/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.util.regex.*;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.api.SequenceStructureBinding;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.ws.ebi.EBIFetchClient;
-
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding
+ ViewSetProvider, JalviewStructureDisplayI
{
AppJmolBinding jmb;
- ScriptWindow scriptWindow;
+ JPanel scriptWindow;
JSplitPane splitPane;
Vector atomsPicked = new Vector();
+ private boolean addingStructures = false;
+
+ /**
+ *
+ * @param file
+ * @param id
+ * @param seq
+ * @param ap
+ * @param loadStatus
+ * @param bounds
+ * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+ */
+ @Deprecated
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds)
{
this(file, id, seq, ap, loadStatus, bounds, null);
}
+ /**
+ * @deprecated
+ */
+ @Deprecated
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds,
String viewid)
{
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
+ this(new String[]
+ { file }, new String[]
+ { id }, new SequenceI[][]
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
+ }
+
+ ViewSelectionMenu seqColourBy;
+
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is
+ * handling them
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ */
+ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
+ boolean leaveColouringToJmol, String loadStatus,
+ Rectangle bounds, String viewid)
+ {
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];
+ for (int i = 0; i < pdbentrys.length; i++)
+ {
+ PDBEntry pdbentry = new PDBEntry();
+ pdbentry.setFile(files[i]);
+ pdbentry.setId(ids[i]);
+ pdbentrys[i] = pdbentry;
+ }
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, seq, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
- this.ap = ap;
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ if (usetoColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
this.setBounds(bounds);
- jmb.setColourBySequence(false);
- seqColour.setSelected(false);
+ initMenus();
viewId = viewid;
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
}
+ private void initMenus()
+ {
+ seqColour.setSelected(jmb.isColourBySequence());
+ viewerColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+
+ seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (!seqColour.isSelected())
+ {
+ seqColour.doClick();
+ }
+ else
+ {
+ // update the jmol display now.
+ seqColour_actionPerformed(null);
+ }
+ }
+ });
+ viewMenu.add(seqColourBy);
+ final ItemListener handler;
+ JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
+ _alignwith, handler = new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setToolTipText(MessageManager
+ .formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[]
+ { new Integer(_alignwith.size()).toString() }));
+ }
+ });
+ handler.itemStateChanged(null);
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+ }
+
+ IProgressIndicator progressBar = null;
+
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
+ final AlignmentPanel ap)
{
+ progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ String alreadyMapped = ap.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
if (alreadyMapped != null)
{
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: "
- + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
-
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new String[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new String[]
+ { pdbentry.getId() }),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
+ // TODO : Fix multiple seq to one chain issue here.
+ ap.getStructureSelectionManager().setMapping(seq, chains,
+ alreadyMapped, AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
ap.seqPanel.seqCanvas.fr.featuresAdded();
{
if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
+ final AppJmol topJmol = ((AppJmol) frames[i]);
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
{
if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
{
- topJmol.jmb.addSequence(seq);
+ topJmol.jmb.addSequence(pe, seq);
+ topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
+ topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
break;
}
}
}
}
// /////////////////////////////////
+ // Check if there are other Jmol views involving this alignment
+ // and prompt user about adding this molecule to one of them
+ Vector existingViews = getJmolsFor(ap);
+ if (existingViews.size() > 0)
+ {
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements())
+ {
+ AppJmol topJmol = (AppJmol) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.add_pdbentry_to_view", new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return;
+ }
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.useAlignmentPanelForSuperposition(ap);
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
+ }
+ // /////////////////////////////////
+ openNewJmol(ap, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq });
+ }
- jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, seq, null, null);
- this.ap = ap;
- setSize(400, 400); // probably should be a configurable/dynamic default here
-
- if (pdbentry.getFile() != null)
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length > 1)
{
- initJmol("load \"" + pdbentry.getFile() + "\"");
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
}
- else
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ worker = null;
{
- Thread worker = new Thread(this);
+ addingStructures = false;
+ worker = new Thread(this);
worker.start();
}
-
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
}
+ /**
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
+
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ AlignmentPanel[] t, list = new AlignmentPanel[0];
+ for (String setid : _aps)
+ {
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+ if (panels != null)
+ {
+ t = new AlignmentPanel[list.length + panels.length];
+ System.arraycopy(list, 0, t, 0, list.length);
+ System.arraycopy(panels, 0, t, list.length, panels.length);
+ list = t;
+ }
+ }
+
+ return list;
+ }
+
+ /**
+ * list of alignment panels to use for superposition
+ */
+ Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
+ /**
+ * list of alignment panels that are used for colouring structures by aligned
+ * sequences
+ */
+ Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
+ /**
+ * set the primary alignmentPanel reference and add another alignPanel to the
+ * list of ones to use for colouring and aligning
+ *
+ * @param nap
+ */
+ public void addAlignmentPanel(AlignmentPanel nap)
+ {
+ if (ap == null)
+ {
+ ap = nap;
+ }
+ if (!_aps.contains(nap.av.getSequenceSetId()))
+ {
+ _aps.add(nap.av.getSequenceSetId());
+ }
+ }
+
+ /**
+ * remove any references held to the given alignment panel
+ *
+ * @param nap
+ */
+ public void removeAlignmentPanel(AlignmentPanel nap)
+ {
+ try
+ {
+ _alignwith.remove(nap);
+ _colourwith.remove(nap);
+ if (ap == nap)
+ {
+ ap = null;
+ for (AlignmentPanel aps : getAllAlignmentPanels())
+ {
+ if (aps != nap)
+ {
+ ap = aps;
+ break;
+ }
+ }
+ }
+ } catch (Exception ex)
+ {
+ }
+ if (ap != null)
+ {
+ buildJmolActionMenu();
+ }
+ }
+
+ public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_alignwith.contains(nap))
+ {
+ _alignwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ {
+ if (_alignwith.contains(nap))
+ {
+ _alignwith.remove(nap);
+ }
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+ boolean enableColourBySeq)
+ {
+ useAlignmentPanelForColourbyseq(nap);
+ jmb.setColourBySequence(enableColourBySeq);
+ seqColour.setSelected(enableColourBySeq);
+ viewerColour.setSelected(!enableColourBySeq);
+ }
+
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_colourwith.contains(nap))
+ {
+ _colourwith.add(nap);
+ }
+ }
+
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
+
+ /**
+ * pdb retrieval thread.
+ */
+ private Thread worker = null;
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param alignFrame
+ * @param align
+ * if true, new structure(s) will be align using associated alignment
+ */
+ private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
+ final String[] chains, final boolean b,
+ final IProgressIndicator alignFrame)
+ {
+ if (pdbentry.getFile() == null)
+ {
+ if (worker != null && worker.isAlive())
+ {
+ // a retrieval is in progress, wait around and add ourselves to the
+ // queue.
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ while (worker != null && worker.isAlive() && _started)
+ {
+ try
+ {
+ Thread.sleep(100 + ((int) Math.random() * 100));
+
+ } catch (Exception e)
+ {
+ }
+
+ }
+ // and call ourselves again.
+ addStructure(pdbentry, seq, chains, b, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ jmb.addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = b;
+ progressBar = alignFrame; // visual indication happens on caller frame.
+ (worker = new Thread(this)).start();
+ return;
+ }
+
+ private Vector getJmolsFor(AlignmentPanel apanel)
+ {
+ Vector result = new Vector();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof AppJmol)
+ {
+ if (((AppJmol) frame).isLinkedWith(apanel))
+ {
+ result.addElement(frame);
+ }
+ }
+ }
+ return result;
+ }
+
void initJmol(String command)
{
jmb.setFinishedInit(false);
this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
getBounds().width, getBounds().height);
- jmb.allocateViewer(renderPanel, "", null, null, "");
+ if (scriptWindow == null)
+ {
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
+ }
+ ;
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
jmb.newJmolPopup(true, "Jmol", true);
+ if (command == null)
+ {
+ command = "";
+ }
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
}
void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
- if (chains==null)
+ if (chains == null)
{
return;
}
- JMenuItem menuItem = new JMenuItem("All");
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
}
centerViewer();
allChainsSelected = false;
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
+ {
centerViewer();
+ }
}
});
boolean allChainsSelected = false;
+ private boolean alignAddedStructures = false;
+
void centerViewer()
{
Vector toshow = new Vector();
jmb.centerViewer(toshow);
}
- void closeViewer()
+ public void closeViewer()
{
jmb.closeViewer();
+ ap = null;
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
}
+ /**
+ * state flag for PDB retrieval thread
+ */
+ private boolean _started = false;
+
public void run()
{
+ _started = true;
String pdbid = "";
// todo - record which pdbids were successfuly imported.
StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
+ String[] curfiles = jmb.getPdbFile(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
for (int pi = 0; pi < jmb.pdbentry.length; pi++)
{
- AlignmentI pdbseq;
- if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId())) != null)
+ String file = jmb.pdbentry[pi].getFile();
+ if (file == null)
{
- String file;
- // just transfer the file name from the first sequence's first
- // PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq.getSequenceAt(
- 0).getPDBId().elementAt(0)).getFile());
- files.append("\"" + file + "\"");
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.pdbentry[pi].getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+ .getId());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'" + pdbid + "'");
+ }
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[pi].setFile(file);
+
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
}
else
{
- errormsgs.append("'" + pdbid + "' ");
+ if (curfiles != null && curfiles.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < curfiles.length; c++)
+ {
+ if (curfiles[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.append(" \"" + Platform.escapeString(file) + "\"");
+ }
}
}
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
}
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
}
+ long lastnotify = jmb.getLoadNotifiesHandled();
if (files.length() > 0)
{
- try
+ if (!addingStructures)
+ {
+
+ try
+ {
+ initJmol("load FILES " + files.toString());
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
{
- initJmol("load FILES " + files.toString());
- } catch (OutOfMemoryError oomerror)
+ StringBuffer cmd = new StringBuffer();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(files.toString());
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ cmd = null;
+ lastnotify = jmb.getLoadNotifiesHandled();
+
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning(
+ "When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + files);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
+
+ // need to wait around until script has finished
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length != jmb.pdbentry.length))
{
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(35);
+ } catch (Exception e)
+ {
+ }
+ }
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ jmb.updateColours(ap);
}
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ alignStructs_withAllAlignPanels();
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ }
+ });
+ alignAddedStructures = false;
+ }
+ addingStructures = false;
+
}
+ _started = false;
+ worker = null;
}
+ @Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{
try
{
- // TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
+ // TODO: cope with multiple PDB files in view
+ BufferedReader in = new BufferedReader(new FileReader(
+ jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
}
}
+ @Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
- for (int pdbe = 0; pdbe<jmb.pdbentry.length; pdbe++) {
- cap.appendText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
+ try
+ {
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ {
+ cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
+ cap.appendText("\n");
+ }
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning(
+ "composing sequence-structure alignments for display in text box.",
+ e);
+ cap.dispose();
+ return;
}
+ jalview.gui.Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- void makePDBImage(int type)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG,
"Make PNG image from view", width, height, null, null);
}
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS,
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
+ }
else
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
+
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
}
if (im.getGraphics() != null)
}
}
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
+
+ @Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
- // Set the colour using the current view for the associated alignframe
- jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures, ap.alignFrame.viewport.alignment);
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector<AlignmentPanel>();
+ }
+ if (jmb.isColourBySequence())
+ {
+ if (!jmb.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && ap != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ }
+ }
}
+ @Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
jmb.colourByChain();
}
+ @Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
jmb.colourByCharge();
}
+ @Override
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
zappoColour.setSelected(true);
jmb.setJalviewColourScheme(new ZappoColourScheme());
}
+ @Override
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
taylorColour.setSelected(true);
jmb.setJalviewColourScheme(new TaylorColourScheme());
}
+ @Override
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
hydroColour.setSelected(true);
jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
+ @Override
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
helixColour.setSelected(true);
jmb.setJalviewColourScheme(new HelixColourScheme());
}
+ @Override
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
strandColour.setSelected(true);
jmb.setJalviewColourScheme(new StrandColourScheme());
}
+ @Override
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
turnColour.setSelected(true);
jmb.setJalviewColourScheme(new TurnColourScheme());
}
+ @Override
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+ @Override
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
new UserDefinedColours(this, null);
}
+ @Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
+ MessageManager.getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
if (showConsole)
{
splitPane.setTopComponent(renderPanel);
splitPane.setBottomComponent(scriptWindow);
this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
}
- splitPane.setDividerLocation(getHeight() - 200);
- splitPane.validate();
}
else
{
if (splitPane != null)
+ {
splitPane.setVisible(false);
+ }
splitPane = null;
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20,
- currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file")
+ + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
- int lines=0;
- for (int e=0;e<jmb.pdbentry.length; e++)
+ int lines = 0;
+ for (int e = 0; e < jmb.pdbentry.length; e++)
{
sb.append(jmb.pdbentry[e].getId());
- if (e<jmb.pdbentry.length-1) {
+ if (e < jmb.pdbentry.length - 1)
+ {
sb.append(",");
}
- if (e==jmb.pdbentry.length-1 || sb.length()>20)
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
{
lines++;
- g.drawString(sb.toString(), 20, currentSize.height/2 - lines*g.getFontMetrics().getHeight());
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
}
}
}
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
+ }
else
- if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
- {
- g.setColor(Color.black);
- g.fillRect(0, 0, currentSize.width, currentSize.height);
- g.setColor(Color.white);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else
{
jmb.viewer.renderScreenImage(g, currentSize, rectClip);
}
}
return viewId;
}
+
public void updateTitleAndMenus()
{
if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ viewerActionMenu.setVisible(true);
+ }
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
+ }
+ }
+
+ protected void buildJmolActionMenu()
+ {
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : viewerActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ viewerActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_withAllAlignPanels();
+ }
+
+ private void alignStructs_withAllAlignPanels()
+ {
+ if (ap == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
+
+ for (AlignmentPanel ap : _alignwith)
+ {
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
+ }
+ jmb.superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
+ {
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
+ }
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
+
+ }
+
}
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
-
+
+ }
+
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (AlignmentPanel ap : getAllAlignmentPanels())
+ {
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
+ }
+ return ap;
+ }
+
+ /**
+ *
+ * @param ap2
+ * @return true if this Jmol instance is linked with the given alignPanel
+ */
+ public boolean isLinkedWith(AlignmentPanel ap2)
+ {
+ return _aps.contains(ap2.av.getSequenceSetId());
+ }
+
+ public boolean isUsedforaligment(AlignmentPanel ap2)
+ {
+
+ return (_alignwith != null) && _alignwith.contains(ap2);
+ }
+
+ public boolean isUsedforcolourby(AlignmentPanel ap2)
+ {
+ return (_colourwith != null) && _colourwith.contains(ap2);
+ }
+
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
+ {
+ return !jmb.isColourBySequence();
+ }
+
+ public JalviewJmolBinding getBinding()
+ {
+ return jmb;
}
}
git://source.jalview.org / jalview.git / blobdiff