X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=78f383ad34eb588632664f1a55e92afca23f4336;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=581c3f94b12f396bf862ddd17c1679c220a51258;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 581c3f9..78f383a 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,322 +1,324 @@
-/*******************************************************************************
- * 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
- *
+/*
+ * 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 .
- *******************************************************************************/
-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
-
- }
-
-}
+ *
+ * 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 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++)
+ {
+ // 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 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 finalise()
+ {
+ jvlite = null;
+ super.finalize();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
+ }
+
+}