/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
*/
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.AlignmentViewPanel;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.Cache;
import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.popup.*;
+public class AppJmol extends GStructureViewer implements Runnable,
+ SequenceStructureBinding, ViewSetProvider
+{
+ AppJmolBinding jmb;
-public class AppJmol
- extends GStructureViewer
- implements StructureListener, JmolStatusListener, Runnable
+ JPanel scriptWindow;
-{
- JmolViewer viewer;
- JmolPopup jmolpopup;
- ScriptWindow scriptWindow;
- PDBEntry pdbentry;
- SequenceI[] sequence;
- String [] chains;
- StructureSelectionManager ssm;
JSplitPane splitPane;
+
RenderPanel renderPanel;
+
AlignmentPanel ap;
- String fileLoadingError;
- boolean colourBySequence = true;
- boolean loadingFromArchive = false;
+
Vector atomsPicked = new Vector();
- public AppJmol(String file, String id,
- SequenceI[] seq,
- AlignmentPanel ap,
- String loadStatus,
- Rectangle bounds)
- {
- loadingFromArchive = true;
- pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
- this.chains = chains;
- this.sequence = seq;
- this.ap = ap;
- this.setBounds(bounds);
+ private boolean addingStructures = false;
+
+ /**
+ *
+ * @param file
+ * @param id
+ * @param seq
+ * @param ap
+ * @param loadStatus
+ * @param bounds
+ * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+ */
+ public AppJmol(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds)
+ {
+ this(file, id, seq, ap, loadStatus, bounds, null);
+ }
+
+ /**
+ * @deprecated
+ */
+ public AppJmol(String file, String id, SequenceI[] seq,
+ AlignmentPanel ap, String loadStatus, Rectangle bounds,
+ String viewid)
+ {
+ this(new String[]
+ { file }, new String[]
+ { id }, new SequenceI[][]
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
+ }
- colourBySequence = false;
- seqColour.setSelected(false);
+ ViewSelectionMenu seqColourBy;
- jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- bounds.width,bounds.height);
+ /**
+ *
+ * @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, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
- initJmol(loadStatus);
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ jmolColour.setSelected(true);
+ }
+ if (usetoColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ jmolColour.setSelected(false);
+ }
+ this.setBounds(bounds);
+ initMenus();
+ viewId = viewid;
+ // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+ // bounds.width,bounds.height);
this.addInternalFrameListener(new InternalFrameAdapter()
{
closeViewer();
}
});
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+
}
-public synchronized void addSequence(SequenceI [] seq)
- {
- Vector v = new Vector();
- for(int i=0; i<sequence.length; i++)
- v.addElement(sequence[i]);
+ private void initMenus()
+ {
+ seqColour.setSelected(jmb.isColourBySequence());
+ jmolColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith==null)
+ {
+ _colourwith=new Vector<AlignmentPanel>();
+ }
+ if (_alignwith==null)
+ {
+ _alignwith=new Vector<AlignmentPanel>();
+ }
+
+ seqColourBy = new ViewSelectionMenu("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("Superpose with ..", this,
+ _alignwith, handler = new ItemListener()
+ {
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setToolTipText("Align structures using "
+ + _alignwith.size() + " linked alignment views");
+ }
+ });
+ handler.itemStateChanged(null);
+ jmolActionMenu.add(alpanels);
+ jmolActionMenu.addMenuListener(new MenuListener()
+ {
- for(int i=0; i<seq.length; i++)
- if(!v.contains(seq[i]))
- v.addElement(seq[i]);
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ handler.itemStateChanged(null);
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
- SequenceI [] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
- }
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
+ }
+ });
+ }
+ 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,
+ final AlignmentPanel ap)
{
- //////////////////////////////////
- //Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ progressBar = ap.alignFrame;
+ // ////////////////////////////////
+ // Is the pdb file already loaded?
+ 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 map sequences to the visible structure?",
- "Map Sequences to Visible Window: " + pdbentry.getId(),
- JOptionPane.YES_NO_OPTION);
+ pdbentry.getId() + " is already displayed."
+ + "\nDo you want to re-use this viewer ?",
+ "Map Sequences to Visible Window: " + pdbentry.getId(),
+ JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr!=null) {
+ // 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();
ap.paintAlignment(true);
}
- //Now this AppJmol is mapped to new sequences. We must add them to
+ // Now this AppJmol is mapped to new sequences. We must add them to
// the exisiting array
- JInternalFrame [] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for(int i=0; i<frames.length; i++)
+ for (int i = 0; i < frames.length; i++)
{
- if(frames[i] instanceof AppJmol)
+ if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol)frames[i]);
- if(topJmol.pdbentry.getFile().equals(alreadyMapped))
- {
- topJmol.addSequence(seq);
- break;
- }
+ 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(pe, seq);
+ topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
+ topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager().sequenceColoursChanged(ap);
+ break;
+ }
+ }
}
}
return;
}
}
- ///////////////////////////////////
-
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
-
- jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
-
- if (pdbentry.getFile() != null)
+ // /////////////////////////////////
+ // 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)
{
- initJmol("load \""+pdbentry.getFile()+"\"");
+ Enumeration jm = existingViews.elements();
+ while (jm.hasMoreElements())
+ {
+ AppJmol topJmol = (AppJmol) jm.nextElement();
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "Do you want to add " + pdbentry.getId()
+ + " to the view called\n'" + topJmol.getTitle()
+ + "'\n", "Align to existing structure view",
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.useAlignmentPanelForSuperposition(ap);
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
+ }
+ }
}
- else
+ // /////////////////////////////////
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ }
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
+ boolean promptUser=pdbentrys.length==1;
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length>1)
{
- Thread worker = new Thread(this);
- worker.start();
+ alignAddedStructures=true;
+ useAlignmentPanelForSuperposition(ap);
}
-
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ worker=null;
+ String filelist="";
+// for (PDBEntry pe: pdbentrys)
+// {
+// if (pe.getFile()==null)
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+// break;
+ }
+// filelist+=" \""+pe.getFile()+"\"";
+
+/* }
+ if (worker==null)
+ {
+ initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
+ }
+*/
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
closeViewer();
}
});
- }
+ }
- void initJmol(String command)
+ /**
+ * 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)
{
- renderPanel = new RenderPanel();
-
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ openNewJmol(ap, pe, seqs);
+ }
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
- pdbentry.getId());
+ /**
+ * list of sequenceSet ids associated with the view
+ */
+ ArrayList<String> _aps = new ArrayList();
- if (pdbentry.getProperty() != null)
+ public AlignmentPanel[] getAllAlignmentPanels()
+ {
+ AlignmentPanel[] t, list = new AlignmentPanel[0];
+ for (String setid : _aps)
{
- if (pdbentry.getProperty().get("method") != null)
+ AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
+ if (panels != null)
{
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
+ 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;
}
- if (pdbentry.getProperty().get("chains") != null)
+ }
+
+ 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)
{
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
+ 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);
+ jmolColour.setSelected(!enableColourBySeq);
+ }
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ addAlignmentPanel(nap);
+ if (!_colourwith.contains(nap))
+ {
+ _colourwith.add(nap);
}
+ }
- this.setTitle(title.toString());
+ public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
+ {
+ if (_colourwith.contains(nap))
+ {
+ _colourwith.remove(nap);
+ }
+ }
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter());
+ /**
+ * 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));
- viewer.setAppletContext("", null, null, "");
+ } catch (Exception e)
+ {
+ }
- viewer.setJmolStatusListener(this);
+ }
+ // 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;
+ }
- jmolpopup = JmolPopup.newJmolPopup(viewer);
+ private Vector getJmolsFor(AlignmentPanel ap2)
+ {
+ Vector otherJmols = new Vector();
+ // Now this AppJmol is mapped to new sequences. We must add them to
+ // the exisiting array
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
- viewer.evalStringQuiet(command);
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
+ AppJmol topJmol = ((AppJmol) frames[i]);
+ if (topJmol.isLinkedWith(ap2))
+ {
+ otherJmols.addElement(topJmol);
+ }
+ }
+ }
+ return otherJmols;
}
+ void initJmol(String command)
+ {
+ jmb.setFinishedInit(false);
+ renderPanel = new RenderPanel();
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ 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)
+ {
+ return;
+ }
JMenuItem menuItem = new JMenuItem("All");
menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
{
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for(int i=0; i<chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- ( (JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- centerViewer();
- allChainsSelected = false;
- }
- });
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ centerViewer();
+ allChainsSelected = false;
+ }
+ });
chainMenu.add(menuItem);
}
boolean allChainsSelected = false;
+
+ private boolean alignAddedStructures = false;
+
void centerViewer()
{
- StringBuffer cmd = new StringBuffer();
- for(int i=0; i<chainMenu.getItemCount(); i++)
+ Vector toshow = new Vector();
+ String lbl;
+ int mlength, p, mnum;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if(item.isSelected())
- cmd.append(":"+item.getText()+" or ");
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.addElement(item.getText());
+ }
}
}
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
-
- viewer.evalStringQuiet("select *;restrict "
- +cmd+";cartoon;center "+cmd);
+ jmb.centerViewer(toshow);
}
void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
-
- //We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager
- .getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getFile());
+ 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
{
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
- initJmol("load "+pdbentry.getFile());
- }
- catch (Exception ex)
+ 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++)
+ {
+ String file = jmb.pdbentry[pi].getFile();
+ if (file == null)
+ {
+ // 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("Fetching PDB " + 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("Finished.", hdl);
+ }
+ if (pdbseq != null)
+ {
+ // 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 + "\"");
+ }
+ else
+ {
+ errormsgs.append("'" + pdbid + "' ");
+ }
+ }
+ else
+ {
+ 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(" \"" + file + "\"");
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
{
ex.printStackTrace();
+ 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);
+
+ }
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ if (files.length() > 0)
+ {
+ 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
+ {
+ 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().length!=jmb.pdbentry.length))
+ {
+ 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)
+ {
+ 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;
}
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
{
try
{
- BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
+ // 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));
String data;
- while ( (data = in.readLine()) != null)
+ while ((data = in.readLine()) != null)
{
- if (
- ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
- )
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
{
out.println(data);
}
}
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550,
- 600);
- cap.setText(
- StructureSelectionManager.getStructureSelectionManager().printMapping(
- pdbentry.getFile())
- );
+ 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, "PDB - Sequence Mapping",
+ 550, 600);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
if (type == jalview.util.ImageMaker.PNG)
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Make PNG image from view",
- width, height,
- null, null);
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Make PNG image from view", width, height, null, null);
}
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.EPS,
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
}
if (im.getGraphics() != null)
{
Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(),
- rect.getSize(), rect);
+ jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
im.writeImage();
}
}
-
-
+ public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ {
+ if (jmolColour.isSelected()) {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
+ }
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
+ jmb.setColourBySequence(seqColour.isSelected());
+ 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);
+ }
+ }
}
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color chain");
+ chainColour.setSelected(true);
+ jmb.colourByChain();
}
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- +"select LYS,ARG;color blue;select CYS;color yellow");
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
}
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new ZappoColourScheme());
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
}
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new TaylorColourScheme());
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
}
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new HydrophobicColourScheme());
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new HelixColourScheme());
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
}
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new StrandColourScheme());
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
}
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new TurnColourScheme());
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
}
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new BuriedColourScheme());
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
}
-
- public void setJalviewColourScheme(ColourSchemeI cs)
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
-
- if(cs==null)
- return;
-
- String res;
- int index;
- Color col;
-
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while(en.hasMoreElements())
- {
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if(index>20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select "+res+";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
- }
-
- viewer.evalStringQuiet(command.toString());
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
}
-
+
public void userColour_actionPerformed(ActionEvent actionEvent)
{
+ userColour.setSelected(true);
new UserDefinedColours(this, null);
}
public void backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour",
- null);
-
+ "Select Background Colour", null);
if (col != null)
{
- viewer.evalStringQuiet("background ["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ jmb.setBackgroundColour(col);
}
}
-
public void jmolHelp_actionPerformed(ActionEvent actionEvent)
{
- try{
- jalview.util.BrowserLauncher.openURL(
- "http://jmol.sourceforge.net/docs/JmolUserGuide/");
- }catch(Exception ex){}
- }
-
-
- //////////////////////////////////
- ///StructureListener
- public String getPdbFile()
- {
- return pdbentry.getFile();
- }
-
- Pattern pattern = Pattern.compile(
- "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
- );
-
- String lastMessage;
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
- matcher.group(1);
- int pdbResNum = Integer.parseInt(matcher.group(2));
- String chainId = matcher.group(3);
-
- if (chainId != null)
- chainId = chainId.substring(1, chainId.length());
- else
+ try
{
- chainId = " ";
- }
-
- if (lastMessage == null || !lastMessage.equals(strInfo))
+ jalview.util.BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
{
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
}
- lastMessage = strInfo;
}
- StringBuffer resetLastRes = new StringBuffer();
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ public void showConsole(boolean showConsole)
{
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
- if (resetLastRes.length() > 0)
+ if (showConsole)
{
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
+ if (splitPane == null)
+ {
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+ splitPane.setTopComponent(renderPanel);
+ splitPane.setBottomComponent(scriptWindow);
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
+ }
- if (!chain.equals(" "))
- {
- eval.append(":" + chain);
- resetLastRes.append(":" + chain);
}
+ else
+ {
+ if (splitPane != null)
+ {
+ splitPane.setVisible(false);
+ }
- eval.append(";wireframe 100;"+eval.toString()+".CA;");
-
- resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.toString());
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
+ splitPane = null;
- return new Color(viewer.getAtomArgb(atomIndex));
- }
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ }
- public void updateColours(Object source)
- {
- colourBySequence( (AlignmentPanel) source);
+ validate();
}
-
-//End StructureListener
-////////////////////////////
-
- String lastCommand;
- FeatureRenderer fr=null;
- public void colourBySequence(AlignmentPanel sourceap)
+ class RenderPanel extends JPanel
{
- this.ap = sourceap;
-
- if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
+ final Dimension currentSize = new Dimension();
- boolean showFeatures = false;
+ final Rectangle rectClip = new Rectangle();
- if (ap.av.showSequenceFeatures)
+ public void paintComponent(Graphics g)
{
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
+ getSize(currentSize);
+ g.getClipBounds(rectClip);
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
+ if (jmb.fileLoadingError != null)
{
- if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s])>-1)
+ 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("Error loading file...", 20, currentSize.height / 2);
+ StringBuffer sb = new StringBuffer();
+ int lines = 0;
+ for (int e = 0; e < jmb.pdbentry.length; e++)
{
- for (int r = 0; r < sequence[s].getLength(); r++)
+ sb.append(jmb.pdbentry[e].getId());
+ if (e < jmb.pdbentry.length - 1)
{
- int pos = mapping[m].getPDBResNum(
- sequence[s].findPosition(r));
-
- if (pos < 1 || pos==lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
-
- if (command.toString().endsWith(":" + mapping[m].getChain()+
- ";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]"))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]");
+ sb.append(",");
+ }
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
}
- break;
}
}
+ 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);
+ }
}
+ }
- if (lastCommand == null || !lastCommand.equals(command.toString()))
+ String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
{
- viewer.evalStringQuiet(command.toString());
+ viewId = System.currentTimeMillis() + "." + this.hashCode();
}
- lastCommand = command.toString();
+ return viewId;
}
- StringBuffer condenseCommand(StringBuffer command, int pos)
+ public void updateTitleAndMenus()
{
- StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
-
- command.delete(0, sb.length());
-
- String start;
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
- if (command.indexOf("-") > -1)
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
- start = command.substring(0,command.indexOf("-"));
+ jmolActionMenu.setVisible(true);
}
- else
+ if (!jmb.isLoadingFromArchive())
{
- start = command.substring(0, command.indexOf(":"));
+ seqColour_actionPerformed(null);
}
-
- sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
-
- return sb;
}
- /////////////////////////////////
- //JmolStatusListener
-
- public String eval(String strEval)
+ protected void buildJmolActionMenu()
{
- // System.out.println(strEval);
- //"# 'eval' is implemented only for the applet.";
- return null;
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector<AlignmentPanel>();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : jmolActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ jmolActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
}
- public void createImage(String file, String type, int quality)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
- System.out.println("JMOL CREATE IMAGE");
+ alignStructs_withAllAlignPanels();
}
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {}
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg)
+ private void alignStructs_withAllAlignPanels()
{
- if(errorMsg!=null)
+ if (ap == null)
{
- fileLoadingError = errorMsg;
- repaint();
return;
}
-
- fileLoadingError = null;
-
- if (fileName != null)
+ ;
+ 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;
- //FILE LOADED OK
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
- ssm.addStructureViewerListener(this);
- Vector chains = new Vector();
- for(int i=0; i<pdbFile.chains.size(); i++)
+ for (AlignmentPanel ap : _alignwith)
{
- chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
+ als[a] = ap.av.getAlignment();
+ alm[a] = -1;
+ alc[a++] = ap.av.getColumnSelection();
}
- setChainMenuItems(chains);
-
- jmolpopup.updateComputedMenus();
-
- if(!loadingFromArchive)
+ jmb.superposeStructures(als, alm, alc);
+ } catch (Exception e)
+ {
+ StringBuffer sp = new StringBuffer();
+ for (AlignmentPanel ap : _alignwith)
{
- viewer.evalStringQuiet(
- "select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
+ sp.append("'" + ap.alignFrame.getTitle() + "' ");
}
- if (fr!=null)
- fr.featuresAdded();
+ Cache.log.info("Couldn't align structures with the " + sp.toString()
+ + "associated alignment panels.", e);
- loadingFromArchive = false;
}
- else
- return;
- }
- public void notifyFrameChanged(int frameNo)
- {
- boolean isAnimationRunning = (frameNo <= -2);
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo)
- {}
-
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
}
- public void sendConsoleMessage(String strStatus)
+ public void setJalviewColourScheme(ColourSchemeI ucs)
{
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
+ jmb.setJalviewColourScheme(ucs);
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
}
- public void handlePopupMenu(int x, int y)
- {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {}
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
{
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
-
- matcher.group(1);
- String resnum = new String(matcher.group(2));
- String chainId = matcher.group(3);
-
- String picked = resnum;
-
- if (chainId != null)
- picked+=(":"+chainId.substring(1, chainId.length()));
-
- picked+=".C";
-
- if (!atomsPicked.contains(picked))
- {
- if(chainId!=null)
- viewer.evalString("select "+picked+";label %n %r:%c");
- else
- viewer.evalString("select "+picked+";label %n %r");
- atomsPicked.addElement(picked);
- }
- else
- {
- viewer.evalString("select "+picked+";label off");
- atomsPicked.removeElement(picked);
- }
-
- if (scriptWindow != null)
+ for (AlignmentPanel ap : getAllAlignmentPanels())
{
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
+ if (ap.av.getAlignment() == alignment)
+ {
+ return ap;
+ }
}
+ return ap;
}
- public void notifyAtomHovered(int atomIndex, String strInfo)
+ /**
+ *
+ * @param ap2
+ * @return true if this Jmol instance is linked with the given alignPanel
+ */
+ public boolean isLinkedWith(AlignmentPanel ap2)
{
- mouseOverStructure(atomIndex, strInfo);
+ return _aps.contains(ap2.av.getSequenceSetId());
}
- public void sendSyncScript(String script, String appletName)
- {}
-
- public void showUrl(String url)
- {}
-
- public void showConsole(boolean showConsole)
+ public boolean isUsedforaligment(AlignmentPanel ap2)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
-
- if(showConsole)
- {
- if(splitPane==null)
- {
- splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
- splitPane.setTopComponent(renderPanel);
- splitPane.setBottomComponent(scriptWindow);
- this.getContentPane().add(splitPane, BorderLayout.CENTER);
- }
-
- splitPane.setDividerLocation(getHeight()-200);
- splitPane.validate();
- }
- else
- {
- if (splitPane != null)
- splitPane.setVisible(false);
-
- splitPane = null;
-
- this.getContentPane().add(renderPanel, BorderLayout.CENTER);
- }
- validate();
+ return (_alignwith != null) && _alignwith.contains(ap2);
}
- public float functionXY(String functionName, int x, int y)
+ public boolean isUsedforcolourby(AlignmentPanel ap2)
{
- return 0;
+ return (_colourwith != null) && _colourwith.contains(ap2);
}
- ///End JmolStatusListener
- ///////////////////////////////
-
-
- class RenderPanel
- extends JPanel
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
{
- final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
- public void paintComponent(Graphics g)
- {
- getSize(currentSize);
- g.getClipBounds(rectClip);
-
- if (viewer == null)
- {
- 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 if(fileLoadingError!=null)
- {
- 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("Error loading file..." + pdbentry.getId(), 20,
- currentSize.height / 2);
- }
- else
- {
- viewer.renderScreenImage(g, currentSize, rectClip);
- }
+ return !jmb.isColourBySequence();
}
- }
+
}
git://source.jalview.org / jalview.git / blobdiff