2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.javascript;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.appletgui.AlignFrame;
27 import jalview.bin.JalviewLite;
28 import jalview.datamodel.SequenceI;
29 import jalview.ext.jmol.JmolCommands;
30 import jalview.structure.AtomSpec;
31 import jalview.structure.StructureListener;
32 import jalview.structure.StructureMapping;
33 import jalview.structure.StructureSelectionManager;
34 import jalview.util.HttpUtils;
36 import java.util.ArrayList;
37 import java.util.List;
40 * Propagate events involving PDB structures associated with sequences to a
41 * javascript function. Generally, the javascript handler is called with a
42 * series of arguments like (eventname, ... ). As of Jalview 2.7, the following
43 * different types of events are supported:
45 * <li>mouseover: javascript function called with arguments
48 * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue
49 * number moused over), String(atom index corresponding to residue)]
53 * <li>colourstruct: javascript function called with arguments
56 * ['colourstruct',String(alignment view id),String(number of javascript message
57 * chunks to collect),String(length of first chunk in set of messages - or zero
62 * The message contains a series of Jmol script commands that will colour
63 * structures according to their associated sequences in the current view. Use
65 * .javascript.JalviewLiteJsApi.getJsMessage('colourstruct',String(alignment
66 * view id)) to retrieve successive chunks of the message.</li>
69 * @author Jim Procter (jprocter)
72 public class MouseOverStructureListener extends JSFunctionExec
73 implements JsCallBack, StructureListener
80 public MouseOverStructureListener(JalviewLite jalviewLite,
81 String listener, String[] modelList)
84 _listenerfn = listener;
88 for (int i = 0; i < modelSet.length; i++)
90 modelSet[i] = resolveModelFile(modelSet[i]);
96 * Returns the first out of: file, file prefixed by document base, or file
97 * prefixed by codebase which can be resolved to a valid URL. If none can,
98 * returns the input parameter value.
102 public String resolveModelFile(String file)
104 // TODO reuse JalviewLite.LoadingThread.addProtocol instead
105 if (HttpUtils.isValidUrl(file))
110 String db = jvlite.getDocumentBase().toString();
111 db = db.substring(0, db.lastIndexOf("/"));
112 String docBaseFile = db + "/" + file;
113 if (HttpUtils.isValidUrl(docBaseFile))
118 String cb = jvlite.getCodeBase() + file;
119 if (HttpUtils.isValidUrl(cb))
128 public String[] getStructureFiles()
133 public void mouseOverStructure(int atomIndex, String strInfo)
136 // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
138 // TODO Auto-generated method stub
143 public void highlightAtoms(List<AtomSpec> atoms)
145 for (AtomSpec atom : atoms)
149 // TODO is this right? StructureSelectionManager passes pdbFile as the
150 // field that is interpreted (in 2.8.2) as pdbId?
151 // JBPComment: yep - this is right! the Javascript harness uses the
152 // absolute pdbFile URI to locate the PDB file in the external viewer
153 executeJavascriptFunction(_listenerfn,
155 { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
156 "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
157 } catch (Exception ex)
159 System.err.println("Couldn't execute callback with " + _listenerfn
160 + " for atomSpec: " + atom);
161 ex.printStackTrace();
167 public synchronized void updateColours(Object srce)
169 final Object source = srce;
170 StructureSelectionManager ssm = StructureSelectionManager
171 .getStructureSelectionManager(jvlite);
173 if (JalviewLite.debug)
176 this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
180 if (source instanceof jalview.api.AlignmentViewPanel)
182 SequenceI[][] sequence = new SequenceI[modelSet.length][];
183 for (int m = 0; m < modelSet.length; m++)
185 StructureMapping[] sm = ssm.getMapping(modelSet[m]);
186 if (sm != null && sm.length > 0)
188 sequence[m] = new SequenceI[sm.length];
189 for (int i = 0; i < sm.length; i++)
191 sequence[m][i] = sm[i].getSequence();
196 sequence[m] = new SequenceI[0];
200 // System.err.println("Mapped '" + modelSet[m] + "' to "
201 // + sequence[m].length + " sequences.");
205 SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
206 .getSequenceRenderer();
207 FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
208 .isShowSequenceFeatures()
209 ? new jalview.appletgui.FeatureRenderer(
210 ((jalview.appletgui.AlignmentPanel) source).av)
214 ((jalview.appletgui.FeatureRenderer) fr).transferSettings(
215 ((jalview.appletgui.AlignmentPanel) source)
216 .getFeatureRenderer());
220 // Form a colour command from the given alignment panel for each distinct
222 ArrayList<String[]> ccomands = new ArrayList<>();
223 ArrayList<String> pdbfn = new ArrayList<>();
224 String[] colcommands = new JmolCommands()
225 .colourBySequence(ssm, modelSet, sequence, sr,
226 (AlignmentViewPanel) source);
227 if (colcommands == null)
232 // for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
233 for (String command : colcommands)
235 // sz += ccset.commands.length;
236 // ccomands.add(command); // ccset.commands);
237 // pdbfn.add(ccset.mapping);
240 String mclass, mhandle;
241 String ccomandset[] = new String[sz];
243 for (String[] ccset : ccomands)
245 System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
248 if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
249 mhandle = ((jalview.appletgui.AlignmentPanel) source).av
253 jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
254 // and notify javascript handler
255 String st[] = new String[] { "colourstruct",
256 "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
257 "" + ccomandset.length, jvlite.arrayToSeparatorList(
258 pdbfn.toArray(new String[pdbfn.size()])) };
261 executeJavascriptFunction(true, _listenerfn, st);
262 } catch (Exception ex)
264 System.err.println("Couldn't execute callback with " + _listenerfn
265 + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
266 + "," + st[3] + "}"); // + ","+st[4]+"\n");
267 ex.printStackTrace();
272 * new Thread(new Runnable() { public void run() { // and send to
273 * javascript handler String st[] = new String[0]; int i = 0; for (String
274 * colcommand : colcommands) { // do sync execution for each chunk try {
275 * executeJavascriptFunction( false, _listenerfn, st = new String[] {
276 * "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
277 * .getViewId(), handle, "" }); } catch (Exception ex) {
278 * System.err.println("Couldn't execute callback with " + _listenerfn +
279 * " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
280 * "\n"); ex.printStackTrace();
289 public AlignFrame getAlignFrame()
291 // associated with all alignframes, always.
296 public String getListenerFunction()
302 public void releaseReferences(Object svl)
305 // TODO Auto-generated method stub
310 public boolean isListeningFor(SequenceI seq)