/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*******************************************************************************/
package jalview.javascript;
import java.awt.Color;
import java.util.ArrayList;
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.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
/**
* 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++)
{
// resolve a real filename
try
{
if (new java.net.URL(modelSet[i]).openConnection() != null)
{
continue;
}
} catch (Exception x)
{
}
;
try
{
String db = jvlite.getDocumentBase().toString();
db = db.substring(0, db.lastIndexOf("/"));
if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
{
modelSet[i] = db + "/" + modelSet[i];
continue;
}
} catch (Exception x)
{
}
;
try
{
if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
.openConnection() != null)
{
modelSet[i] = jvlite.getCodeBase() + modelSet[i];
continue;
}
} catch (Exception x)
{
}
;
}
}
}
@Override
public String[] getPdbFile()
{
return modelSet;
}
@Override
public void mouseOverStructure(int atomIndex, String strInfo)
{
// StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
// chain, pdbfile)
// TODO Auto-generated method stub
}
@Override
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbId)
{
String[] st = new String[0];
try
{
executeJavascriptFunction(_listenerfn, st = new String[]
{ "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
"" + atomIndex });
} 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();
}
}
@Override
public synchronized void updateColours(Object srce)
{
final Object source = srce;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(jvlite);
// if (jvlite.debug)
// {
// 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
.getShowSequenceFeatures() ? 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, fr,
((AlignmentViewPanel) source).getAlignment());
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 Color getColour(int atomIndex, int pdbResNum, String chain,
String pdbId)
{
return null;
}
@Override
public AlignFrame getAlignFrame()
{
// associated with all alignframes, always.
return null;
}
@Override
public String getListenerFunction()
{
return _listenerfn;
}
public void finalise()
{
jvlite=null;
super.finalize();
}
@Override
public void releaseReferences(Object svl)
{
// TODO Auto-generated method stub
}
}