/*
* 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.javascript;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.appletgui.AlignFrame;
import jalview.bin.JalviewLite;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolCommands;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import java.util.ArrayList;
import java.util.List;
/**
* Propagate events involving PDB structures associated with sequences to a
* javascript function. Generally, the javascript handler is called with a
* series of arguments like (eventname, ... ). As of Jalview 2.7, the following
* different types of events are supported:
*
* - mouseover: javascript function called with arguments
*
*
* ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue
* number moused over), String(atom index corresponding to residue)]
*
*
*
* - colourstruct: javascript function called with arguments
*
*
* ['colourstruct',String(alignment view id),String(number of javascript message
* chunks to collect),String(length of first chunk in set of messages - or zero
* for null message)]
*
*
*
* The message contains a series of Jmol script commands that will colour
* structures according to their associated sequences in the current view. Use
* jalview
* .javascript.JalviewLiteJsApi.getJsMessage('colourstruct',String(alignment
* view id)) to retrieve successive chunks of the message.
*
*
* @author Jim Procter (jprocter)
*
*/
public class MouseOverStructureListener extends JSFunctionExec
implements JsCallBack, StructureListener
{
String _listenerfn;
String[] modelSet;
public MouseOverStructureListener(JalviewLite jalviewLite,
String listener, String[] modelList)
{
super(jalviewLite);
_listenerfn = listener;
modelSet = modelList;
if (modelSet != null)
{
for (int i = 0; i < modelSet.length; i++)
{
modelSet[i] = resolveModelFile(modelSet[i]);
}
}
}
/**
* Returns the first out of: file, file prefixed by document base, or file
* prefixed by codebase which can be resolved to a valid URL. If none can,
* returns the input parameter value.
*
* @param file
*/
public String resolveModelFile(String file)
{
// TODO reuse JalviewLite.LoadingThread.addProtocol instead
if (HttpUtils.isValidUrl(file))
{
return file;
}
String db = jvlite.getDocumentBase().toString();
db = db.substring(0, db.lastIndexOf("/"));
String docBaseFile = db + "/" + file;
if (HttpUtils.isValidUrl(docBaseFile))
{
return docBaseFile;
}
String cb = jvlite.getCodeBase() + file;
if (HttpUtils.isValidUrl(cb))
{
return cb;
}
return file;
}
@Override
public String[] getStructureFiles()
{
return modelSet;
}
public void mouseOverStructure(int atomIndex, String strInfo)
{
// StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
// chain, pdbfile)
// TODO Auto-generated method stub
}
@Override
public void highlightAtoms(List atoms)
{
for (AtomSpec atom : atoms)
{
try
{
// TODO is this right? StructureSelectionManager passes pdbFile as the
// field that is interpreted (in 2.8.2) as pdbId?
// JBPComment: yep - this is right! the Javascript harness uses the
// absolute pdbFile URI to locate the PDB file in the external viewer
executeJavascriptFunction(_listenerfn,
new String[]
{ "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
"" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
} catch (Exception ex)
{
System.err.println("Couldn't execute callback with " + _listenerfn
+ " for atomSpec: " + atom);
ex.printStackTrace();
}
}
}
@Override
public synchronized void updateColours(Object srce)
{
final Object source = srce;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(jvlite);
if (JalviewLite.debug)
{
System.err.println(
this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
ssm.reportMapping();
}
if (source instanceof jalview.api.AlignmentViewPanel)
{
SequenceI[][] sequence = new SequenceI[modelSet.length][];
for (int m = 0; m < modelSet.length; m++)
{
StructureMapping[] sm = ssm.getMapping(modelSet[m]);
if (sm != null && sm.length > 0)
{
sequence[m] = new SequenceI[sm.length];
for (int i = 0; i < sm.length; i++)
{
sequence[m][i] = sm[i].getSequence();
}
}
else
{
sequence[m] = new SequenceI[0];
}
// if (jvlite.debug)
// {
// System.err.println("Mapped '" + modelSet[m] + "' to "
// + sequence[m].length + " sequences.");
// }
}
SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
.getSequenceRenderer();
FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
.isShowSequenceFeatures()
? new jalview.appletgui.FeatureRenderer(
((jalview.appletgui.AlignmentPanel) source).av)
: null;
if (fr != null)
{
((jalview.appletgui.FeatureRenderer) fr).transferSettings(
((jalview.appletgui.AlignmentPanel) source)
.getFeatureRenderer());
}
;
// Form a colour command from the given alignment panel for each distinct
// structure
ArrayList ccomands = new ArrayList();
ArrayList pdbfn = new ArrayList();
StructureMappingcommandSet[] colcommands = JmolCommands
.getColourBySequenceCommand(ssm, modelSet, sequence, sr,
(AlignmentViewPanel) source);
if (colcommands == null)
{
return;
}
int sz = 0;
for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
{
sz += ccset.commands.length;
ccomands.add(ccset.commands);
pdbfn.add(ccset.mapping);
}
String mclass, mhandle;
String ccomandset[] = new String[sz];
sz = 0;
for (String[] ccset : ccomands)
{
System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
sz += ccset.length;
}
if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
mhandle = ((jalview.appletgui.AlignmentPanel) source).av
.getViewId(),
ccomandset))
{
jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
// and notify javascript handler
String st[] = new String[] { "colourstruct",
"" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
"" + ccomandset.length, jvlite.arrayToSeparatorList(
pdbfn.toArray(new String[pdbfn.size()])) };
try
{
executeJavascriptFunction(true, _listenerfn, st);
} catch (Exception ex)
{
System.err.println("Couldn't execute callback with " + _listenerfn
+ " using args { " + st[0] + ", " + st[1] + ", " + st[2]
+ "," + st[3] + "}"); // + ","+st[4]+"\n");
ex.printStackTrace();
}
}
/*
* new Thread(new Runnable() { public void run() { // and send to
* javascript handler String st[] = new String[0]; int i = 0; for (String
* colcommand : colcommands) { // do sync execution for each chunk try {
* executeJavascriptFunction( false, _listenerfn, st = new String[] {
* "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
* .getViewId(), handle, "" }); } catch (Exception ex) {
* System.err.println("Couldn't execute callback with " + _listenerfn +
* " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
* "\n"); ex.printStackTrace();
*
* } } } }).start();
*/
}
}
@Override
public AlignFrame getAlignFrame()
{
// associated with all alignframes, always.
return null;
}
@Override
public String getListenerFunction()
{
return _listenerfn;
}
@Override
public void releaseReferences(Object svl)
{
// TODO Auto-generated method stub
}
@Override
public boolean isListeningFor(SequenceI seq)
{
return true;
}
}