X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=1c0dfe6c2e534bddc3d733588bfdc9542c17e5a0;hb=678a8ac35bb269d80cda081bec11e7b403c9811a;hp=dcca874286f0cd78afc91108171a829c4d368fa0;hpb=f8456d4c0b253ae32a4b569e12bb8bf7f7096d65;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index dcca874..1c0dfe6 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,258 +1,420 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.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;
-
-public class AppJmol extends GStructureViewer implements StructureListener,
- JmolStatusListener, Runnable, SequenceStructureBinding
-
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+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.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+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.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+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.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+public class AppJmol extends StructureViewerBase
{
- JmolViewer viewer;
-
- JmolPopup jmolpopup;
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
- ScriptWindow scriptWindow;
+ private static final String SPACE = " ";
- PDBEntry pdbentry;
+ private static final String BACKSLASH = "\"";
- SequenceI[] sequence;
+ AppJmolBinding jmb;
- String[] chains;
-
- StructureSelectionManager ssm;
+ JPanel scriptWindow;
JSplitPane splitPane;
RenderPanel renderPanel;
- AlignmentPanel ap;
-
- String fileLoadingError;
+ ViewSelectionMenu seqColourBy;
- boolean colourBySequence = true;
-
- boolean loadingFromArchive = false;
-
- Vector atomsPicked = new Vector();
-
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
- {
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
-
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
+ /**
+ *
+ * @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)
{
- loadingFromArchive = true;
- pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
- this.sequence = seq;
- this.ap = ap;
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];
+ for (int i = 0; i < pdbentrys.length; i++)
+ {
+ // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+ PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+ files[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);
+
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (usetoColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
this.setBounds(bounds);
- colourBySequence = false;
- seqColour.setSelected(false);
- viewId = viewid;
+ initMenus();
+ setViewId(viewid);
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
- initJmol(loadStatus);
-
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+
}
- public synchronized void addSequence(SequenceI[] seq)
+ private void initMenus()
{
- Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
-
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
+ seqColour.setSelected(jmb.isColourBySequence());
+ viewerColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector();
+ }
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
- }
+ seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
+ new ItemListener()
+ {
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
- {
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ @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()
+ {
- if (alreadyMapped != null)
+ @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()
{
- 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);
-
- if (option == JOptionPane.YES_OPTION)
+
+ @Override
+ public void menuSelected(MenuEvent e)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
+ handler.itemStateChanged(null);
+ }
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppJmol)
- {
- AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.pdbentry.getFile().equals(alreadyMapped))
- {
- topJmol.addSequence(seq);
- break;
- }
- }
- }
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ // TODO Auto-generated method stub
- return;
}
- }
- // /////////////////////////////////
+ });
+ }
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
- this.setSize(400, 400);
- // jalview.gui.Desktop.addInternalFrame(this, "Jmol
- // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
- // : ""), 400, 400);
+ 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)
+ {
+ progressBar = ap.alignFrame;
+ String pdbId = pdbentry.getId();
- if (pdbentry.getFile() != null)
+ /*
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
+ */
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- initJmol("load \"" + pdbentry.getFile() + "\"");
+ return;
}
- else
+
+ /*
+ * Check if there are other Jmol views involving this alignment and prompt
+ * user about adding this molecule to one of them
+ */
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
+ {
+ return;
+ }
+
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ }
+
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
+ protected boolean hasPdbId(String pdbId)
+ {
+ return jmb.hasPdbId(pdbId);
+ }
+
+ 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)
{
- 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();
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
+
}
- 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());
+ /**
+ * Returns a list of any Jmol viewers. The list is restricted to those linked
+ * to the given alignment panel if it is not null.
+ */
+ @Override
+ protected List getViewersFor(AlignmentPanel apanel)
+ {
+ List result = new ArrayList();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
- if (pdbentry.getProperty() != null)
+ for (JInternalFrame frame : frames)
{
- if (pdbentry.getProperty().get("method") != null)
+ if (frame instanceof AppJmol)
{
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
}
}
+ return result;
+ }
- this.setTitle(title.toString());
- jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+ 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);
- // * OK, but safer to assign htmlName, URL bases, comandOptions, and
- // statusListener now.
-
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter(), "", null, null, "", this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
+ if (scriptWindow == null)
+ {
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
+ }
- viewer.evalStringQuiet(command);
+ jmb.allocateViewer(renderPanel, true, "", null, null, "",
+ scriptWindow, null);
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
+ {
+ command = "";
+ }
+ jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
+ jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
-
- JMenuItem menuItem = new JMenuItem("All");
+ if (chains == null)
+ {
+ return;
+ }
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
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;
@@ -261,15 +423,18 @@ public class AppJmol extends GStructureViewer implements StructureListener,
chainMenu.add(menuItem);
- for (int c = 0; c < chains.size(); c++)
+ for (String chain : chains)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
+ {
centerViewer();
+ }
}
});
@@ -281,121 +446,310 @@ public class AppJmol extends GStructureViewer implements StructureListener,
void centerViewer()
{
- jmolHistory(false);
- StringBuffer cmd = new StringBuffer();
- String lbl;
- int mlength, p,mnum;
+ Vector toshow = new Vector();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
- { lbl = item.getText();
- mlength = 0;
- do
{
- p = mlength;
- mlength = lbl.indexOf(":", p);
- } while (p < mlength && mlength < (lbl.length() - 2));
- if (pdbentry.getId().equals(lbl.substring(0,mlength)))
- {
- mnum = 1+getModelNum(pdbentry.getFile());
- if (mnum>0)
- {cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + mnum + " or ");
- }
- }
+ toshow.addElement(item.getText());
}
}
}
+ jmb.centerViewer(toshow);
+ }
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
+ @Override
+ public void closeViewer(boolean closeExternalViewer)
+ {
+ // Jmol does not use an external viewer
+ if (jmb != null)
+ {
+ jmb.closeViewer();
+ }
+ setAlignmentPanel(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;
+ }
- viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
- jmolHistory(true);
+ @Override
+ public void run()
+ {
+ _started = true;
+ try
+ {
+ List files = fetchPdbFiles();
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
+ {
+ _started = false;
+ worker = null;
+ }
}
- private int getModelNum(String modelFileName)
+
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List files)
{
- String[] mfn = getPdbFile();
- if (mfn == null)
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(BACKSLASH)
+ .append(Platform.escapeString(s)).append(BACKSLASH);
+ }
+ String filesString = fileList.toString();
+
+ if (!addingStructures)
+ {
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ 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 " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
+
+ // need to wait around until script has finished
+ int waitMax = JMOL_LOAD_TIMEOUT;
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length == files.size()))
{
- return -1;
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
+ {
+ }
+ if (waitTotal > waitMax)
+ {
+ System.err
+ .println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+// System.err.println("finished: " + jmb.isFinishedInit()
+// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+// + "; files: " + files.toString());
+ jmb.getPdbFile();
+ break;
+ }
}
- for (int i = 0; i < mfn.length; i++)
+
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
- if (mfn[i].equalsIgnoreCase(modelFileName))
- return i;
+ alignAddedStructures();
}
- return -1;
+ addingStructures = false;
}
- void closeViewer()
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- // remove listeners for all structures in viewer
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (jmb.viewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ }
+ });
+ alignAddedStructures = false;
}
- public void run()
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * @return
+ */
+ List fetchPdbFiles()
{
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List files = new ArrayList();
+ String pdbid = "";
try
{
+ String[] filesInViewer = jmb.getPdbFile();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- AlignmentI pdbseq;
- if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
- {
- // just transfer the file name from the first seuqence's first PDBEntry
- pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile());
- initJmol("load " + pdbentry.getFile());
- }
- else
+ Pdb pdbclient = new Pdb();
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " could not be retrieved. Please try downloading the file manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
+ String file = jmb.getPdbEntry(pi).getFile();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.getPdbEntry(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);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
+ {
+ 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(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ jmb.getPdbEntry(pi).setFile(file);
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
+ {
+ if (filesInViewer[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.add(file);
+ }
+ }
}
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
- oomerror);
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
+ if (errormsgs.length() > 0)
+ {
+ 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);
+ }
+ return files;
}
+ @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);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
+ BufferedReader in = null;
try
{
- BufferedReader in = new BufferedReader(new FileReader(pdbentry
- .getFile()));
+ // TODO: cope with multiple PDB files in view
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -411,702 +765,226 @@ public class AppJmol extends GStructureViewer implements StructureListener,
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
}
}
+ @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);
- cap.setText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(pdbentry.getFile()));
+ try
+ {
+ cap.appendText(jmb.printMappings());
+ } 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.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null, null, 0, false);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
- 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.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle(), null, 0, false);
}
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(), null, 0, false);
}
if (im.getGraphics() != null)
{
- Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+ jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
im.writeImage();
}
}
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- jmolHistory(false);
- viewer.evalStringQuiet("select *;color chain");
- jmolHistory(true);
+ if (viewerColour.isSelected())
+ {
+ // disable automatic sequence colouring.
+ jmb.setColourBySequence(false);
+ }
}
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- jmolHistory(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
- jmolHistory(true);
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TurnColourScheme());
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new BuriedColourScheme());
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
- {
- jmolHistory(false);
- 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())
+ jmb.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
{
- 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() + "];");
+ _colourwith = new Vector();
}
-
- viewer.evalStringQuiet(command.toString());
- jmolHistory(true);
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- new UserDefinedColours(this, null);
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
-
- if (col != null)
- {
- jmolHistory(false);
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- jmolHistory(true);
- }
- }
- private void jmolHistory(boolean enable)
- {
- viewer.setBooleanProperty("history", enable);
- }
-
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
- {
- try
- {
- jalview.util.BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
- } catch (Exception ex)
+ if (jmb.isColourBySequence())
{
- }
- }
- String[] modelFileNames = null;
-
- // ////////////////////////////////
- // /StructureListener
- public String[] getPdbFile()
- {
- if (modelFileNames == null)
- {
- String mset[] = new String[viewer.getModelCount()];
- for (int i = 0; i < mset.length; i++)
+ if (!jmb.isLoadingFromArchive())
{
- try {
- String mname = viewer.getModelFileName(i);
- if (mname==null)
- {
- System.err.println("Model "+i+" has no filename!");
- continue;
- }
- File fpath = new File(mname);
- mset[i] = fpath.toString();
- } catch (Exception e)
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
{
- System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!");
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
}
}
- modelFileNames = mset;
- }
- return modelFileNames;
- }
-
- Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?");
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- // copied from AppJmol - will be refactored to binding eventually
- int pdbResNum;
- int mdlSep = strInfo.indexOf("/");
- int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
- if (chainSeparator == -1)
- {
- chainSeparator = strInfo.indexOf(".");
- if (mdlSep > -1 && mdlSep < chainSeparator)
- {
- chainSeparator1 = chainSeparator;
- chainSeparator = mdlSep;
- }
- }
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
-
- String chainId;
-
- if (strInfo.indexOf(":") > -1)
- chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
- else
- {
- chainId = " ";
- }
-
- String pdbfilename = pdbentry.getFile();
- if (mdlSep > -1)
- {
- if (chainSeparator1 == -1)
- {
- chainSeparator1 = strInfo.indexOf(".", mdlSep);
- }
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
- try
- {
- // recover PDB filename for the model hovered over.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
- } catch (Exception e)
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
{
+ jmb.colourBySequence(ap);
}
- ;
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
- lastMessage = strInfo;
-/*
- * Old Implementation based on Pattern regex.
- 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
- {
- chainId = " ";
}
- String mdlId = matcher.group(4);
- String pdbfilename = pdbentry.getFile();
-
- if (mdlId!=null && mdlId.length()>0)
- {
- try {
- // recover PDB filename for the model hovered over.
- pdbfilename = viewer.getModelFileName(new Integer(mdlId).intValue()-1);
- } catch (Exception e) {};
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
- }
- lastMessage = strInfo; */
}
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- int mdlNum = 1+getModelNum(pdbfile);
- if (mdlNum==0)
- {
- return;
- }
-
- jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum); // +modelNum
-
- if (!chain.equals(" "))
- {
- eval.append(":");
- resetLastRes.append(":");
- eval.append(chain);
- resetLastRes.append(chain);
- }
- // if (mdlNum != 0)
- {
- eval.append(" /" + (mdlNum));
- resetLastRes.append(" /" + (mdlNum));
- }
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.toString());
- jmolHistory(true);
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
-
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- public void updateColours(Object source)
+ @Override
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence((AlignmentPanel) source);
+ chainColour.setSelected(true);
+ jmb.colourByChain();
}
- // End StructureListener
- // //////////////////////////
-
- String lastCommand;
-
- FeatureRenderer fr = null;
-
- public void colourBySequence(AlignmentPanel sourceap)
- {
- this.ap = sourceap;
-
- if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
- return;
-
- String[] files = getPdbFile();
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
- {
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
-
- int lastPos = -1;
- for (int sp, s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
- {
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // No mapping to gaps in sequence.
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(asp, r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, asp, r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
- }
- }
- jmolHistory(false);
-
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- jmolHistory(true);
- lastCommand = command.toString();
- }
-
- StringBuffer condenseCommand(StringBuffer command, int pos)
+ @Override
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
-
- command.delete(0, sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
}
- // ///////////////////////////////
- // JmolStatusListener
-
- public String eval(String strEval)
+ @Override
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
- // System.out.println(strEval);
- // "# 'eval' is implemented only for the applet.";
- return null;
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
}
- public void createImage(String file, String type, int quality)
+ @Override
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
- System.out.println("JMOL CREATE IMAGE");
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
}
- public void notifyFileLoaded(String fullPathName, String fileName2,
- String modelName, String errorMsg, int modelParts)
+ @Override
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
- if (errorMsg != null)
- {
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
-
- fileLoadingError = null;
- modelFileNames = null;
-
- String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
- boolean modelsloaded=false;
- for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
- {
- String fileName = modelfilenames[modelnum];
-
- if (fileName != null)
- {
- modelsloaded=true;
- // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
- if (pdbentry.getFile().equals(fileName))
- {
- // TODO: do some checking using the modelPts number of parts against our
- // own estimate of the number of chains
- // FILE LOADED OK
- MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
- .getFile(), AppletFormatAdapter.FILE);
- Vector chains = new Vector();
- for (int i = 0; i < pdbFile.chains.size(); i++)
- {
- chains
- .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id));
- }
- setChainMenuItems(chains);
-
- if (!loadingFromArchive)
- {
- viewer
- .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
- }
- if (fr != null)
- fr.featuresAdded();
-
- loadingFromArchive = false;
- }
- else {
- // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
- // and try to find a home - either on a matching sequence or as a new sequence.
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
- "PDB");
- // parse pdb file into a chain, etc.
- // locate best match for pdb in associated views and add mapping to
- // ssm
- modelsloaded=true;
- }
- }
- }
- if (modelsloaded)
- {
- ssm.addStructureViewerListener(this);
- jmolpopup.updateComputedMenus();
- }
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
- public void sendConsoleEcho(String strEcho)
+ @Override
+ public void helixColour_actionPerformed(ActionEvent actionEvent)
{
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
}
- public void sendConsoleMessage(String strStatus)
+ @Override
+ public void strandColour_actionPerformed(ActionEvent actionEvent)
{
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
}
- public void notifyScriptTermination(String strStatus, int msWalltime)
+ @Override
+ public void turnColour_actionPerformed(ActionEvent actionEvent)
{
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
}
- public void handlePopupMenu(int x, int y)
+ @Override
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
- jmolpopup.show(x, y);
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
}
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
{
- notifyAtomPicked(iatom, strMeasure, null);
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
}
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
+ @Override
+ public void userColour_actionPerformed(ActionEvent actionEvent)
{
- if (strData != null)
- {
- Cache.log.info("Non null pick data string: " + strData
- + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
- }
- /*
- 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()));
-*/
- int chainSeparator = strInfo.indexOf(":");
- int p=0;
- if (chainSeparator == -1)
- chainSeparator = strInfo.indexOf(".");
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
- String mdlString="";
- if ((p=strInfo.indexOf(":")) > -1)
- picked += strInfo.substring(p + 1, strInfo
- .indexOf("."));
-
- if ((p=strInfo.indexOf("/"))> -1)
- {
- mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
- }
- picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
- jmolHistory(false);
- if (!atomsPicked.contains(picked))
- {
- // TODO: re-instate chain ID separator dependent labelling for both applet and application
-// 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);
- }
- jmolHistory(true);
- if (scriptWindow != null)
- {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
+ userColour.setSelected(true);
+ new UserDefinedColours(this, null);
}
- public void notifyAtomHovered(int atomIndex, String strInfo, String data)
+ @Override
+ public void backGround_actionPerformed(ActionEvent actionEvent)
{
- if (data != null)
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
+ if (col != null)
{
- Cache.log.info("Non null hover data string: " + data
- + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+ jmb.setBackgroundColour(col);
}
- mouseOverStructure(atomIndex, strInfo);
}
@Override
- public void showUrl(String url)
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher.openURL(url);
- } catch (IOException e)
+ jalview.util.BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
- // TODO: 2.6 : warn user if browser was not configured.
}
}
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
if (showConsole)
{
@@ -1116,15 +994,19 @@ public class AppJmol extends GStructureViewer implements StructureListener,
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;
@@ -1134,156 +1016,178 @@ public class AppJmol extends GStructureViewer implements StructureListener,
validate();
}
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
-
- // /End JmolStatusListener
- // /////////////////////////////
-
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
+ @Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
- g.getClipBounds(rectClip);
- if (viewer == null)
+ if (jmb != null && jmb.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("Retrieving PDB data....", 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.getPdbCount(); e++)
+ {
+ sb.append(jmb.getPdbEntry(e).getId());
+ if (e < jmb.getPdbCount() - 1)
+ {
+ sb.append(",");
+ }
+
+ if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
+ }
+ }
}
- else if (fileLoadingError != null)
+ 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("Error loading file..." + pdbentry.getId(), 20,
- currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
- viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
- String viewId = null;
-
- public String getViewId()
+ public void updateTitleAndMenus()
{
- if (viewId == null)
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
{
- viewId = System.currentTimeMillis() + "." + this.hashCode();
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
+
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
+ {
+ viewerActionMenu.setVisible(true);
+ }
+ if (!jmb.isLoadingFromArchive())
+ {
+ seqColour_actionPerformed(null);
}
- return viewId;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
@Override
- public String createImage(String fileName, String type,
- Object textOrBytes, int quality)
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
- // TODO Auto-generated method stub
- return null;
+ alignStructs_withAllAlignPanels();
}
- @Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ private void alignStructs_withAllAlignPanels()
{
- // TODO Auto-generated method stub
- return null;
+ if (getAlignmentPanel() == null)
+ {
+ return;
+ }
+ ;
+ if (_alignwith.size() == 0)
+ {
+ _alignwith.add(getAlignmentPanel());
+ }
+ ;
+ 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);
+
+ }
+
}
@Override
- public Hashtable getRegistryInfo()
+ public void setJalviewColourScheme(ColourSchemeI ucs)
{
- // TODO Auto-generated method stub
- return null;
+ jmb.setJalviewColourScheme(ucs);
+
}
- @Override
- public void notifyCallback(int type, Object[] data)
+ /**
+ *
+ * @param alignment
+ * @return first alignment panel displaying given alignment, or the default
+ * alignment panel
+ */
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
{
- try
+ for (AlignmentPanel ap : getAllAlignmentPanels())
{
- switch (type)
+ if (ap.av.getAlignment() == alignment)
{
- case JmolConstants.CALLBACK_LOADSTRUCT:
- notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5])
- .intValue());
-
- break;
- case JmolConstants.CALLBACK_PICK:
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
- (String) data[0]);
- // also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
- (String) data[0]);
- break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String) data[2], ((Integer) data[3])
- .intValue());
- break;
- case JmolConstants.CALLBACK_ECHO:
- sendConsoleEcho((String) data[1]);
- break;
- case JmolConstants.CALLBACK_MESSAGE:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
- break;
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_CLICK:
- default:
- System.err.println("Unhandled callback " + type + " " + data);
- break;
+ return ap;
}
- } catch (Exception e)
- {
- Cache.log.warn("Squashed Jmol callback handler error: ", e);
}
+ return getAlignmentPanel();
}
@Override
- public boolean notifyEnabled(int callbackPick)
+ public AAStructureBindingModel getBinding()
{
- switch (callbackPick)
- {
- case JmolConstants.CALLBACK_ECHO:
- case JmolConstants.CALLBACK_LOADSTRUCT:
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_MESSAGE:
- case JmolConstants.CALLBACK_PICK:
- case JmolConstants.CALLBACK_SCRIPT:
- case JmolConstants.CALLBACK_HOVER:
- case JmolConstants.CALLBACK_ERROR:
- return true;
- case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
- case JmolConstants.CALLBACK_MINIMIZATION:
- case JmolConstants.CALLBACK_RESIZE:
- case JmolConstants.CALLBACK_SYNC:
- }
- return false;
+ return this.jmb;
}
@Override
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
+ public String getStateInfo()
{
- Cache.log.debug("Ignoring set-callback request to associate "
- + callbackType + " with function " + callbackFunction);
+ return jmb == null ? null : jmb.viewer.getStateInfo();
+ }
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
}
}