X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=8ee22964da54980984e13c3f151dda1b403f81ad;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=09303c760d791fb90d9fdce2387b6ecfd2f7d581;hpb=4c5b46336a4a57c09b4a1d2ab13c81b0958a6c9e;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 09303c7..8ee2296 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,49 +1,63 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 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.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 + JmolStatusListener, SequenceStructureBinding, + JmolSelectionListener, ComponentListener, + StructureSelectionManagerProvider { /** @@ -52,6 +66,12 @@ 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 @@ -80,6 +100,8 @@ public abstract class JalviewJmolBinding implements StructureListener, public Vector chainNames; + Hashtable chainFile; + /** * array of target chains for seuqences - tied to pdbentry and sequence[] */ @@ -113,7 +135,7 @@ public abstract class JalviewJmolBinding implements StructureListener, public PDBEntry[] pdbentry; /** - * datasource protocol for access to PDBEntry + * datasource protocol for access to PDBEntrylatest */ String protocol = null; @@ -124,13 +146,15 @@ 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; @@ -148,8 +172,10 @@ 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); @@ -210,8 +236,9 @@ public abstract class JalviewJmolBinding implements StructureListener, p = mlength; mlength = lbl.indexOf(":", p); } while (p < mlength && mlength < (lbl.length() - 2)); + // TODO: lookup each pdb id and recover proper model number for it. cmd.append(":" + lbl.substring(mlength + 1) + " /" - + getModelNum(lbl.substring(0, mlength)) + " or "); + + (1 + getModelNum((String) chainFile.get(lbl))) + " or "); } if (cmd.length() > 0) cmd.setLength(cmd.length() - 4); @@ -222,15 +249,21 @@ 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); lastCommand = null; viewer = null; + releaseUIResources(); } + /** + * called by JalviewJmolbinding after closeViewer is called - release any + * resources and references so they can be garbage collected. + */ + protected abstract void releaseUIResources(); + public void colourByChain() { colourBySequence = false; @@ -282,198 +315,301 @@ public abstract class JalviewJmolBinding implements StructureListener, public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols) { + superposeStructures(new AlignmentI[] + { alignment }, new int[] + { refStructure }, new ColumnSelection[] + { hiddenCols }); + } + + public void superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, ColumnSelection[] _hiddenCols) + { + assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); + String[] files = getPdbFile(); - if (refStructure >= files.length) + // 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("Invalid reference structure value " - + refStructure); - refStructure = -1; + System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); + return; } - if (refStructure < -1) + StringBuffer selectioncom = new StringBuffer(); + // In principle - nSeconds specifies the speed of animation for each + // superposition - but is seems to behave weirdly, so we don't specify it. + String nSeconds = " "; + if (files.length > 10) { - refStructure = -1; + nSeconds = " 0.00001 "; } - StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer(); - - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) + else { - - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + nSeconds = " " + (2.0 / files.length) + " "; + // if (nSeconds).substring(0,5)+" "; } - - int commonrpositions[][] = new int[files.length][alignment.getWidth()]; - String isel[] = new String[files.length]; - // reference structure - all others are superposed in it - String[] targetC = new String[files.length]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + // see JAL-1345 - should really automatically turn off the animation for + // large numbers of structures, but Jmol doesn't seem to allow that. + nSeconds = " "; + // union of all aligned positions are collected together. + for (int a = 0; a < _alignment.length; a++) { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + int refStructure = _refStructure[a]; + AlignmentI alignment = _alignment[a]; + ColumnSelection hiddenCols = _hiddenCols[a]; + if (a > 0 + && selectioncom.length() > 0 + && !selectioncom.substring(selectioncom.length() - 1).equals( + "|")) + { + selectioncom.append("|"); + } + // process this alignment + if (refStructure >= files.length) + { + System.err.println("Invalid reference structure value " + + refStructure); + refStructure = -1; + } + if (refStructure < -1) + { + refStructure = -1; + } + StringBuffer command = new StringBuffer(); - if (mapping == null || mapping.length < 1) - continue; + boolean matched[] = new boolean[alignment.getWidth()]; + for (int m = 0; m < matched.length; m++) + { - int lastPos = -1; - for (int s = 0; s < sequence[pdbfnum].length; s++) + matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + } + + int commonrpositions[][] = new int[files.length][alignment.getWidth()]; + String isel[] = new String[files.length]; + // reference structure - all others are superposed in it + String[] targetC = new String[files.length]; + String[] chainNames = new String[files.length]; + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - for (int sp, m = 0; m < mapping.length; m++) + 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) { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + throw new Error("Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016"); + } + int lastPos = -1; + for (int s = 0; s < sequence[pdbfnum].length; s++) + { + for (int sp, m = 0; m < mapping.length; m++) { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) + if (mapping[m].getSequence() == sequence[pdbfnum][s] + && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) { - if (!matched[r]) + if (refStructure == -1) { - continue; + refStructure = pdbfnum; } - matched[r] = false; // assume this is not a good site - if (r >= asp.getLength()) + SequenceI asp = alignment.getSequenceAt(sp); + for (int r = 0; r < matched.length; r++) { - continue; - } + if (!matched[r]) + { + continue; + } + matched[r] = false; // assume this is not a good site + if (r >= asp.getLength()) + { + continue; + } - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + { + // no mapping to gaps in sequence + continue; + } + int t = asp.findPosition(r); // sequence position + int apos = mapping[m].getAtomNum(t); + int pos = mapping[m].getPDBResNum(t); + + if (pos < 1 || pos == lastPos) + { + // can't align unmapped sequence + continue; + } + matched[r] = true; // this is a good ite + lastPos = pos; + // just record this residue position + commonrpositions[pdbfnum][r] = pos; + } + // create model selection suffix + isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1"; + if (mapping[m].getChain() == null + || mapping[m].getChain().trim().length() == 0) { - // no mapping to gaps in sequence - continue; + targetC[pdbfnum] = ""; } - int t = asp.findPosition(r); // sequence position - int apos = mapping[m].getAtomNum(t); - int pos = mapping[m].getPDBResNum(t); - - if (pos < 1 || pos == lastPos) + else { - // can't align unmapped sequence - continue; + targetC[pdbfnum] = ":" + mapping[m].getChain(); } - matched[r] = true; // this is a good ite - lastPos = pos; - // just record this residue position - commonrpositions[pdbfnum][r] = pos; + chainNames[pdbfnum] = mapping[m].getPdbId() + + targetC[pdbfnum]; + // move on to next pdb file + s = sequence[pdbfnum].length; + break; } - // create model selection suffix - isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1"; - if (mapping[m].getChain() == null - || mapping[m].getChain().trim().length() == 0) - { - targetC[pdbfnum] = ""; - } - else - { - targetC[pdbfnum] = ":" + mapping[m].getChain(); - } - // move on to next pdb file - s = sequence[pdbfnum].length; - break; } } } - } - String[] selcom = new String[files.length]; - int nmatched = 0; - // generate select statements to select regions to superimpose structures - { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + + // TODO: consider bailing if nmatched less than 4 because superposition + // not + // well defined. + // TODO: refactor superposable position search (above) from jmol selection + // construction (below) + + String[] selcom = new String[files.length]; + int nmatched = 0; + // generate select statements to select regions to superimpose structures { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - molsel.append("{"); - for (int r = 0; r < matched.length; r++) + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - if (matched[r]) + String chainCd = targetC[pdbfnum]; + int lpos = -1; + boolean run = false; + StringBuffer molsel = new StringBuffer(); + molsel.append("{"); + for (int r = 0; r < matched.length; r++) { - if (pdbfnum == 0) + if (matched[r]) { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) - { - // discontinuity - if (lpos != -1) + if (pdbfnum == 0) { - molsel.append(lpos); - molsel.append(chainCd); - // molsel.append("} {"); - molsel.append("|"); + nmatched++; } - } - else - { - // continuous run - and lpos >-1 - if (!run) + if (lpos != commonrpositions[pdbfnum][r] - 1) { - // at the beginning, so add dash - molsel.append(lpos); - molsel.append("-"); + // discontinuity + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + // molsel.append("} {"); + molsel.append("|"); + } } - run = true; + else + { + // continuous run - and lpos >-1 + if (!run) + { + // at the beginning, so add dash + molsel.append(lpos); + molsel.append("-"); + } + run = true; + } + lpos = commonrpositions[pdbfnum][r]; + // molsel.append(lpos); + } + } + // add final selection phrase + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + molsel.append("}"); + } + if (molsel.length() > 1) + { + selcom[pdbfnum] = molsel.toString(); + selectioncom.append("(("); + selectioncom.append(selcom[pdbfnum].substring(1, + selcom[pdbfnum].length() - 1)); + selectioncom.append(" )& "); + selectioncom.append(pdbfnum + 1); + selectioncom.append(".1)"); + if (pdbfnum < files.length - 1) + { + selectioncom.append("|"); } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); + } else { + selcom[pdbfnum] = null; } } - // add final selection phrase - if (lpos != -1) + } + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + if (pdbfnum == refStructure || selcom[pdbfnum]==null || selcom[refStructure]==null) { - molsel.append(lpos); - molsel.append(chainCd); - molsel.append("}"); + continue; } - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("(("); - selectioncom.append(selcom[pdbfnum].substring(1, - selcom[pdbfnum].length() - 1)); - selectioncom.append(" )& "); - selectioncom.append(pdbfnum + 1); - selectioncom.append(".1)"); - if (pdbfnum < files.length - 1) + command.append("echo "); + command.append("\"Superposing ("); + command.append(chainNames[pdbfnum]); + command.append(") against reference ("); + command.append(chainNames[refStructure]); + command.append(")\";\ncompare "+nSeconds); + command.append("{"); + command.append(1 + pdbfnum); + command.append(".1} {"); + command.append(1 + refStructure); + command.append(".1} SUBSET {*.CA | *.P} ATOMS "); + + // form the matched pair strings + String sep = ""; + for (int s = 0; s < 2; s++) { - selectioncom.append("|"); + command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); } + command.append(" ROTATE TRANSLATE;\n"); } - } - // TODO: consider bailing if nmatched less than 4 because superposition not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - if (pdbfnum == refStructure) + if (selectioncom.length() > 0) { - continue; + System.out.println("Select regions:\n" + selectioncom.toString()); + evalStateCommand("select *; cartoons off; backbone; select (" + + selectioncom.toString() + "); cartoons; "); + // selcom.append("; ribbons; "); + System.out + .println("Superimpose command(s):\n" + command.toString()); + + evalStateCommand(command.toString()); } - command.append("compare "); - command.append("{"); - command.append(1 + pdbfnum); - command.append(".1} {"); - command.append(1 + refStructure); - command.append(".1} SUBSET {*.CA | *.P} ATOMS "); - - // form the matched pair strings - String sep = ""; - for (int s = 0; s < 2; s++) + } + if (selectioncom.length() > 0) + {// finally, mark all regions that were superposed. + if (selectioncom.substring(selectioncom.length() - 1).equals("|")) { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); + selectioncom.setLength(selectioncom.length() - 1); } - command.append(" ROTATE TRANSLATE;\n"); + System.out.println("Select regions:\n" + selectioncom.toString()); + evalStateCommand("select *; cartoons off; backbone; select (" + + selectioncom.toString() + "); cartoons; "); + // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); } - System.out.println("Select regions:\n" + selectioncom.toString()); - evalStateCommand("select *; cartoons off; backbone; select (" - + selectioncom.toString() + "); cartoons; "); - // selcom.append("; ribbons; "); - System.out.println("Superimpose command(s):\n" + command.toString()); - - evalStateCommand(command.toString()); - - // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); } public void evalStateCommand(String command) @@ -492,87 +628,33 @@ public abstract class JalviewJmolBinding implements StructureListener, * using the getFeatureRenderer() and getSequenceRenderer() renderers but only * if colourBySequence is enabled. */ - public void colourBySequence(boolean showFeatures, AlignmentI alignment) + public void colourBySequence(boolean showFeatures, + jalview.api.AlignmentViewPanel alignmentv) { - if (!colourBySequence) + if (!colourBySequence || !loadingFinished) return; if (ssm == null) { return; } String[] files = getPdbFile(); - SequenceRenderer sr = getSequenceRenderer(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); FeatureRenderer fr = null; if (showFeatures) { - fr = getFeatureRenderer(); + 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) - 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() @@ -585,30 +667,6 @@ 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"); @@ -655,9 +713,12 @@ public abstract class JalviewJmolBinding implements StructureListener, * returns the current featureRenderer that should be used to colour the * structures * + * @param alignment + * * @return */ - public abstract FeatureRenderer getFeatureRenderer(); + public abstract FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment); /** * instruct the Jalview binding to update the pdbentries vector if necessary @@ -702,10 +763,34 @@ 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] @@ -733,9 +818,12 @@ public abstract class JalviewJmolBinding implements StructureListener, * returns the current sequenceRenderer that should be used to colour the * structures * + * @param alignment + * * @return */ - public abstract SequenceRenderer getSequenceRenderer(); + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); // /////////////////////////////// // JmolStatusListener @@ -830,6 +918,7 @@ public abstract class JalviewJmolBinding implements StructureListener, public void mouseOverStructure(int atomIndex, String strInfo) { int pdbResNum; + int alocsep = strInfo.indexOf("^"); int mdlSep = strInfo.indexOf("/"); int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; @@ -842,9 +931,18 @@ public abstract class JalviewJmolBinding implements StructureListener, chainSeparator = mdlSep; } } - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); + // handle insertion codes + if (alocsep != -1) + { + pdbResNum = Integer.parseInt(strInfo.substring( + strInfo.indexOf("]") + 1, alocsep)); + } + else + { + pdbResNum = Integer.parseInt(strInfo.substring( + strInfo.indexOf("]") + 1, chainSeparator)); + } String chainId; if (strInfo.indexOf(":") > -1) @@ -868,8 +966,19 @@ 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) { } @@ -947,47 +1056,48 @@ 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()); @@ -1000,24 +1110,25 @@ 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; } @@ -1051,9 +1162,9 @@ public abstract class JalviewJmolBinding implements StructureListener, String[] oldmodels = modelFileNames; modelFileNames = null; chainNames = new Vector(); + 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) { @@ -1127,7 +1238,9 @@ 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 @@ -1138,7 +1251,6 @@ 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; @@ -1148,20 +1260,22 @@ 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++) { - chainNames.addElement(new String(pdb.id + ":" - + ((MCview.PDBChain) pdb.chains.elementAt(i)).id)); + String chid = new String(pdb.id + ":" + + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); + chainFile.put(chid, fileName); + chainNames.addElement(chid); } notifyLoaded = true; } @@ -1193,13 +1307,12 @@ 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); if (notifyLoaded) { - FeatureRenderer fr = getFeatureRenderer(); + FeatureRenderer fr = getFeatureRenderer(null); if (fr != null) { fr.featuresAdded(); @@ -1207,6 +1320,7 @@ public abstract class JalviewJmolBinding implements StructureListener, refreshGUI(); loadNotifiesHandled++; } + setLoadingFromArchive(false); } public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) @@ -1314,7 +1428,7 @@ public abstract class JalviewJmolBinding implements StructureListener, * @param codeBase * @param commandOptions */ - public void allocateViewer(Component renderPanel, boolean jmolfileio, + public void allocateViewer(Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, String commandOptions) { @@ -1337,11 +1451,15 @@ public abstract class JalviewJmolBinding implements StructureListener, * @param buttonsToShow * - buttons to show on the console, in ordr */ - public void allocateViewer(Component renderPanel, boolean jmolfileio, + public void allocateViewer(Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, 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, @@ -1351,9 +1469,8 @@ public abstract class JalviewJmolBinding implements StructureListener, if (consolePanel != null) { consolePanel.addComponentListener(this); - - } + } } @@ -1362,39 +1479,48 @@ public abstract class JalviewJmolBinding implements StructureListener, protected org.jmol.api.JmolAppConsoleInterface console = null; -@Override -public void componentResized(ComponentEvent e) -{ - -} + public void componentResized(ComponentEvent e) + { -@Override -public void componentMoved(ComponentEvent e) -{ - -} + } -@Override -public void componentShown(ComponentEvent e) -{ - showConsole(true); -} + public void componentMoved(ComponentEvent e) + { -@Override -public void componentHidden(ComponentEvent e) -{ - showConsole(false); -} + } + public void componentShown(ComponentEvent e) + { + showConsole(true); + } + + public void componentHidden(ComponentEvent e) + { + showConsole(false); + } public void setLoadingFromArchive(boolean loadingFromArchive) { 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) @@ -1542,4 +1668,22 @@ public void componentHidden(ComponentEvent e) 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 + + } }