/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.SwingUtilities;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.viewer.Viewer;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsModelI;
import jalview.api.SequenceRenderer;
import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AppJmol;
import jalview.gui.IProgressIndicator;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.AtomSpec;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.ws.dbsources.Pdb;
import javajs.util.BS;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
private String lastMessage;
/*
* when true, try to search the associated datamodel for sequences that are
* associated with any unknown structures in the Jmol view.
*/
private boolean associateNewStructs = false;
private Vector atomsPicked = new Vector<>();
private String lastCommand;
private boolean loadedInline;
private StringBuffer resetLastRes = new StringBuffer();
public Viewer jmolViewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
setStructureCommands(new JmolCommands());
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(),
* "", this);
*
* jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
*/
}
public JalviewJmolBinding(StructureSelectionManager ssm,
SequenceI[][] seqs, Viewer theViewer)
{
super(ssm, seqs);
jmolViewer = theViewer;
jmolViewer.setJmolStatusListener(this);
jmolViewer.addSelectionListener(this);
setStructureCommands(new JmolCommands());
}
/**
* construct a title string for the viewer window based on the data jalview
* knows about
*
* @return
*/
public String getViewerTitle()
{
return getViewerTitle("Jmol", true);
}
private String jmolScript(String script)
{
Console.debug(">>Jmol>> " + script);
String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
Console.debug("< executeCommand(StructureCommandI command,
boolean getReply)
{
if (command == null)
{
return null;
}
String cmd = command.getCommand();
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(cmd))
{
jmolScript(cmd + "\n");
}
jmolHistory(true);
lastCommand = cmd;
return null;
}
public void createImage(String file, String type, int quality)
{
System.out.println("JMOL CREATE IMAGE");
}
@Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
System.out.println("JMOL CREATE IMAGE");
return null;
}
@Override
public String eval(String strEval)
{
// System.out.println(strEval);
// "# 'eval' is implemented only for the applet.";
return null;
}
// End StructureListener
// //////////////////////////
@Override
public float[][] functionXY(String functionName, int x, int y)
{
return null;
}
@Override
public float[][][] functionXYZ(String functionName, int nx, int ny,
int nz)
{
// TODO Auto-generated method stub
return null;
}
/**
* map between index of model filename returned from getPdbFile and the first
* index of models from this file in the viewer. Note - this is not trimmed -
* use getPdbFile to get number of unique models.
*/
private int _modelFileNameMap[];
@Override
public synchronized String[] getStructureFiles()
{
if (jmolViewer == null)
{
return new String[0];
}
if (modelFileNames == null)
{
int modelCount = jmolViewer.ms.mc;
String filePath = null;
List mset = new ArrayList<>();
for (int i = 0; i < modelCount; ++i)
{
/*
* defensive check for null as getModelFileName can return null even when model
* count ms.mc is > 0
*/
filePath = jmolViewer.ms.getModelFileName(i);
if (filePath != null && !mset.contains(filePath))
{
mset.add(filePath);
}
}
if (!mset.isEmpty())
{
modelFileNames = mset.toArray(new String[mset.size()]);
}
}
return modelFileNames;
}
/**
* map from string to applet
*/
@Override
public Map getRegistryInfo()
{
// TODO Auto-generated method stub
return null;
}
// ///////////////////////////////
// JmolStatusListener
public void handlePopupMenu(int x, int y)
{
// jmolpopup.show(x, y);
// jmolpopup.jpiShow(x, y);
}
/**
* Highlight zero, one or more atoms on the structure
*/
@Override
public void highlightAtoms(List atoms)
{
if (atoms != null)
{
if (resetLastRes.length() > 0)
{
jmolScript(resetLastRes.toString());
resetLastRes.setLength(0);
}
for (AtomSpec atom : atoms)
{
highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
atom.getChain(), atom.getPdbFile());
}
}
}
// jmol/ssm only
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
String modelId = getModelIdForFile(pdbfile);
if (modelId.isEmpty())
{
return;
}
jmolHistory(false);
StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
selection.append("select ").append(String.valueOf(pdbResNum));
selection.append(":");
if (!chain.equals(" "))
{
selection.append(chain);
}
selection.append(" /").append(modelId);
cmd.append(selection).append(";wireframe 100;").append(selection)
.append(" and not hetero;").append("spacefill 200;select none");
resetLastRes.append(selection).append(";wireframe 0;").append(selection)
.append(" and not hetero; spacefill 0;");
jmolScript(cmd.toString());
jmolHistory(true);
}
private boolean debug = true;
private void jmolHistory(boolean enable)
{
jmolScript("History " + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)
{
loadedInline = true;
// TODO: re JAL-623
// viewer.loadInline(strModel, isAppend);
// could do this:
// construct fake fullPathName and fileName so we can identify the file
// later.
// Then, construct pass a reader for the string to Jmol.
// ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
// fileName, null, reader, false, null, null, 0);
jmolViewer.openStringInline(string);
}
protected void mouseOverStructure(int atomIndex, final String strInfo)
{
int pdbResNum;
int alocsep = strInfo.indexOf("^");
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;
}
}
// handle insertion codes
if (alocsep != -1)
{
pdbResNum = Integer.parseInt(
strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
}
else
{
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 = modelFileNames[0]; // default is first model
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.
int mnumber = Integer.valueOf(mdlId).intValue() - 1;
if (_modelFileNameMap != null)
{
int _mp = _modelFileNameMap.length - 1;
while (mnumber < _modelFileNameMap[_mp])
{
_mp--;
}
pdbfilename = modelFileNames[_mp];
}
else
{
if (mnumber >= 0 && mnumber < modelFileNames.length)
{
pdbfilename = modelFileNames[mnumber];
}
if (pdbfilename == null)
{
pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
}
} catch (Exception e)
{
}
}
/*
* highlight position on alignment(s); if some text is returned, show this as a
* second line on the structure hover tooltip
*/
String label = getSsm().mouseOverStructure(pdbResNum, chainId,
pdbfilename);
if (label != null)
{
// change comma to pipe separator (newline token for Jmol)
label = label.replace(',', '|');
StringTokenizer toks = new StringTokenizer(strInfo, " ");
StringBuilder sb = new StringBuilder();
sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
.append(chainId).append("/1");
sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
.append(toks.nextToken());
sb.append("|").append(label).append("\"");
executeCommand(new StructureCommand(sb.toString()), false);
}
}
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
if (strInfo.equals(lastMessage))
{
return;
}
lastMessage = strInfo;
if (data != null)
{
System.err.println("Ignoring additional hover info: " + data
+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
/*
* { if (history != null && strStatus != null &&
* !strStatus.equals("Script completed")) { history.append("\n" + strStatus); }
* }
*/
public void notifyAtomPicked(int atomIndex, String strInfo,
String strData)
{
/**
* this implements the toggle label behaviour copied from the original
* structure viewer, mc_view
*/
if (strData != null)
{
System.err.println("Ignoring additional pick data string " + strData);
}
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, 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))
{
jmolScript("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
{
jmolViewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
jmolHistory(true);
// TODO: in application this happens
//
// if (scriptWindow != null)
// {
// scriptWindow.sendConsoleMessage(strInfo);
// scriptWindow.sendConsoleMessage("\n");
// }
}
@Override
public void notifyCallback(CBK type, Object[] data)
{
/*
* ensure processed in AWT thread to avoid risk of deadlocks
*/
SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
processCallback(type, data);
}
});
}
/**
* Processes one callback notification from Jmol
*
* @param type
* @param data
*/
protected void processCallback(CBK type, Object[] data)
{
try
{
switch (type)
{
case LOADSTRUCT:
notifyFileLoaded((String) data[1], (String) data[2],
(String) data[3], (String) data[4],
((Integer) data[5]).intValue());
break;
case PICK:
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
// deliberate fall through
case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
break;
case SCRIPT:
notifyScriptTermination((String) data[2],
((Integer) data[3]).intValue());
break;
case ECHO:
sendConsoleEcho((String) data[1]);
break;
case MESSAGE:
sendConsoleMessage(
(data == null) ? ((String) null) : (String) data[1]);
break;
case ERROR:
// System.err.println("Ignoring error callback.");
break;
case SYNC:
case RESIZE:
refreshGUI();
break;
case MEASURE:
case CLICK:
default:
System.err.println(
"Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
{
System.err.println("Squashed Jmol callback handler error:");
e.printStackTrace();
}
}
@Override
public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
case ECHO:
case LOADSTRUCT:
case MEASURE:
case MESSAGE:
case PICK:
case SCRIPT:
case HOVER:
case ERROR:
return true;
default:
return false;
}
}
// incremented every time a load notification is successfully handled -
// lightweight mechanism for other threads to detect when they can start
// referrring to new structures.
private long loadNotifiesHandled = 0;
public long getLoadNotifiesHandled()
{
return loadNotifiesHandled;
}
public void notifyFileLoaded(String fullPathName, String fileName2,
String modelName, String errorMsg, int modelParts)
{
if (errorMsg != null)
{
fileLoadingError = errorMsg;
refreshGUI();
return;
}
// TODO: deal sensibly with models loaded inLine:
// modelName will be null, as will fullPathName.
// the rest of this routine ignores the arguments, and simply interrogates
// the Jmol view to find out what structures it contains, and adds them to
// the structure selection manager.
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
boolean notifyLoaded = false;
String[] modelfilenames = getStructureFiles();
if (modelfilenames == null)
{
// Jmol is still loading files!
return;
}
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
int oldm = 0;
for (int i = 0; i < oldmodels.length; i++)
{
for (int n = 0; n < modelfilenames.length; n++)
{
if (modelfilenames[n] == oldmodels[i])
{
oldmodels[i] = null;
break;
}
}
if (oldmodels[i] != null)
{
oldm++;
}
}
if (oldm > 0)
{
String[] oldmfn = new String[oldm];
oldm = 0;
for (int i = 0; i < oldmodels.length; i++)
{
if (oldmodels[i] != null)
{
oldmfn[oldm++] = oldmodels[i];
}
}
// deregister the Jmol instance for these structures - we'll add
// ourselves again at the end for the current structure set.
getSsm().removeStructureViewerListener(this, oldmfn);
}
}
refreshPdbEntries();
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
StructureFile pdb = null;
String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
{
// calculate essential attributes for the pdb data imported inline.
// prolly need to resolve modelnumber properly - for now just use our
// 'best guess'
pdbfile = jmolViewer.getData(
"" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
// model
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
addSequence(pe, getSequence()[pe]);
if (fileName == null)
{
if (false)
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
}
else
{
File fl = new File(getPdbEntry(pe).getFile());
matches = fl.equals(new File(fileName));
if (matches)
{
foundEntry = true;
// TODO: Jmol can in principle retrieve from CLASSLOADER but
// this
// needs
// to be tested. See mantis bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
protocol = DataSourceType.FILE;
}
} catch (Exception e)
{
} catch (Error e)
{
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
}
if (matches)
{
stashFoundChains(pdb, fileName);
notifyLoaded = true;
}
}
if (!foundEntry && associateNewStructs)
{
// 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 = jmolViewer.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
// if properly registered then
notifyLoaded = true;
}
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
// if (jmolpopup != null)
// {
// // potential for deadlock here:
// // jmolpopup.updateComputedMenus();
// }
if (!isLoadingFromArchive())
{
jmolScript(
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
getSsm().addStructureViewerListener(this);
if (notifyLoaded)
{
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
((AppJmol) getViewer()).getAlignmentPanel().av
.applyFeaturesStyle(colours);
}
refreshGUI();
loadNotifiesHandled++;
}
setLoadingFromArchive(false);
}
protected IProgressIndicator getIProgressIndicator()
{
return null;
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
}
public abstract void notifyScriptTermination(String strStatus,
int msWalltime);
/**
* display a message echoed from the jmol viewer
*
* @param strEcho
*/
public abstract void sendConsoleEcho(String strEcho); /*
* { showConsole(true);
*
* history.append("\n" + strEcho); }
*/
// /End JmolStatusListener
// /////////////////////////////
/**
* @param strStatus
* status message - usually the response received after a script
* executed
*/
public abstract void sendConsoleMessage(String strStatus);
@Override
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
System.err.println("Ignoring set-callback request to associate "
+ callbackType + " with function " + callbackFunction);
}
public void showHelp()
{
showUrl("http://wiki.jmol.org"
// BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
, "jmolHelp");
}
/**
* open the URL somehow
*
* @param target
*/
public abstract void showUrl(String url, String target);
/**
* called to show or hide the associated console window container.
*
* @param show
*/
public abstract void showConsole(boolean show);
public static Viewer getJmolData(JmolParser jmolParser)
{
return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
"-x -o -n", jmolParser);
}
/**
*
*
*
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* in applet context)
* @param htmlName
* @param documentBase
* @param codeBase
* @param commandOptions
*/
public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions)
{
allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
codeBase, commandOptions, null, null);
}
/**
*
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* in applet context)
* @param htmlName
* @param documentBase
* @param codeBase
* @param commandOptions
* @param consolePanel
* - panel to contain Jmol console
* @param buttonsToShow
* - buttons to show on the console, in order
*/
public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions, final Container consolePanel,
String buttonsToShow)
{
System.err.println("Allocating Jmol Viewer: " + commandOptions);
if (commandOptions == null)
{
commandOptions = "";
}
jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null),
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
try
{
console = createJmolConsole(consolePanel, buttonsToShow);
} catch (Throwable e)
{
System.err.println("Could not create Jmol application console. "
+ e.getMessage());
e.printStackTrace();
}
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
}
}
protected abstract JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow);
// BH 2018 -- Jmol console is not working due to problems with styled
// documents.
protected org.jmol.api.JmolAppConsoleInterface console = null;
@Override
public int[] resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
return null;
}
/**
*
*/
protected void closeConsole()
{
if (console != null)
{
try
{
console.setVisible(false);
} catch (Error e)
{
} catch (Exception x)
{
}
;
console = null;
}
}
/**
* ComponentListener method
*/
@Override
public void componentMoved(ComponentEvent e)
{
}
/**
* ComponentListener method
*/
@Override
public void componentResized(ComponentEvent e)
{
}
/**
* ComponentListener method
*/
@Override
public void componentShown(ComponentEvent e)
{
showConsole(true);
}
/**
* ComponentListener method
*/
@Override
public void componentHidden(ComponentEvent e)
{
showConsole(false);
}
@Override
protected String getModelIdForFile(String pdbFile)
{
if (modelFileNames == null)
{
return "";
}
for (int i = 0; i < modelFileNames.length; i++)
{
if (modelFileNames[i].equalsIgnoreCase(pdbFile))
{
return String.valueOf(i + 1);
}
}
return "";
}
@Override
protected ViewerType getViewerType()
{
return ViewerType.JMOL;
}
@Override
protected String getModelId(int pdbfnum, String file)
{
return String.valueOf(pdbfnum + 1);
}
/**
* Returns ".spt" - the Jmol session file extension
*
* @return
* @see https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
@Override
public String getSessionFileExtension()
{
return ".spt";
}
@Override
public void selectionChanged(BS arg0)
{
// TODO Auto-generated method stub
}
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
{
return new jalview.gui.SequenceRenderer(avp.getAlignViewport());
}
@Override
public String getHelpURL()
{
return "http://wiki.jmol.org"; // BH 2018
}
}