X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=4ac247c9204f93257e4365bedc2cf8a988c19a1a;hb=fd8ca94295a0f1fe8300112b90439d19f8cb683e;hp=67327c13b26aed3f956a86c4c5b7bbf9e3c251e6;hpb=2da92b61300307562cb8bec70a72f0b0527aa3b3;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 67327c1..4ac247c 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * * 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 @@ -17,35 +17,46 @@ */ package jalview.ext.jmol; -import java.io.File; -import java.net.URL; -import java.util.*; -import java.applet.Applet; -import java.awt.*; -import java.awt.event.*; - -import javax.swing.JPanel; - import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.SequenceStructureBinding; -import jalview.datamodel.*; -import jalview.structure.*; -import jalview.io.*; +import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; + +import java.awt.Color; +import java.awt.Container; +import java.awt.event.ComponentEvent; +import java.awt.event.ComponentListener; +import java.io.File; +import java.net.URL; +import java.security.AccessControlException; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Map; +import java.util.Vector; -import org.jmol.api.*; import org.jmol.adapter.smarter.SmarterJmolAdapter; - -import org.jmol.popup.*; -import org.jmol.viewer.JmolConstants; -import org.jmol.viewer.Viewer; - -import jalview.schemes.*; +import org.jmol.api.JmolAppConsoleInterface; +import org.jmol.api.JmolSelectionListener; +import org.jmol.api.JmolStatusListener; +import org.jmol.api.JmolViewer; +import org.jmol.constant.EnumCallback; +import org.jmol.popup.JmolPopup; public abstract class JalviewJmolBinding implements StructureListener, JmolStatusListener, SequenceStructureBinding, - JmolSelectionListener, ComponentListener + JmolSelectionListener, ComponentListener, + StructureSelectionManagerProvider { /** @@ -54,6 +65,12 @@ public abstract class JalviewJmolBinding implements StructureListener, * time. */ private boolean loadingFromArchive = false; + + /** + * second flag to indicate if the jmol viewer should ignore sequence colouring + * events from the structure manager because the GUI is still setting up + */ + private boolean loadingFinished = true; /** * state flag used to check if the Jmol viewer's paint method can be called @@ -128,13 +145,15 @@ public abstract class JalviewJmolBinding implements StructureListener, */ public SequenceI[][] sequence; - StructureSelectionManager ssm; + public StructureSelectionManager ssm; public JmolViewer viewer; - public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs, - String[][] chains, String protocol) + public JalviewJmolBinding(StructureSelectionManager ssm, + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, + String protocol) { + this.ssm = ssm; this.sequence = sequenceIs; this.chains = chains; this.pdbentry = pdbentry; @@ -152,8 +171,10 @@ public abstract class JalviewJmolBinding implements StructureListener, */ } - public JalviewJmolBinding(JmolViewer viewer2) + public JalviewJmolBinding(StructureSelectionManager ssm, + JmolViewer viewer2) { + this.ssm = ssm; viewer = viewer2; viewer.setJmolStatusListener(this); viewer.addSelectionListener(this); @@ -227,8 +248,7 @@ public abstract class JalviewJmolBinding implements StructureListener, { viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); // remove listeners for all structures in viewer - StructureSelectionManager.getStructureSelectionManager() - .removeStructureViewerListener(this, this.getPdbFile()); + ssm.removeStructureViewerListener(this, this.getPdbFile()); // and shut down jmol viewer.evalStringQuiet("zap"); viewer.setJmolStatusListener(null); @@ -303,9 +323,42 @@ public abstract class JalviewJmolBinding implements StructureListener, public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { + assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); + String[] files = getPdbFile(); + // check to see if we are still waiting for Jmol files + long starttime=System.currentTimeMillis(); + boolean waiting=true; + do { + waiting=false; + for (String file:files) + { + try { + // HACK - in Jalview 2.8 this call may not be threadsafe so we catch + // every possible exception + StructureMapping[] sm = ssm.getMapping(file); + if (sm == null || sm.length == 0) + { + waiting = true; + } + } catch (Exception x) + { + waiting = true; + } catch (Error q) + { + waiting = true; + } + } + // we wait around for a reasonable time before we give up + } while (waiting && System.currentTimeMillis()<(10000+1000*files.length+starttime)); + if (waiting) + { + System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); + return; + } StringBuffer selectioncom = new StringBuffer(); - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); + + // union of all aligned positions are collected together. for (int a = 0; a < _alignment.length; a++) { @@ -347,7 +400,8 @@ public abstract class JalviewJmolBinding implements StructureListener, for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - + // RACE CONDITION - getMapping only returns Jmol loaded filenames once + // Jmol callback has completed. if (mapping == null || mapping.length < 1) continue; @@ -551,7 +605,7 @@ public abstract class JalviewJmolBinding implements StructureListener, public void colourBySequence(boolean showFeatures, jalview.api.AlignmentViewPanel alignmentv) { - if (!colourBySequence) + if (!colourBySequence || !loadingFinished) return; if (ssm == null) { @@ -567,70 +621,14 @@ public abstract class JalviewJmolBinding implements StructureListener, fr = getFeatureRenderer(alignmentv); } AlignmentI alignment = alignmentv.getAlignment(); - StringBuffer command = new StringBuffer(); - - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - continue; - int lastPos = -1; - for (int s = 0; s < sequence[pdbfnum].length; s++) + for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands + .getColourBySequenceCommand(ssm, files, sequence, sr, fr, + alignment)) + for (String cbyseq : cpdbbyseq.commands) { - for (int sp, m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) - { - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < asp.getLength(); r++) - { - // no mapping to gaps in sequence - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) - { - continue; - } - int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - - if (pos < 1 || pos == lastPos) - continue; - - lastPos = pos; - - Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); - - if (showFeatures && fr != null) - col = fr.findFeatureColour(col, sequence[pdbfnum][s], r); - String newSelcom = (mapping[m].getChain() != " " ? ":" - + mapping[m].getChain() : "") - + "/" - + (pdbfnum + 1) - + ".1" - + ";color[" - + col.getRed() - + "," - + col.getGreen() - + "," - + col.getBlue() + "]"; - if (command.toString().endsWith(newSelcom)) - { - command = condenseCommand(command.toString(), pos); - continue; - } - // TODO: deal with case when buffer is too large for Jmol to parse - // - execute command and flush - - command.append(";select " + pos); - command.append(newSelcom); - } - break; - } - } + evalStateCommand(cbyseq); } - } - evalStateCommand(command.toString()); } public boolean isColourBySequence() @@ -643,30 +641,6 @@ public abstract class JalviewJmolBinding implements StructureListener, this.colourBySequence = colourBySequence; } - StringBuffer condenseCommand(String command, int pos) - { - - StringBuffer sb = new StringBuffer(command.substring(0, - command.lastIndexOf("select") + 7)); - - command = command.substring(sb.length()); - - String start; - - if (command.indexOf("-") > -1) - { - start = command.substring(0, command.indexOf("-")); - } - else - { - start = command.substring(0, command.indexOf(":")); - } - - sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); - - return sb; - } - public void createImage(String file, String type, int quality) { System.out.println("JMOL CREATE IMAGE"); @@ -763,10 +737,34 @@ public abstract class JalviewJmolBinding implements StructureListener, String mset[] = new String[viewer.getModelCount()]; _modelFileNameMap = new int[mset.length]; int j = 1; - mset[0] = viewer.getModelFileName(0); + String m = viewer.getModelFileName(0); + if (m != null) + { + try + { + mset[0] = new File(m).getAbsolutePath(); + } catch (AccessControlException x) + { + // usually not allowed to do this in applet, so keep raw handle + mset[0] = m; + // System.err.println("jmolBinding: Using local file string from Jmol: "+m); + } + } for (int i = 1; i < mset.length; i++) { - mset[j] = viewer.getModelFileName(i); + m = viewer.getModelFileName(i); + if (m != null) + { + try + { + mset[j] = new File(m).getAbsolutePath(); + } catch (AccessControlException x) + { + // usually not allowed to do this in applet, so keep raw handle + mset[j] = m; + // System.err.println("jmolBinding: Using local file string from Jmol: "+m); + } + } _modelFileNameMap[j] = i; // record the model index for the filename // skip any additional models in the same file (NMR structures) if ((mset[j] == null ? mset[j] != mset[j - 1] @@ -942,8 +940,19 @@ public abstract class JalviewJmolBinding implements StructureListener, try { // recover PDB filename for the model hovered over. - pdbfilename = viewer - .getModelFileName(new Integer(mdlId).intValue() - 1); + int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId) + .intValue() - 1; + while (mnumber < _modelFileNameMap[_mp]) + { + _mp--; + } + pdbfilename = modelFileNames[_mp]; + if (pdbfilename == null) + { + pdbfilename = new File(viewer.getModelFileName(mnumber)) + .getAbsolutePath(); + } + } catch (Exception e) { } @@ -1021,47 +1030,48 @@ public abstract class JalviewJmolBinding implements StructureListener, } - public void notifyCallback(int type, Object[] data) + @Override + public void notifyCallback(EnumCallback type, Object[] data) { try { switch (type) { - case JmolConstants.CALLBACK_LOADSTRUCT: + case LOADSTRUCT: notifyFileLoaded((String) data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer) data[5]).intValue()); break; - case JmolConstants.CALLBACK_PICK: + case PICK: notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: + case HOVER: notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); break; - case JmolConstants.CALLBACK_SCRIPT: + case SCRIPT: notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue()); break; - case JmolConstants.CALLBACK_ECHO: + case ECHO: sendConsoleEcho((String) data[1]); break; - case JmolConstants.CALLBACK_MESSAGE: + case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) : (String) data[1]); break; - case JmolConstants.CALLBACK_ERROR: + case ERROR: // System.err.println("Ignoring error callback."); break; - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_RESIZE: + case SYNC: + case RESIZE: refreshGUI(); break; - case JmolConstants.CALLBACK_MEASURE: + case MEASURE: - case JmolConstants.CALLBACK_CLICK: + case CLICK: default: System.err.println("Unhandled callback " + type + " " + data[1].toString()); @@ -1074,24 +1084,25 @@ public abstract class JalviewJmolBinding implements StructureListener, } } - public boolean notifyEnabled(int callbackPick) + @Override + public boolean notifyEnabled(EnumCallback callbackPick) { switch (callbackPick) { - case JmolConstants.CALLBACK_ECHO: - case JmolConstants.CALLBACK_LOADSTRUCT: - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_MESSAGE: - case JmolConstants.CALLBACK_PICK: - case JmolConstants.CALLBACK_SCRIPT: - case JmolConstants.CALLBACK_HOVER: - case JmolConstants.CALLBACK_ERROR: + case ECHO: + case LOADSTRUCT: + case MEASURE: + case MESSAGE: + case PICK: + case SCRIPT: + case HOVER: + case ERROR: return true; - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: + case RESIZE: + case SYNC: + case CLICK: + case ANIMFRAME: + case MINIMIZATION: } return false; } @@ -1128,7 +1139,6 @@ public abstract class JalviewJmolBinding implements StructureListener, chainFile = new Hashtable(); boolean notifyLoaded = false; String[] modelfilenames = getPdbFile(); - ssm = StructureSelectionManager.getStructureSelectionManager(); // first check if we've lost any structures if (oldmodels != null && oldmodels.length > 0) { @@ -1202,7 +1212,9 @@ public abstract class JalviewJmolBinding implements StructureListener, } else { - if (matches = pdbentry[pe].getFile().equals(fileName)) + File fl; + if (matches = (fl = new File(pdbentry[pe].getFile())) + .equals(new File(fileName))) { foundEntry = true; // TODO: Jmol can in principle retrieve from CLASSLOADER but @@ -1213,7 +1225,6 @@ public abstract class JalviewJmolBinding implements StructureListener, String protocol = AppletFormatAdapter.URL; try { - File fl = new java.io.File(pdbentry[pe].getFile()); if (fl.exists()) { protocol = AppletFormatAdapter.FILE; @@ -1223,21 +1234,21 @@ public abstract class JalviewJmolBinding implements StructureListener, } catch (Error e) { } - ; - pdb = ssm.setMapping(sequence[pe], chains[pe], - pdbentry[pe].getFile(), protocol); + // Explicitly map to the filename used by Jmol ; + pdb = ssm.setMapping(sequence[pe], chains[pe], fileName, + protocol); + // pdbentry[pe].getFile(), protocol); } } if (matches) { - pdbentry[pe].setId(pdb.id); // add an entry for every chain in the model for (int i = 0; i < pdb.chains.size(); i++) { String chid = new String(pdb.id + ":" + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); - chainFile.put(chid, pdbentry[pe].getFile()); + chainFile.put(chid, fileName); chainNames.addElement(chid); } notifyLoaded = true; @@ -1270,7 +1281,6 @@ public abstract class JalviewJmolBinding implements StructureListener, { viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); } - setLoadingFromArchive(false); // register ourselves as a listener and notify the gui that it needs to // update itself. ssm.addStructureViewerListener(this); @@ -1284,6 +1294,7 @@ public abstract class JalviewJmolBinding implements StructureListener, refreshGUI(); loadNotifiesHandled++; } + setLoadingFromArchive(false); } public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) @@ -1419,6 +1430,10 @@ public abstract class JalviewJmolBinding implements StructureListener, String commandOptions, final Container consolePanel, String buttonsToShow) { + if (commandOptions == null) + { + commandOptions = ""; + } viewer = JmolViewer.allocateViewer(renderPanel, (jmolfileio ? new SmarterJmolAdapter() : null), htmlName + ((Object) this).toString(), documentBase, codeBase, @@ -1462,10 +1477,24 @@ public abstract class JalviewJmolBinding implements StructureListener, { this.loadingFromArchive = loadingFromArchive; } - + + /** + * + * @return true if Jmol is still restoring state or loading is still going on (see setFinsihedLoadingFromArchive) + */ public boolean isLoadingFromArchive() { - return loadingFromArchive; + return loadingFromArchive && !loadingFinished; + } + + /** + * modify flag which controls if sequence colouring events are honoured by the binding. + * Should be true for normal operation + * @param finishedLoading + */ + public void setFinishedLoadingFromArchive(boolean finishedLoading) + { + loadingFinished = finishedLoading; } public void setBackgroundColour(java.awt.Color col) @@ -1613,4 +1642,22 @@ public abstract class JalviewJmolBinding implements StructureListener, chains[pe] = null; } } + + /** + * + * @param pdbfile + * @return text report of alignment between pdbfile and any associated + * alignment sequences + */ + public String printMapping(String pdbfile) + { + return ssm.printMapping(pdbfile); + } + + @Override + public void resizeInnerPanel(String data) + { + // Jalview doesn't honour resize panel requests + + } }