/*
- * 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.regex.*;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
+import java.util.Locale;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Console;
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.*;
-
-
-public class AppJmol
- extends GStructureViewer
- implements StructureListener, JmolStatusListener, Runnable
-
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.fts.service.alphafold.AlphafoldRestClient;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structure.StructureCommand;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class AppJmol extends StructureViewerBase
{
- 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);
-
- colourBySequence = false;
- seqColour.setSelected(false);
-
- jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- bounds.width,bounds.height);
-
- initJmol(loadStatus);
-
- this.addInternalFrameListener(new InternalFrameAdapter()
- {
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
- {
- closeViewer();
- }
- });
- }
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
-public synchronized void addSequence(SequenceI [] seq)
- {
- Vector v = new Vector();
- for(int i=0; i<sequence.length; i++)
- v.addElement(sequence[i]);
+ private static final String SPACE = " ";
- for(int i=0; i<seq.length; i++)
- if(!v.contains(seq[i]))
- v.addElement(seq[i]);
+ private static final String QUOTE = "\"";
- SequenceI [] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
- }
+ AppJmolBinding jmb;
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String [] chains, AlignmentPanel ap)
- {
- //////////////////////////////////
- //Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .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);
+ JPanel scriptWindow;
- if (option == JOptionPane.YES_OPTION)
- {
- StructureSelectionManager.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
- // the exisiting array
- JInternalFrame [] frames = Desktop.instance.getAllFrames();
+ JSplitPane splitPane;
- 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;
- }
- }
- }
+ RenderPanel renderPanel;
- return;
- }
+ /**
+ *
+ * @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(StructureViewerModel viewerModel, AlignmentPanel ap,
+ String sessionFile, String viewid)
+ {
+ Map<File, StructureData> pdbData = viewerModel.getFileData();
+ PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()];
+ SequenceI[][] seqs = new SequenceI[pdbData.size()][];
+ int i = 0;
+ for (StructureData data : pdbData.values())
+ {
+ PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+ PDBEntry.Type.PDB, data.getFilePath());
+ pdbentrys[i] = pdbentry;
+ List<SequenceI> sequencesForPdb = data.getSeqList();
+ seqs[i] = sequencesForPdb
+ .toArray(new SequenceI[sequencesForPdb.size()]);
+ i++;
}
- ///////////////////////////////////
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
+ // TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
- jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400);
-
- if (pdbentry.getFile() != null)
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (viewerModel.isAlignWithPanel())
{
- initJmol("load \""+pdbentry.getFile()+"\"");
+ useAlignmentPanelForSuperposition(ap);
}
- else
+ initMenus();
+ boolean useToColour = viewerModel.isColourWithAlignPanel();
+ boolean leaveColouringToJmol = viewerModel.isColourByViewer();
+ if (leaveColouringToJmol || !useToColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (useToColour)
{
- Thread worker = new Thread(this);
- worker.start();
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
}
+ this.setBounds(viewerModel.getX(), viewerModel.getY(),
+ viewerModel.getWidth(), viewerModel.getHeight());
+ setViewId(viewid);
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("load FILES ").append(QUOTE)
+ .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE);
+ initJmol(cmd.toString());
}
-
- void initJmol(String command)
- {
- renderPanel = new RenderPanel();
-
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":" +
- pdbentry.getId());
-
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
- }
-
- this.setTitle(title.toString());
-
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter());
-
-
- viewer.setAppletContext("", null, null, "");
-
- viewer.setJmolStatusListener(this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer);
-
- viewer.evalStringQuiet(command);
- }
-
-
- void setChainMenuItems(Vector chains)
+ @Override
+ protected void initMenus()
{
- chainMenu.removeAll();
-
- JMenuItem menuItem = new JMenuItem("All");
- menuItem.addActionListener(new ActionListener()
- {
- 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;
- }
- });
+ super.initMenus();
- chainMenu.add(menuItem);
-
- for (int c = 0; c < chains.size(); c++)
- {
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
- menuItem.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- centerViewer();
- }
- });
-
- chainMenu.add(menuItem);
- }
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
- boolean allChainsSelected = false;
- void centerViewer()
+ /**
+ * display a single PDB structure in a new Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ final AlignmentPanel ap)
{
- StringBuffer cmd = new StringBuffer();
- 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 ");
- }
- }
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
+ setProgressIndicator(ap.alignFrame);
- viewer.evalStringQuiet("select *;restrict "
- +cmd+";cartoon;center "+cmd);
+ openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+ new SequenceI[][]
+ { seq });
}
- void closeViewer()
+ private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+ PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
{
- 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());
- }
+ setProgressIndicator(ap.alignFrame);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
- public void run()
- {
- try
+ alignAddedStructures = alignAdded;
+ if (pdbentrys.length > 1)
{
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
- initJmol("load "+pdbentry.getFile());
+ useAlignmentPanelForSuperposition(ap);
}
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ this.addInternalFrameListener(new InternalFrameAdapter()
{
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ( (data = in.readLine()) != null)
- {
- if (
- ! (data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)
- )
- {
- out.println(data);
- }
- }
- out.close();
- }
- catch (Exception ex)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- ex.printStackTrace();
+ closeViewer(false);
}
- }
- }
+ });
- 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())
- );
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * create a new Jmol containing several structures optionally superimposed
+ * using the given alignPanel.
+ *
+ * @param ap
+ * @param alignAdded
+ * - true to superimpose
+ * @param pe
+ * @param seqs
*/
- public void eps_actionPerformed(ActionEvent e)
+ public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+ SequenceI[][] seqs)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ openNewJmol(ap, alignAdded, pe, seqs);
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
- void makePDBImage(int type)
+ void initJmol(String command)
{
- int width = getWidth();
- int height = getHeight();
-
- jalview.util.ImageMaker im;
-
- 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);
- }
- else
+ 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)
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.EPS,
- "Make EPS file from view",
- width, height,
- null, this.getTitle());
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
}
- if (im.getGraphics() != null)
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
{
- Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(),
- rect.getSize(), rect);
- im.writeImage();
+ command = "";
}
+ jmb.executeCommand(new StructureCommand(command), false);
+ jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
+ jmb.setFinishedInit(true);
}
-
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color chain");
- }
-
- 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");
- }
-
- 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)
+ @Override
+ public void run()
{
- 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())
+ _started = true;
+ try
{
- 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());
- }
-
- 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)
+ List<String> files = jmb.fetchPdbFiles(this);
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
{
- viewer.evalStringQuiet("background ["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ _started = false;
+ worker = null;
}
}
-
- 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)
+ /**
+ * 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<String> files)
{
- 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
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
{
- chainId = " ";
+ fileList.append(SPACE).append(QUOTE)
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
+ String filesString = fileList.toString();
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- 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)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
-
- if (resetLastRes.length() > 0)
+ if (!addingStructures)
{
- viewer.evalStringQuiet(resetLastRes.toString());
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Console.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Console.error("Couldn't open Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
+ }
}
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
-
- if (!chain.equals(" "))
+ else
{
- eval.append(":" + chain);
- resetLastRes.append(":" + chain);
- }
-
- 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;
-
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- public void updateColours(Object source)
- {
- colourBySequence( (AlignmentPanel) source);
- }
-
-
-//End StructureListener
-////////////////////////////
-
- String lastCommand;
- FeatureRenderer fr=null;
- public void colourBySequence(AlignmentPanel sourceap)
- {
- this.ap = sourceap;
-
- if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final StructureCommand command = new StructureCommand(cmd.toString());
+ lastnotify = jmb.getLoadNotifiesHandled();
- if (mapping.length < 1)
- return;
-
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
- {
- showFeatures = true;
- if (fr == null)
+ try
{
- fr = new jalview.gui.FeatureRenderer(ap);
+ jmb.executeCommand(command, false);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Console.debug("File locations are " + filesString);
+ return;
+ } catch (Exception ex)
+ {
+ Console.error("Couldn't add files to Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
}
- StringBuffer command = new StringBuffer();
-
- int lastPos = -1;
- for (int sp,s = 0; s < sequence.length; s++)
+ // 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.getStructureFiles() != null
+ && jmb.getStructureFiles().length == files.size()))
{
- for (int m = 0; m < mapping.length; m++)
+ try
{
- 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);
-
- 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() + "]");
+ Console.debug("Waiting around for jmb notify.");
+ waitTotal += waitFor;
- }
- break;
- }
+ // Thread.sleep() throws an exception in JS
+ Thread.sleep(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.getStructureFiles();
+ break;
}
}
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- lastCommand = command.toString();
- }
-
- StringBuffer condenseCommand(StringBuffer command, int pos)
- {
- StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
-
- command.delete(0, sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentViewPanel ap : _colourwith)
{
- start = command.substring(0,command.indexOf("-"));
+ jmb.updateColours(ap);
}
- else
+ // do superposition if asked to
+ if (alignAddedStructures)
{
- start = command.substring(0, command.indexOf(":"));
+ alignAddedStructures();
}
-
- sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
-
- return sb;
+ addingStructures = false;
}
- /////////////////////////////////
- //JmolStatusListener
-
- public String eval(String strEval)
- {
- // System.out.println(strEval);
- //"# 'eval' is implemented only for the applet.";
- return null;
- }
-
- public void createImage(String file, String type, int quality)
- {
- System.out.println("JMOL CREATE IMAGE");
- }
-
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {}
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg)
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
{
- if(errorMsg!=null)
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- fileLoadingError = errorMsg;
- repaint();
- return;
- }
-
- fileLoadingError = null;
-
- if (fileName != null)
- {
-
- //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++)
+ @Override
+ public void run()
{
- chains.addElement(((MCview.PDBChain)pdbFile.chains.elementAt(i)).id);
- }
- setChainMenuItems(chains);
-
- jmolpopup.updateComputedMenus();
-
- if(!loadingFromArchive)
- {
- viewer.evalStringQuiet(
- "select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
+ if (jmb.jmolViewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructsWithAllAlignPanels();
+ }
}
- if (fr!=null)
- fr.featuresAdded();
-
- 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)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- 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)
+ /**
+ * Outputs the Jmol viewer image as an image file, after prompting the user to
+ * choose a file and (for EPS) choice of Text or Lineart character rendering
+ * (unless a preference for this is set)
+ *
+ * @param type
+ */
+ @Override
+ public void makePDBImage(ImageMaker.TYPE type)
{
- notifyAtomPicked(iatom, strMeasure);
+ int width = getWidth();
+ int height = getHeight();
+ ImageWriterI writer = new ImageWriterI()
+ {
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ jmb.jmolViewer.renderScreenImage(g, width, height);
+ }
+ };
+ String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
+ ImageExporter exporter = new ImageExporter(writer,
+ getProgressIndicator(), type, getTitle());
+ exporter.doExport(null, this, width, height, view);
}
- public void notifyNewDefaultModeMeasurement(int count, String strInfo)
- {}
-
- public void notifyAtomPicked(int atomIndex, String strInfo)
+ @Override
+ public void showHelp_actionPerformed()
{
- 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+=".CA";
-
-
- if (!atomsPicked.contains(picked))
+ try
{
- if(chainId!=null)
- viewer.evalString("select "+picked+";label %n %r:%c");
- else
- viewer.evalString("select "+picked+";label %n %r");
- atomsPicked.addElement(picked);
- }
- else
+ BrowserLauncher // BH 2018
+ .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
{
- viewer.evalString("select "+picked+";label off");
- atomsPicked.removeElement(picked);
+ System.err.println("Show Jmol help failed with: " + ex.getMessage());
}
-
- if (scriptWindow != null)
- {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo)
- {
- mouseOverStructure(atomIndex, strInfo);
}
- public void sendSyncScript(String script, String appletName)
- {}
-
- public void showUrl(String url)
- {}
-
+ @Override
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
-
- if(showConsole)
+ if (showConsole)
{
- if(splitPane==null)
+ 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();
}
- splitPane.setDividerLocation(getHeight()-200);
- splitPane.validate();
}
else
{
if (splitPane != null)
+ {
splitPane.setVisible(false);
+ }
splitPane = null;
validate();
}
- public float functionXY(String functionName, int x, int y)
- {
- return 0;
- }
-
- ///End JmolStatusListener
- ///////////////////////////////
-
-
- class RenderPanel
- extends JPanel
+ 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.hasFileLoadingError())
{
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.jmolViewer == 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.jmolViewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
+ @Override
+ public AAStructureBindingModel getBinding()
+ {
+ return this.jmb;
+ }
+
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
+ @Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
}
git://source.jalview.org / jalview.git / blobdiff