel.setLayout(new BorderLayout());
+ *
+ * _listPanel.add(ops,BorderLayout.SOUTH);
+ * _listPanel.add(j,BorderLayout.NORTH);
+ * _listPanel.add(listScroller,BorderLayout.CENTER);
+ *
+ * goPanel.add(_createButton, BorderLayout.CENTER);
+ *
+ * JSplitPane split = new
+ * JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
+ * getContentPane().setLayout(new BorderLayout()); getContentPane().add(split,
+ * BorderLayout.CENTER); getContentPane().add(_tools, BorderLayout.NORTH);
+ *
+ * setVisible(true); DropTarget dt = new DropTarget(vp, this);
+ *
+ * vp.addVARNAListener(this); }
+ */
+ public static String generateDefaultName()
+ {
+ return "User file #" + _nextID++;
+ }
+
+ public RNA getRNA()
+ {
+ return (RNA) _sideList.getSelectedValue();
+ }
+
+ public String[][] getParameterInfo()
+ {
+ String[][] info =
{
- console.sendConsoleMessage(strStatus);
- }
+ // 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;
}
- @Override
- public void showUrl(String url, String target)
+ public void init()
{
+ vp.setBackground(_backgroundColor);
+ _error = true;
+ }
+
+ @SuppressWarnings("unused")
+ private Color getSafeColor(String col, Color def)
+ {
+ Color result;
try
{
- jalview.util.BrowserLauncher.openURL(url);
+ result = Color.decode(col);
} catch (Exception e)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
- // TODO: 2.6 : warn user if browser was not configured.
+ try
+ {
+ result = Color.getColor(col, def);
+ } catch (Exception e2)
+ {
+ return def;
+ }
}
+ return result;
}
- @Override
- public void refreshGUI()
+ public VARNAPanel get_varnaPanel()
{
- // appJmolWindow.repaint();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- appJmolWindow.updateTitleAndMenus();
- appJmolWindow.revalidate();
- }
- });
+ return vp;
}
- public void updateColours(Object source)
+ public void set_varnaPanel(VARNAPanel surface)
{
- AlignmentPanel ap = (AlignmentPanel) source,topap;
- // ignore events from unrelated or non-user interactive frames
- if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap))
- return;
- if (!isLoadingFromArchive()) {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
- }
+ vp = surface;
+ }
+
+ public String get_seq()
+ {
+ return _seq.getText();
}
- public void notifyScriptTermination(String strStatus, int msWalltime)
+ public void set_seq(String _seq)
{
- // todo - script termination doesn't happen ?
- // if (console != null)
- // console.notifyScriptTermination(strStatus,
- // msWalltime);
+ this._seq.setText(_seq);
}
- public void showUrl(String url)
+ public String get_str()
{
- showUrl(url, "jmol");
+ return _str.getText();
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
+ public void set_str(String _str)
{
+ this._str.setText(_str);
+ }
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ public JLabel get_info()
+ {
+ return _info;
}
- public void selectionChanged(BitSet arg0)
+ public void set_info(JLabel _info)
+ {
+ this._info = _info;
+ }
+
+ /*
+ * public static void main(String[] args) { AppVarnaBinding d = new
+ * AppVarnaBinding(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ * d.pack(); d.setVisible(true); }
+ */
+
+ public void dragEnter(DropTargetDragEvent arg0)
{
// TODO Auto-generated method stub
}
- public void refreshPdbEntries()
+ public void dragExit(DropTargetEvent arg0)
{
// TODO Auto-generated method stub
}
- public void showConsole(boolean b)
+ public void dragOver(DropTargetDragEvent arg0)
{
- appJmolWindow.showConsole(b);
+ // TODO Auto-generated method stub
+
}
- /**
- * add the given sequences to the mapping scope for the given pdb file handle
- *
- * @param pdbFile
- * - pdbFile identifier
- * @param seq
- * - set of sequences it can be mapped to
- */
- public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+ public void drop(DropTargetDropEvent dtde)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ try
{
- if (pdbentry[pe].getFile().equals(pdbFile))
+ Transferable tr = dtde.getTransferable();
+ DataFlavor[] flavors = tr.getTransferDataFlavors();
+ for (int i = 0; i < flavors.length; i++)
{
- addSequence(pe, seq);
+ 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(path);
+ _rnaList.add(bck.config, bck.rna, bck.name, true);
+ } catch (ExceptionLoadingFailed e3)
+ {
+ int mn = 1;
+ Collection<RNA> mdls = fr.orsay.lri.varna.factories.RNAFactory
+ .loadSecStr(path);
+ for (RNA r : mdls)
+ {
+ r.drawRNA(vp.getConfig());
+ String name = r.getName();
+ if (name.equals(""))
+ {
+ name = path.substring(path
+ .lastIndexOf(File.separatorChar) + 1);
+ }
+ if (mdls.size() > 1)
+ {
+ name += " (Model " + mn++ + ")";
+ }
+ _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();
}
+
}
- @Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
- Container consolePanel, String buttonsToShow)
+ public void dropActionChanged(DropTargetDragEvent arg0)
{
- return new AppConsole(viewer, consolePanel, buttonsToShow);
}
- @Override
- protected void releaseUIResources()
+ private class BackupHolder
{
- appJmolWindow = null;
- if (console != null)
+ private DefaultListModel _rnaList;
+
+ private ArrayList<RNA> _rnas = new ArrayList<RNA>();
+
+ JList _l;
+
+ public BackupHolder(DefaultListModel rnaList, JList l)
{
- try
+ _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 (select)
{
- console.setVisible(false);
- } catch (Error e)
+ _l.removeSelectionInterval(0, _rnaList.size());
+ }
+ if (name.equals(""))
{
- } catch (Exception x)
+ name = generateDefaultName();
+ }
+ FullBackup bck = new FullBackup(c, r, name);
+ _rnas.add(0, r);
+ _rnaList.add(0, bck);
+ 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)
+ {
+ }
+ vp.showRNA(r);
+ vp.repaint();
+ }
+ 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 onLayoutChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void onUINewStructure(VARNAConfig v, RNA r)
+ {
+ // patch to fix infinite loop
+ // The problem is that onUINewStructure is called when user clicks
+ // check with Yann about whether Jalview should do anything with this event.
+ // e.g. if user has used VARNA's menu to import a structure .. Jalview may
+ // need to be told which structure is displayed.
+
+ // _rnaList.add(v, r, "", true);
+ }
+
+ 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);
;
- console = null;
+ _sideList.ensureIndexIsVisible(index);
+ /*
+ * TODO 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
+
+ }
+
+ @Override
+ public Color getColour(int atomIndex, int pdbResNum, String chain,
+ String pdbId)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String[] getPdbFile()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbId)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseOverStructure(int atomIndex, String strInfo)
+ {
+ // TODO Auto-generated method stub
}
@Override
public void releaseReferences(Object svl)
{
- if (svl instanceof SeqPanel) {
- appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
- };
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void updateColours(Object source)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void componentHidden(ComponentEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void componentMoved(ComponentEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void componentResized(ComponentEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void componentShown(ComponentEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onStructureRedrawn()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
}
}
+
+/*
+ * public static void main(String[] args) { JTextField str = new
+ * JTextField("ATGC");
+ *
+ * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
+ * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
+ */
git://source.jalview.org / jalview.git / blobdiff