X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=4f833bc83c5a46ef9b238bade084c377b7c11639;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=085e50dd8f444fe17ff77ea13a2338b90b7242f9;hpb=ce89ec35928a6cb2f05a655c44c39a0249beb2d6;p=jalview.git diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java index 085e50d..4f833bc 100644 --- a/src/jalview/javascript/MouseOverStructureListener.java +++ b/src/jalview/javascript/MouseOverStructureListener.java @@ -1,305 +1,321 @@ -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: - * - * - * @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 - - } - -} +/* + * 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[] getPdbFile() + { + 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, 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 AlignFrame getAlignFrame() + { + // associated with all alignframes, always. + return null; + } + + @Override + public String getListenerFunction() + { + 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; + } + +}