+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.javascript;
-import java.awt.Color;
-
+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:
+ * <ul>
+ * <li>mouseover: javascript function called with arguments
+ *
+ * <pre>
+ * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue
+ * number moused over), String(atom index corresponding to residue)]
+ * </pre>
+ *
+ * </li>
+ * <li>colourstruct: javascript function called with arguments
+ *
+ * <pre>
+ * ['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)]
+ * </pre>
+ *
+ * <br>
+ * 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.</li>
+ * </ul>
+ *
+ * @author Jim Procter (jprocter)
+ *
+ */
public class MouseOverStructureListener extends JSFunctionExec implements
JsCallBack, StructureListener
{
String _listenerfn;
- public MouseOverStructureListener(JalviewLite applet, String listenerCb)
+
+ 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)
{
- super(applet);
- _listenerfn = listenerCb;
-
+ // 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[] getPdbFile()
{
- // TODO Auto-generated method stub
- return null;
+ return modelSet;
}
- @Override
public void mouseOverStructure(int atomIndex, String strInfo)
{
-
- // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex, chain, pdbfile)
+
+ // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
+ // chain, pdbfile)
// TODO Auto-generated method stub
}
@Override
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbId)
+ public void highlightAtoms(List<AtomSpec> atoms)
{
- String[] st=new String[0];
- try {
- executeJavascriptFunction(_listenerfn, st = new String[] { "mouseover",""+pdbId, ""+chain, ""+(pdbResNum), ""+atomIndex});
- } catch (Exception ex)
+ for (AtomSpec atom : atoms)
{
- System.err.println("Couldn't execute callback with "+_listenerfn+" using args { "+st[0]+", "+st[1]+", "+st[2]+","+st[3]+"\n");
- ex.printStackTrace();
-
+ 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 void updateColours(Object source)
+ public synchronized void updateColours(Object srce)
{
- // TODO Auto-generated method stub
+ 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<String[]> ccomands = new ArrayList<String[]>();
+ ArrayList<String> pdbfn = new ArrayList<String>();
+ 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
{
return _listenerfn;
}
+
+ public void finalize() throws Throwable
+ {
+ jvlite = null;
+ super.finalize();
+ }
+
@Override
public void releaseReferences(Object svl)
{
+
// TODO Auto-generated method stub
-
+
+ }
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
}
}
git://source.jalview.org / jalview.git / blobdiff