-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
- *******************************************************************************/
-package jalview.javascript;\r
-\r
-import java.awt.Color;\r
-import java.util.ArrayList;\r
-\r
-import jalview.api.AlignmentViewPanel;\r
-import jalview.api.FeatureRenderer;\r
-import jalview.api.SequenceRenderer;\r
-import jalview.appletgui.AlignFrame;\r
-import jalview.bin.JalviewLite;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.ext.jmol.JmolCommands;\r
-import jalview.structure.StructureListener;\r
-import jalview.structure.StructureMapping;\r
-import jalview.structure.StructureMappingcommandSet;\r
-import jalview.structure.StructureSelectionManager;\r
-\r
-/**\r
- * Propagate events involving PDB structures associated with sequences to a\r
- * javascript function. Generally, the javascript handler is called with a\r
- * series of arguments like (eventname, ... ). As of Jalview 2.7, the following\r
- * different types of events are supported:\r
- * <ul>\r
- * <li>mouseover: javascript function called with arguments <pre>\r
- * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue\r
- * number moused over), String(atom index corresponding to residue)]</pre></li>\r
- * <li>colourstruct: javascript function called with arguments <pre>\r
- * ['colourstruct',String(alignment view id),String(number of javascript message\r
- * chunks to collect),String(length of first chunk in set of messages - or zero\r
- * for null message)]</pre><br>\r
- * The message contains a series of Jmol script commands that will colour\r
- * structures according to their associated sequences in the current view. Use\r
- * jalview\r
- * .javascript.JalviewLiteJsApi.getJsMessage('colourstruct',String(alignment\r
- * view id)) to retrieve successive chunks of the message.</li>\r
- * </ul>\r
- * \r
- * @author Jim Procter (jprocter)\r
- * \r
- */\r
-public class MouseOverStructureListener extends JSFunctionExec implements\r
- JsCallBack, StructureListener\r
-{\r
-\r
- String _listenerfn;\r
-\r
- String[] modelSet;\r
-\r
- public MouseOverStructureListener(JalviewLite jalviewLite,\r
- String listener, String[] modelList)\r
- {\r
- super(jalviewLite);\r
- _listenerfn = listener;\r
- modelSet = modelList;\r
- if (modelSet != null)\r
- {\r
- for (int i = 0; i < modelSet.length; i++)\r
- {\r
- // resolve a real filename\r
- try\r
- {\r
- if (new java.net.URL(modelSet[i]).openConnection() != null)\r
- {\r
- continue;\r
- }\r
- } catch (Exception x)\r
- {\r
- }\r
- ;\r
- try\r
- {\r
- String db = jvlite.getDocumentBase().toString();\r
- db = db.substring(0, db.lastIndexOf("/"));\r
- if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)\r
- {\r
- modelSet[i] = db + "/" + modelSet[i];\r
- continue;\r
- }\r
- } catch (Exception x)\r
- {\r
- }\r
- ;\r
- try\r
- {\r
- if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])\r
- .openConnection() != null)\r
- {\r
- modelSet[i] = jvlite.getCodeBase() + modelSet[i];\r
- continue;\r
- }\r
- } catch (Exception x)\r
- {\r
- }\r
- ;\r
-\r
- }\r
- }\r
- }\r
-\r
- @Override\r
- public String[] getPdbFile()\r
- {\r
- return modelSet;\r
- }\r
-\r
- @Override\r
- public void mouseOverStructure(int atomIndex, String strInfo)\r
- {\r
-\r
- // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,\r
- // chain, pdbfile)\r
- // TODO Auto-generated method stub\r
-\r
- }\r
-\r
- @Override\r
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,\r
- String pdbId)\r
- {\r
- String[] st = new String[0];\r
- try\r
- {\r
- executeJavascriptFunction(_listenerfn, st = new String[]\r
- { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),\r
- "" + atomIndex });\r
- } catch (Exception ex)\r
- {\r
- System.err.println("Couldn't execute callback with " + _listenerfn\r
- + " using args { " + st[0] + ", " + st[1] + ", " + st[2]\r
- + "," + st[3] + "\n");\r
- ex.printStackTrace();\r
-\r
- }\r
-\r
- }\r
-\r
- @Override\r
- public synchronized void updateColours(Object srce)\r
- {\r
- final Object source = srce;\r
- StructureSelectionManager ssm = StructureSelectionManager\r
- .getStructureSelectionManager(jvlite);\r
- // if (jvlite.debug)\r
- // {\r
- // ssm.reportMapping();\r
- // }\r
- if (source instanceof jalview.api.AlignmentViewPanel)\r
- {\r
- SequenceI[][] sequence = new SequenceI[modelSet.length][];\r
- for (int m = 0; m < modelSet.length; m++)\r
- {\r
- StructureMapping[] sm = ssm.getMapping(modelSet[m]);\r
- if (sm != null && sm.length > 0)\r
- {\r
- sequence[m] = new SequenceI[sm.length];\r
- for (int i = 0; i < sm.length; i++)\r
- {\r
- sequence[m][i] = sm[i].getSequence();\r
- }\r
- }\r
- else\r
- {\r
- sequence[m] = new SequenceI[0];\r
- }\r
- // if (jvlite.debug)\r
- // {\r
- // System.err.println("Mapped '" + modelSet[m] + "' to "\r
- // + sequence[m].length + " sequences.");\r
- // }\r
- }\r
-\r
- SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)\r
- .getSequenceRenderer();\r
- FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av\r
- .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(\r
- ((jalview.appletgui.AlignmentPanel) source).av) : null;\r
- if (fr != null)\r
- {\r
- ((jalview.appletgui.FeatureRenderer) fr)\r
- .transferSettings(((jalview.appletgui.AlignmentPanel) source)\r
- .getFeatureRenderer());\r
- }\r
- ;\r
-\r
- \r
- // Form a colour command from the given alignment panel for each distinct structure \r
- ArrayList<String[]> ccomands=new ArrayList<String[]>();\r
- ArrayList<String> pdbfn=new ArrayList<String>();\r
- StructureMappingcommandSet[] colcommands=JmolCommands.getColourBySequenceCommand(\r
- ssm, modelSet, sequence, sr, fr,\r
- ((AlignmentViewPanel) source).getAlignment());\r
- if (colcommands==null) {\r
- return;\r
- }\r
- int sz=0;\r
- for (jalview.structure.StructureMappingcommandSet ccset: colcommands) {\r
- sz+=ccset.commands.length;\r
- ccomands.add(ccset.commands);\r
- pdbfn.add(ccset.mapping);\r
- }\r
- \r
- String mclass,mhandle;\r
- String ccomandset[] = new String[sz];\r
- sz=0;\r
- for (String[] ccset: ccomands) {\r
- System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);\r
- sz+=ccset.length;\r
- }\r
- if (jvlite.isJsMessageSetChanged(mclass="colourstruct",mhandle=((jalview.appletgui.AlignmentPanel) source).av\r
- .getViewId(), ccomandset)) {\r
- jvlite.setJsMessageSet(mclass, mhandle , ccomandset);\r
- // and notify javascript handler\r
- String st[] = new String[]\r
- {\r
- "colourstruct",\r
- ""\r
- + ((jalview.appletgui.AlignmentPanel) source).av\r
- .getViewId(), ""+ccomandset.length, jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn.size()]))\r
- };\r
- try\r
- {\r
- executeJavascriptFunction(\r
- true,\r
- _listenerfn,st\r
-);\r
- } catch (Exception ex)\r
- {\r
- System.err.println("Couldn't execute callback with "\r
- + _listenerfn + " using args { " + st[0] + ", "\r
- + st[1] + ", " + st[2] + "," + st[3]+"}"); // + ","+st[4]+"\n");\r
- ex.printStackTrace();\r
-\r
- }\r
- }\r
-/* new Thread(new Runnable()\r
- {\r
- public void run()\r
- {\r
- // and send to javascript handler\r
- String st[] = new String[0];\r
- int i = 0;\r
- for (String colcommand : colcommands)\r
- {\r
- // do sync execution for each chunk\r
- try\r
- {\r
- executeJavascriptFunction(\r
- false,\r
- _listenerfn,\r
- st = new String[]\r
- {\r
- "colourstruct",\r
- ""\r
- + ((jalview.appletgui.AlignmentPanel) source).av\r
- .getViewId(), handle, "" });\r
- } catch (Exception ex)\r
- {\r
- System.err.println("Couldn't execute callback with "\r
- + _listenerfn + " using args { " + st[0] + ", "\r
- + st[1] + ", " + st[2] + "," + st[3] + "\n");\r
- ex.printStackTrace();\r
-\r
- }\r
- }\r
- }\r
- }).start();\r
- */\r
- }\r
-\r
- }\r
-\r
- @Override\r
- public Color getColour(int atomIndex, int pdbResNum, String chain,\r
- String pdbId)\r
- {\r
- return null;\r
- }\r
-\r
- @Override\r
- public AlignFrame getAlignFrame()\r
- {\r
- // associated with all alignframes, always.\r
- return null;\r
- }\r
-\r
- @Override\r
- public String getListenerFunction()\r
- {\r
- return _listenerfn;\r
- }\r
-\r
- public void finalise()\r
- {\r
- jvlite=null;\r
- super.finalize();\r
- }\r
- @Override\r
- public void releaseReferences(Object svl)\r
- {\r
- \r
- // TODO Auto-generated method stub\r
-\r
- }\r
-\r
-}\r
+ *
+ * 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 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 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;
+
+ 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;
+ }
+
+ public void mouseOverStructure(int atomIndex, String strInfo)
+ {
+
+ // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,
+ // chain, pdbfile)
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void highlightAtoms(List<AtomSpec> 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<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 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
+
+ }
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff