From b4f141d24f090c73e5608214cef2e1dd2c3e21ad Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 5 May 2011 13:56:53 +0000 Subject: [PATCH] separation of jmol script command generation from jmol binding --- src/jalview/ext/jmol/JalviewJmolBinding.java | 3155 +++++++++++++------------- src/jalview/ext/jmol/JmolCommands.java | 135 ++ 2 files changed, 1667 insertions(+), 1623 deletions(-) create mode 100644 src/jalview/ext/jmol/JmolCommands.java diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 8ea1c5d..8e1ede4 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,1626 +1,1535 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 - * 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.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 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.*; - -public abstract class JalviewJmolBinding implements StructureListener, - JmolStatusListener, SequenceStructureBinding, - JmolSelectionListener, ComponentListener - -{ - /** - * set if Jmol state is being restored from some source - instructs binding - * not to apply default display style when structure set is updated for first - * time. - */ - private boolean loadingFromArchive = false; - - /** - * state flag used to check if the Jmol viewer's paint method can be called - */ - private boolean finishedInit = false; - - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } - - boolean allChainsSelected = false; - - /** - * when true, try to search the associated datamodel for sequences that are - * associated with any unknown structures in the Jmol view. - */ - private boolean associateNewStructs = false; - - Vector atomsPicked = new Vector(); - - public Vector chainNames; - - Hashtable chainFile; - - /** - * array of target chains for seuqences - tied to pdbentry and sequence[] - */ - protected String[][] chains; - - boolean colourBySequence = true; - - StringBuffer eval = new StringBuffer(); - - public String fileLoadingError; - - /** - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - int frameNo = 0; - - protected JmolPopup jmolpopup; - - String lastCommand; - - String lastMessage; - - boolean loadedInline; - - /** - * current set of model filenames loaded in the Jmol instance - */ - String[] modelFileNames = null; - - public PDBEntry[] pdbentry; - - /** - * datasource protocol for access to PDBEntrylatest - */ - String protocol = null; - - StringBuffer resetLastRes = new StringBuffer(); - - /** - * sequences mapped to each pdbentry - */ - public SequenceI[][] sequence; - - StructureSelectionManager ssm; - - public JmolViewer viewer; - - public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs, - String[][] chains, String protocol) - { - this.sequence = sequenceIs; - this.chains = chains; - this.pdbentry = pdbentry; - this.protocol = protocol; - if (chains == null) - { - this.chains = new String[pdbentry.length][]; - } - /* - * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), - * "jalviewJmol", ap.av.applet .getDocumentBase(), - * ap.av.applet.getCodeBase(), "", this); - * - * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); - */ - } - - public JalviewJmolBinding(JmolViewer viewer2) - { - viewer = viewer2; - viewer.setJmolStatusListener(this); - viewer.addSelectionListener(this); - } - - /** - * construct a title string for the viewer window based on the data jalview - * knows about - * - * @return - */ - public String getViewerTitle() - { - if (sequence == null || pdbentry == null || sequence.length < 1 - || pdbentry.length < 1 || sequence[0].length < 1) - { - return ("Jalview Jmol Window"); - } - // TODO: give a more informative title when multiple structures are - // displayed. - StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":" - + pdbentry[0].getId()); - - if (pdbentry[0].getProperty() != null) - { - if (pdbentry[0].getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbentry[0].getProperty().get("method")); - } - if (pdbentry[0].getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbentry[0].getProperty().get("chains")); - } - } - return title.toString(); - } - - /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' - * - * @param chainList - * list of chains to make visible - */ - public void centerViewer(Vector chainList) - { - StringBuffer cmd = new StringBuffer(); - String lbl; - int mlength, p; - for (int i = 0, iSize = chainList.size(); i < iSize; i++) - { - mlength = 0; - lbl = (String) chainList.elementAt(i); - do - { - 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) + " /" - + (1 + getModelNum((String) chainFile.get(lbl))) + " or "); - } - if (cmd.length() > 0) - cmd.setLength(cmd.length() - 4); - evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd); - } - - public void closeViewer() - { - viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); - // remove listeners for all structures in viewer - StructureSelectionManager.getStructureSelectionManager() - .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; - // TODO: colour by chain should colour each chain distinctly across all - // visible models - // TODO: http://issues.jalview.org/browse/JAL-628 - evalStateCommand("select *;color chain"); - } - - public void colourByCharge() - { - colourBySequence = false; - evalStateCommand("select *;color white;select ASP,GLU;color red;" - + "select LYS,ARG;color blue;select CYS;color yellow"); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. - */ - public void superposeStructures(AlignmentI alignment) - { - superposeStructures(alignment, -1, null); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) - * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - */ - public void superposeStructures(AlignmentI alignment, int refStructure) - { - superposeStructures(alignment, refStructure, null); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) - * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - * @param hiddenCols - * TODO - */ - 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) - { - String[] files = getPdbFile(); - 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++) - { - 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(); - - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) - { - - 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++) - { - 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 (int sp, m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) - { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) - { - 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))) - { - // 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) - { - targetC[pdbfnum] = ""; - } - else - { - targetC[pdbfnum] = ":" + mapping[m].getChain(); - } - chainNames[pdbfnum] = mapping[m].getPdbId() - + targetC[pdbfnum]; - // 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++) - { - 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 (matched[r]) - { - if (pdbfnum == 0) - { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) - { - // discontinuity - if (lpos != -1) - { - molsel.append(lpos); - molsel.append(chainCd); - // molsel.append("} {"); - molsel.append("|"); - } - } - 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("}"); - } - 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("|"); - } - } - } - // 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) - { - continue; - } - command.append("echo "); - command.append("\"Superposing ("); - command.append(chainNames[pdbfnum]); - command.append(") against reference ("); - command.append(chainNames[refStructure]); - command.append(")\";\ncompare "); - 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++) - { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - } - command.append(" ROTATE TRANSLATE;\n"); - } - 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()); - } - if (selectioncom.length() > 0) - {// finally, mark all regions that were superposed. - if (selectioncom.substring(selectioncom.length() - 1).equals("|")) - { - selectioncom.setLength(selectioncom.length() - 1); - } - 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()); - } - } - - public void evalStateCommand(String command) - { - jmolHistory(false); - if (lastCommand == null || !lastCommand.equals(command)) - { - viewer.evalStringQuiet(command + "\n"); - } - jmolHistory(true); - lastCommand = command; - } - - /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. - */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) - { - if (!colourBySequence) - return; - if (ssm == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - 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 (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(command.toString()); - } - - public boolean isColourBySequence() - { - return colourBySequence; - } - - public void setColourBySequence(boolean colourBySequence) - { - 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"); - } - - public String createImage(String fileName, String type, - Object textOrBytes, int quality) - { - System.out.println("JMOL CREATE IMAGE"); - return null; - } - - public String eval(String strEval) - { - // System.out.println(strEval); - // "# 'eval' is implemented only for the applet."; - return null; - } - - // End StructureListener - // ////////////////////////// - - public float[][] functionXY(String functionName, int x, int y) - { - return null; - } - - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) - { - // TODO Auto-generated method stub - return null; - } - - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (getModelNum(pdbfile) < 0) - return null; - // TODO: verify atomIndex is selecting correct model. - return new Color(viewer.getAtomArgb(atomIndex)); - } - - /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - - /** - * instruct the Jalview binding to update the pdbentries vector if necessary - * prior to matching the jmol view's contents to the list of structure files - * Jalview knows about. - */ - public abstract void refreshPdbEntries(); - - private int getModelNum(String modelFileName) - { - String[] mfn = getPdbFile(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) - { - if (mfn[i].equalsIgnoreCase(modelFileName)) - return i; - } - return -1; - } - - /** - * map between index of model filename returned from getPdbFile and the first - * index of models from this file in the viewer. Note - this is not trimmed - - * use getPdbFile to get number of unique models. - */ - private int _modelFileNameMap[]; - - // //////////////////////////////// - // /StructureListener - public synchronized String[] getPdbFile() - { - if (viewer == null) - { - return new String[0]; - } - if (modelFileNames == null) - { - - String mset[] = new String[viewer.getModelCount()]; - _modelFileNameMap = new int[mset.length]; - int j = 1; - mset[0] = viewer.getModelFileName(0); - for (int i = 1; i < mset.length; i++) - { - mset[j] = viewer.getModelFileName(i); - _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] - : (mset[j - 1] == null || !mset[j].equals(mset[j - 1])))) - { - j++; - } - } - modelFileNames = new String[j]; - System.arraycopy(mset, 0, modelFileNames, 0, j); - } - return modelFileNames; - } - - /** - * map from string to applet - */ - public Map getRegistryInfo() - { - // TODO Auto-generated method stub - return null; - } - - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - // /////////////////////////////// - // JmolStatusListener - - public void handlePopupMenu(int x, int y) - { - jmolpopup.show(x, y); - } - - // jmol/ssm only - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (modelFileNames == null) - { - return; - } - - // look up file model number for this pdbfile - int mdlNum = 0; - String fn; - // may need to adjust for URLencoding here - we don't worry about that yet. - while (mdlNum < modelFileNames.length - && !pdbfile.equals(modelFileNames[mdlNum])) - { - // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn); - mdlNum++; - } - if (mdlNum == modelFileNames.length) - { - return; - } - - jmolHistory(false); - // if (!pdbfile.equals(pdbentry.getFile())) - // return; - if (resetLastRes.length() > 0) - { - viewer.evalStringQuiet(resetLastRes.toString()); - } - - eval.setLength(0); - eval.append("select " + pdbResNum); // +modelNum - - resetLastRes.setLength(0); - resetLastRes.append("select " + pdbResNum); // +modelNum - - eval.append(":"); - resetLastRes.append(":"); - if (!chain.equals(" ")) - { - eval.append(chain); - resetLastRes.append(chain); - } - { - eval.append(" /" + (mdlNum + 1)); - resetLastRes.append("/" + (mdlNum + 1)); - } - eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); - - resetLastRes.append(";wireframe 0;" + resetLastRes.toString() - + " and not hetero; spacefill 0;"); - - eval.append("spacefill 200;select none"); - - viewer.evalStringQuiet(eval.toString()); - jmolHistory(true); - - } - - boolean debug = true; - - private void jmolHistory(boolean enable) - { - viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off")); - } - - public void loadInline(String string) - { - loadedInline = true; - // TODO: re JAL-623 - // viewer.loadInline(strModel, isAppend); - // could do this: - // construct fake fullPathName and fileName so we can identify the file - // later. - // Then, construct pass a reader for the string to Jmol. - // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, - // fileName, null, reader, false, null, null, 0); - viewer.openStringInline(string); - } - - public void mouseOverStructure(int atomIndex, String strInfo) - { - int pdbResNum; - int alocsep = strInfo.indexOf("^"); - int mdlSep = strInfo.indexOf("/"); - int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; - - if (chainSeparator == -1) - { - chainSeparator = strInfo.indexOf("."); - if (mdlSep > -1 && mdlSep < chainSeparator) - { - chainSeparator1 = chainSeparator; - chainSeparator = mdlSep; - } - } - // 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) - chainId = strInfo.substring(strInfo.indexOf(":") + 1, - strInfo.indexOf(".")); - else - { - chainId = " "; - } - - String pdbfilename = modelFileNames[frameNo]; // default is first or current - // model - if (mdlSep > -1) - { - if (chainSeparator1 == -1) - { - chainSeparator1 = strInfo.indexOf(".", mdlSep); - } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); - try - { - // recover PDB filename for the model hovered over. - pdbfilename = viewer - .getModelFileName(new Integer(mdlId).intValue() - 1); - } catch (Exception e) - { - } - ; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); - - lastMessage = strInfo; - } - - public void notifyAtomHovered(int atomIndex, String strInfo, String data) - { - if (data != null) - { - System.err.println("Ignoring additional hover info: " + data - + " (other info: '" + strInfo + "' pos " + atomIndex + ")"); - } - mouseOverStructure(atomIndex, strInfo); - } - - /* - * { if (history != null && strStatus != null && - * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); - * } } - */ - - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) - { - /** - * this implements the toggle label behaviour copied from the original - * structure viewer, MCView - */ - if (strData != null) - { - System.err.println("Ignoring additional pick data string " + strData); - } - int chainSeparator = strInfo.indexOf(":"); - int p = 0; - if (chainSeparator == -1) - chainSeparator = strInfo.indexOf("."); - - String picked = strInfo.substring(strInfo.indexOf("]") + 1, - chainSeparator); - String mdlString = ""; - if ((p = strInfo.indexOf(":")) > -1) - picked += strInfo.substring(p + 1, strInfo.indexOf(".")); - - if ((p = strInfo.indexOf("/")) > -1) - { - mdlString += strInfo.substring(p, strInfo.indexOf(" #")); - } - picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" - + mdlString + "))"; - jmolHistory(false); - - if (!atomsPicked.contains(picked)) - { - viewer.evalStringQuiet("select " + picked + ";label %n %r:%c"); - atomsPicked.addElement(picked); - } - else - { - viewer.evalString("select " + picked + ";label off"); - atomsPicked.removeElement(picked); - } - jmolHistory(true); - // TODO: in application this happens - // - // if (scriptWindow != null) - // { - // scriptWindow.sendConsoleMessage(strInfo); - // scriptWindow.sendConsoleMessage("\n"); - // } - - } - - public void notifyCallback(int type, Object[] data) - { - try - { - switch (type) - { - case JmolConstants.CALLBACK_LOADSTRUCT: - notifyFileLoaded((String) data[1], (String) data[2], - (String) data[3], (String) data[4], - ((Integer) data[5]).intValue()); - - break; - case JmolConstants.CALLBACK_PICK: - notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: - notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - break; - case JmolConstants.CALLBACK_SCRIPT: - notifyScriptTermination((String) data[2], - ((Integer) data[3]).intValue()); - break; - case JmolConstants.CALLBACK_ECHO: - sendConsoleEcho((String) data[1]); - break; - case JmolConstants.CALLBACK_MESSAGE: - sendConsoleMessage((data == null) ? ((String) null) - : (String) data[1]); - break; - case JmolConstants.CALLBACK_ERROR: - // System.err.println("Ignoring error callback."); - break; - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_RESIZE: - refreshGUI(); - break; - case JmolConstants.CALLBACK_MEASURE: - - case JmolConstants.CALLBACK_CLICK: - default: - System.err.println("Unhandled callback " + type + " " - + data[1].toString()); - break; - } - } catch (Exception e) - { - System.err.println("Squashed Jmol callback handler error:"); - e.printStackTrace(); - } - } - - public boolean notifyEnabled(int 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: - return true; - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: - } - return false; - } - - // incremented every time a load notification is successfully handled - - // lightweight mechanism for other threads to detect when they can start - // referrring to new structures. - private long loadNotifiesHandled = 0; - - public long getLoadNotifiesHandled() - { - return loadNotifiesHandled; - } - - public void notifyFileLoaded(String fullPathName, String fileName2, - String modelName, String errorMsg, int modelParts) - { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - refreshGUI(); - return; - } - // TODO: deal sensibly with models loaded inLine: - // modelName will be null, as will fullPathName. - - // the rest of this routine ignores the arguments, and simply interrogates - // the Jmol view to find out what structures it contains, and adds them to - // the structure selection manager. - fileLoadingError = null; - 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) - { - int oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - for (int n = 0; n < modelfilenames.length; n++) - { - if (modelfilenames[n] == oldmodels[i]) - { - oldmodels[i] = null; - break; - } - } - if (oldmodels[i] != null) - { - oldm++; - } - } - if (oldm > 0) - { - String[] oldmfn = new String[oldm]; - oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - if (oldmodels[i] != null) - { - oldmfn[oldm++] = oldmodels[i]; - } - } - // deregister the Jmol instance for these structures - we'll add - // ourselves again at the end for the current structure set. - ssm.removeStructureViewerListener(this, oldmfn); - } - } - refreshPdbEntries(); - for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) - { - String fileName = modelfilenames[modelnum]; - boolean foundEntry = false; - MCview.PDBfile pdb = null; - String pdbfile = null, pdbfhash = null; - // model was probably loaded inline - so check the pdb file hashcode - if (loadedInline) - { - // calculate essential attributes for the pdb data imported inline. - // prolly need to resolve modelnumber properly - for now just use our - // 'best guess' - pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum]) - + ".0", "PDB"); - pdbfhash = "" + pdbfile.hashCode(); - } - if (pdbentry != null) - { - // search pdbentries and sequences to find correct pdbentry for this - // model - for (int pe = 0; pe < pdbentry.length; pe++) - { - boolean matches = false; - if (fileName == null) - { - if (false) - // see JAL-623 - need method of matching pasted data up - { - pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile, - AppletFormatAdapter.PASTE); - pdbentry[modelnum].setFile("INLINE" + pdb.id); - matches = true; - foundEntry = true; - } - } - else - { - if (matches = pdbentry[pe].getFile().equals(fileName)) - { - foundEntry = true; - // TODO: Jmol can in principle retrieve from CLASSLOADER but - // this - // needs - // to be tested. See mantis bug - // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 - String protocol = AppletFormatAdapter.URL; - try - { - File fl = new java.io.File(pdbentry[pe].getFile()); - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) - { - } - ; - pdb = ssm.setMapping(sequence[pe], chains[pe], - 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()); - chainNames.addElement(chid); - } - notifyLoaded = true; - } - } - } - if (!foundEntry && associateNewStructs) - { - // this is a foreign pdb file that jalview doesn't know about - add - // it to the dataset and try to find a home - either on a matching - // sequence or as a new sequence. - String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1", - "PDB"); - // parse pdb file into a chain, etc. - // locate best match for pdb in associated views and add mapping to - // ssm - // if properly registered then - notifyLoaded = true; - - } - } - // FILE LOADED OK - // so finally, update the jmol bits and pieces - if (jmolpopup != null) - { - // potential for deadlock here: - // jmolpopup.updateComputedMenus(); - } - if (!isLoadingFromArchive()) - { - viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); - } - // register ourselves as a listener and notify the gui that it needs to - // update itself. - ssm.addStructureViewerListener(this); - if (notifyLoaded) - { - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); - loadNotifiesHandled++; - } - setLoadingFromArchive(false); - } - - public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) - { - notifyAtomPicked(iatom, strMeasure, null); - } - - public abstract void notifyScriptTermination(String strStatus, - int msWalltime); - - /** - * display a message echoed from the jmol viewer - * - * @param strEcho - */ - public abstract void sendConsoleEcho(String strEcho); /* - * { showConsole(true); - * - * history.append("\n" + - * strEcho); } - */ - - // /End JmolStatusListener - // ///////////////////////////// - - /** - * @param strStatus - * status message - usually the response received after a script - * executed - */ - public abstract void sendConsoleMessage(String strStatus); - - public void setCallbackFunction(String callbackType, - String callbackFunction) - { - System.err.println("Ignoring set-callback request to associate " - + callbackType + " with function " + callbackFunction); - - } - - /** - * function to colour all structures using the given Jalview colourscheme. - * This disables the colourBySequence flag but does not record the - * colourscheme used for use later. - * - * @param cs - */ - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - - if (cs == null) - return; - - String res; - int index; - Color col; - jmolHistory(false); - // TODO: Switch between nucleotide or aa selection expressions - Enumeration en = ResidueProperties.aa3Hash.keys(); - StringBuffer command = new StringBuffer("select *;color white;"); - while (en.hasMoreElements()) - { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); - if (index > 20) - continue; - - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - - command.append("select " + res + ";color[" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - } - - evalStateCommand(command.toString()); - jmolHistory(true); - } - - public void showHelp() - { - showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp"); - } - - /** - * open the URL somehow - * - * @param target - */ - public abstract void showUrl(String url, String target); - - /** - * called when the binding thinks the UI needs to be refreshed after a Jmol - * state change. this could be because structures were loaded, or because an - * error has occured. - */ - public abstract void refreshGUI(); - - /** - * called to show or hide the associated console window container. - * - * @param show - */ - public abstract void showConsole(boolean show); - - /** - * @param renderPanel - * @param jmolfileio - * - when true will initialise jmol's file IO system (should be false - * in applet context) - * @param htmlName - * @param documentBase - * @param codeBase - * @param commandOptions - */ - public void allocateViewer(Container renderPanel, boolean jmolfileio, - String htmlName, URL documentBase, URL codeBase, - String commandOptions) - { - allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, - codeBase, commandOptions, null, null); - } - - /** - * - * @param renderPanel - * @param jmolfileio - * - when true will initialise jmol's file IO system (should be false - * in applet context) - * @param htmlName - * @param documentBase - * @param codeBase - * @param commandOptions - * @param consolePanel - * - panel to contain Jmol console - * @param buttonsToShow - * - buttons to show on the console, in ordr - */ - public void allocateViewer(Container renderPanel, boolean jmolfileio, - String htmlName, URL documentBase, URL codeBase, - String commandOptions, final Container consolePanel, - String buttonsToShow) - { +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 + * 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.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 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.*; + +public abstract class JalviewJmolBinding implements StructureListener, + JmolStatusListener, SequenceStructureBinding, + JmolSelectionListener, ComponentListener + +{ + /** + * set if Jmol state is being restored from some source - instructs binding + * not to apply default display style when structure set is updated for first + * time. + */ + private boolean loadingFromArchive = false; + + /** + * state flag used to check if the Jmol viewer's paint method can be called + */ + private boolean finishedInit = false; + + public boolean isFinishedInit() + { + return finishedInit; + } + + public void setFinishedInit(boolean finishedInit) + { + this.finishedInit = finishedInit; + } + + boolean allChainsSelected = false; + + /** + * when true, try to search the associated datamodel for sequences that are + * associated with any unknown structures in the Jmol view. + */ + private boolean associateNewStructs = false; + + Vector atomsPicked = new Vector(); + + public Vector chainNames; + + Hashtable chainFile; + + /** + * array of target chains for seuqences - tied to pdbentry and sequence[] + */ + protected String[][] chains; + + boolean colourBySequence = true; + + StringBuffer eval = new StringBuffer(); + + public String fileLoadingError; + + /** + * the default or current model displayed if the model cannot be identified + * from the selection message + */ + int frameNo = 0; + + protected JmolPopup jmolpopup; + + String lastCommand; + + String lastMessage; + + boolean loadedInline; + + /** + * current set of model filenames loaded in the Jmol instance + */ + String[] modelFileNames = null; + + public PDBEntry[] pdbentry; + + /** + * datasource protocol for access to PDBEntrylatest + */ + String protocol = null; + + StringBuffer resetLastRes = new StringBuffer(); + + /** + * sequences mapped to each pdbentry + */ + public SequenceI[][] sequence; + + StructureSelectionManager ssm; + + public JmolViewer viewer; + + public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + String[][] chains, String protocol) + { + this.sequence = sequenceIs; + this.chains = chains; + this.pdbentry = pdbentry; + this.protocol = protocol; + if (chains == null) + { + this.chains = new String[pdbentry.length][]; + } + /* + * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), + * "jalviewJmol", ap.av.applet .getDocumentBase(), + * ap.av.applet.getCodeBase(), "", this); + * + * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); + */ + } + + public JalviewJmolBinding(JmolViewer viewer2) + { + viewer = viewer2; + viewer.setJmolStatusListener(this); + viewer.addSelectionListener(this); + } + + /** + * construct a title string for the viewer window based on the data jalview + * knows about + * + * @return + */ + public String getViewerTitle() + { + if (sequence == null || pdbentry == null || sequence.length < 1 + || pdbentry.length < 1 || sequence[0].length < 1) + { + return ("Jalview Jmol Window"); + } + // TODO: give a more informative title when multiple structures are + // displayed. + StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":" + + pdbentry[0].getId()); + + if (pdbentry[0].getProperty() != null) + { + if (pdbentry[0].getProperty().get("method") != null) + { + title.append(" Method: "); + title.append(pdbentry[0].getProperty().get("method")); + } + if (pdbentry[0].getProperty().get("chains") != null) + { + title.append(" Chain:"); + title.append(pdbentry[0].getProperty().get("chains")); + } + } + return title.toString(); + } + + /** + * prepare the view for a given set of models/chains. chainList contains + * strings of the form 'pdbfilename:Chaincode' + * + * @param chainList + * list of chains to make visible + */ + public void centerViewer(Vector chainList) + { + StringBuffer cmd = new StringBuffer(); + String lbl; + int mlength, p; + for (int i = 0, iSize = chainList.size(); i < iSize; i++) + { + mlength = 0; + lbl = (String) chainList.elementAt(i); + do + { + 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) + " /" + + (1 + getModelNum((String) chainFile.get(lbl))) + " or "); + } + if (cmd.length() > 0) + cmd.setLength(cmd.length() - 4); + evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd); + } + + public void closeViewer() + { + viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); + // remove listeners for all structures in viewer + StructureSelectionManager.getStructureSelectionManager() + .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; + // TODO: colour by chain should colour each chain distinctly across all + // visible models + // TODO: http://issues.jalview.org/browse/JAL-628 + evalStateCommand("select *;color chain"); + } + + public void colourByCharge() + { + colourBySequence = false; + evalStateCommand("select *;color white;select ASP,GLU;color red;" + + "select LYS,ARG;color blue;select CYS;color yellow"); + } + + /** + * superpose the structures associated with sequences in the alignment + * according to their corresponding positions. + */ + public void superposeStructures(AlignmentI alignment) + { + superposeStructures(alignment, -1, null); + } + + /** + * superpose the structures associated with sequences in the alignment + * according to their corresponding positions. ded) + * + * @param refStructure + * - select which pdb file to use as reference (default is -1 - the + * first structure in the alignment) + */ + public void superposeStructures(AlignmentI alignment, int refStructure) + { + superposeStructures(alignment, refStructure, null); + } + + /** + * superpose the structures associated with sequences in the alignment + * according to their corresponding positions. ded) + * + * @param refStructure + * - select which pdb file to use as reference (default is -1 - the + * first structure in the alignment) + * @param hiddenCols + * TODO + */ + 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) + { + String[] files = getPdbFile(); + 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++) + { + 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(); + + boolean matched[] = new boolean[alignment.getWidth()]; + for (int m = 0; m < matched.length; m++) + { + + 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++) + { + 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 (int sp, m = 0; m < mapping.length; m++) + { + if (mapping[m].getSequence() == sequence[pdbfnum][s] + && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + { + if (refStructure == -1) + { + refStructure = pdbfnum; + } + SequenceI asp = alignment.getSequenceAt(sp); + for (int r = 0; r < matched.length; r++) + { + 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))) + { + // 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) + { + targetC[pdbfnum] = ""; + } + else + { + targetC[pdbfnum] = ":" + mapping[m].getChain(); + } + chainNames[pdbfnum] = mapping[m].getPdbId() + + targetC[pdbfnum]; + // 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++) + { + 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 (matched[r]) + { + if (pdbfnum == 0) + { + nmatched++; + } + if (lpos != commonrpositions[pdbfnum][r] - 1) + { + // discontinuity + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + // molsel.append("} {"); + molsel.append("|"); + } + } + 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("}"); + } + 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("|"); + } + } + } + // 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) + { + continue; + } + command.append("echo "); + command.append("\"Superposing ("); + command.append(chainNames[pdbfnum]); + command.append(") against reference ("); + command.append(chainNames[refStructure]); + command.append(")\";\ncompare "); + 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++) + { + command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); + } + command.append(" ROTATE TRANSLATE;\n"); + } + 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()); + } + if (selectioncom.length() > 0) + {// finally, mark all regions that were superposed. + if (selectioncom.substring(selectioncom.length() - 1).equals("|")) + { + selectioncom.setLength(selectioncom.length() - 1); + } + 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()); + } + } + + public void evalStateCommand(String command) + { + jmolHistory(false); + if (lastCommand == null || !lastCommand.equals(command)) + { + viewer.evalStringQuiet(command + "\n"); + } + jmolHistory(true); + lastCommand = command; + } + + /** + * colour any structures associated with sequences in the given alignment + * using the getFeatureRenderer() and getSequenceRenderer() renderers but only + * if colourBySequence is enabled. + */ + public void colourBySequence(boolean showFeatures, + jalview.api.AlignmentViewPanel alignmentv) + { + if (!colourBySequence) + return; + if (ssm == null) + { + return; + } + String[] files = getPdbFile(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); + + FeatureRenderer fr = null; + if (showFeatures) + { + fr = getFeatureRenderer(alignmentv); + } + AlignmentI alignment = alignmentv.getAlignment(); + + for (String cbyseq : JmolCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment)) { + evalStateCommand(cbyseq); + } + } + + public boolean isColourBySequence() + { + return colourBySequence; + } + + public void setColourBySequence(boolean colourBySequence) + { + this.colourBySequence = colourBySequence; + } + + public void createImage(String file, String type, int quality) + { + System.out.println("JMOL CREATE IMAGE"); + } + + public String createImage(String fileName, String type, + Object textOrBytes, int quality) + { + System.out.println("JMOL CREATE IMAGE"); + return null; + } + + public String eval(String strEval) + { + // System.out.println(strEval); + // "# 'eval' is implemented only for the applet."; + return null; + } + + // End StructureListener + // ////////////////////////// + + public float[][] functionXY(String functionName, int x, int y) + { + return null; + } + + public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) + { + // TODO Auto-generated method stub + return null; + } + + public Color getColour(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + if (getModelNum(pdbfile) < 0) + return null; + // TODO: verify atomIndex is selecting correct model. + return new Color(viewer.getAtomArgb(atomIndex)); + } + + /** + * returns the current featureRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment); + + /** + * instruct the Jalview binding to update the pdbentries vector if necessary + * prior to matching the jmol view's contents to the list of structure files + * Jalview knows about. + */ + public abstract void refreshPdbEntries(); + + private int getModelNum(String modelFileName) + { + String[] mfn = getPdbFile(); + if (mfn == null) + { + return -1; + } + for (int i = 0; i < mfn.length; i++) + { + if (mfn[i].equalsIgnoreCase(modelFileName)) + return i; + } + return -1; + } + + /** + * map between index of model filename returned from getPdbFile and the first + * index of models from this file in the viewer. Note - this is not trimmed - + * use getPdbFile to get number of unique models. + */ + private int _modelFileNameMap[]; + + // //////////////////////////////// + // /StructureListener + public synchronized String[] getPdbFile() + { + if (viewer == null) + { + return new String[0]; + } + if (modelFileNames == null) + { + + String mset[] = new String[viewer.getModelCount()]; + _modelFileNameMap = new int[mset.length]; + int j = 1; + mset[0] = viewer.getModelFileName(0); + for (int i = 1; i < mset.length; i++) + { + mset[j] = viewer.getModelFileName(i); + _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] + : (mset[j - 1] == null || !mset[j].equals(mset[j - 1])))) + { + j++; + } + } + modelFileNames = new String[j]; + System.arraycopy(mset, 0, modelFileNames, 0, j); + } + return modelFileNames; + } + + /** + * map from string to applet + */ + public Map getRegistryInfo() + { + // TODO Auto-generated method stub + return null; + } + + /** + * returns the current sequenceRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); + + // /////////////////////////////// + // JmolStatusListener + + public void handlePopupMenu(int x, int y) + { + jmolpopup.show(x, y); + } + + // jmol/ssm only + public void highlightAtom(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + if (modelFileNames == null) + { + return; + } + + // look up file model number for this pdbfile + int mdlNum = 0; + String fn; + // may need to adjust for URLencoding here - we don't worry about that yet. + while (mdlNum < modelFileNames.length + && !pdbfile.equals(modelFileNames[mdlNum])) + { + // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn); + mdlNum++; + } + if (mdlNum == modelFileNames.length) + { + return; + } + + jmolHistory(false); + // if (!pdbfile.equals(pdbentry.getFile())) + // return; + if (resetLastRes.length() > 0) + { + viewer.evalStringQuiet(resetLastRes.toString()); + } + + eval.setLength(0); + eval.append("select " + pdbResNum); // +modelNum + + resetLastRes.setLength(0); + resetLastRes.append("select " + pdbResNum); // +modelNum + + eval.append(":"); + resetLastRes.append(":"); + if (!chain.equals(" ")) + { + eval.append(chain); + resetLastRes.append(chain); + } + { + eval.append(" /" + (mdlNum + 1)); + resetLastRes.append("/" + (mdlNum + 1)); + } + eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); + + resetLastRes.append(";wireframe 0;" + resetLastRes.toString() + + " and not hetero; spacefill 0;"); + + eval.append("spacefill 200;select none"); + + viewer.evalStringQuiet(eval.toString()); + jmolHistory(true); + + } + + boolean debug = true; + + private void jmolHistory(boolean enable) + { + viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off")); + } + + public void loadInline(String string) + { + loadedInline = true; + // TODO: re JAL-623 + // viewer.loadInline(strModel, isAppend); + // could do this: + // construct fake fullPathName and fileName so we can identify the file + // later. + // Then, construct pass a reader for the string to Jmol. + // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, + // fileName, null, reader, false, null, null, 0); + viewer.openStringInline(string); + } + + public void mouseOverStructure(int atomIndex, String strInfo) + { + int pdbResNum; + int alocsep = strInfo.indexOf("^"); + int mdlSep = strInfo.indexOf("/"); + int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; + + if (chainSeparator == -1) + { + chainSeparator = strInfo.indexOf("."); + if (mdlSep > -1 && mdlSep < chainSeparator) + { + chainSeparator1 = chainSeparator; + chainSeparator = mdlSep; + } + } + // 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) + chainId = strInfo.substring(strInfo.indexOf(":") + 1, + strInfo.indexOf(".")); + else + { + chainId = " "; + } + + String pdbfilename = modelFileNames[frameNo]; // default is first or current + // model + if (mdlSep > -1) + { + if (chainSeparator1 == -1) + { + chainSeparator1 = strInfo.indexOf(".", mdlSep); + } + String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, + chainSeparator1) : strInfo.substring(mdlSep + 1); + try + { + // recover PDB filename for the model hovered over. + pdbfilename = viewer + .getModelFileName(new Integer(mdlId).intValue() - 1); + } catch (Exception e) + { + } + ; + } + if (lastMessage == null || !lastMessage.equals(strInfo)) + ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); + + lastMessage = strInfo; + } + + public void notifyAtomHovered(int atomIndex, String strInfo, String data) + { + if (data != null) + { + System.err.println("Ignoring additional hover info: " + data + + " (other info: '" + strInfo + "' pos " + atomIndex + ")"); + } + mouseOverStructure(atomIndex, strInfo); + } + + /* + * { if (history != null && strStatus != null && + * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); + * } } + */ + + public void notifyAtomPicked(int atomIndex, String strInfo, String strData) + { + /** + * this implements the toggle label behaviour copied from the original + * structure viewer, MCView + */ + if (strData != null) + { + System.err.println("Ignoring additional pick data string " + strData); + } + int chainSeparator = strInfo.indexOf(":"); + int p = 0; + if (chainSeparator == -1) + chainSeparator = strInfo.indexOf("."); + + String picked = strInfo.substring(strInfo.indexOf("]") + 1, + chainSeparator); + String mdlString = ""; + if ((p = strInfo.indexOf(":")) > -1) + picked += strInfo.substring(p + 1, strInfo.indexOf(".")); + + if ((p = strInfo.indexOf("/")) > -1) + { + mdlString += strInfo.substring(p, strInfo.indexOf(" #")); + } + picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" + + mdlString + "))"; + jmolHistory(false); + + if (!atomsPicked.contains(picked)) + { + viewer.evalStringQuiet("select " + picked + ";label %n %r:%c"); + atomsPicked.addElement(picked); + } + else + { + viewer.evalString("select " + picked + ";label off"); + atomsPicked.removeElement(picked); + } + jmolHistory(true); + // TODO: in application this happens + // + // if (scriptWindow != null) + // { + // scriptWindow.sendConsoleMessage(strInfo); + // scriptWindow.sendConsoleMessage("\n"); + // } + + } + + public void notifyCallback(int type, Object[] data) + { + try + { + switch (type) + { + case JmolConstants.CALLBACK_LOADSTRUCT: + notifyFileLoaded((String) data[1], (String) data[2], + (String) data[3], (String) data[4], + ((Integer) data[5]).intValue()); + + break; + case JmolConstants.CALLBACK_PICK: + notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], + (String) data[0]); + // also highlight in alignment + case JmolConstants.CALLBACK_HOVER: + notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], + (String) data[0]); + break; + case JmolConstants.CALLBACK_SCRIPT: + notifyScriptTermination((String) data[2], + ((Integer) data[3]).intValue()); + break; + case JmolConstants.CALLBACK_ECHO: + sendConsoleEcho((String) data[1]); + break; + case JmolConstants.CALLBACK_MESSAGE: + sendConsoleMessage((data == null) ? ((String) null) + : (String) data[1]); + break; + case JmolConstants.CALLBACK_ERROR: + // System.err.println("Ignoring error callback."); + break; + case JmolConstants.CALLBACK_SYNC: + case JmolConstants.CALLBACK_RESIZE: + refreshGUI(); + break; + case JmolConstants.CALLBACK_MEASURE: + + case JmolConstants.CALLBACK_CLICK: + default: + System.err.println("Unhandled callback " + type + " " + + data[1].toString()); + break; + } + } catch (Exception e) + { + System.err.println("Squashed Jmol callback handler error:"); + e.printStackTrace(); + } + } + + public boolean notifyEnabled(int 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: + return true; + case JmolConstants.CALLBACK_RESIZE: + case JmolConstants.CALLBACK_SYNC: + case JmolConstants.CALLBACK_CLICK: + case JmolConstants.CALLBACK_ANIMFRAME: + case JmolConstants.CALLBACK_MINIMIZATION: + } + return false; + } + + // incremented every time a load notification is successfully handled - + // lightweight mechanism for other threads to detect when they can start + // referrring to new structures. + private long loadNotifiesHandled = 0; + + public long getLoadNotifiesHandled() + { + return loadNotifiesHandled; + } + + public void notifyFileLoaded(String fullPathName, String fileName2, + String modelName, String errorMsg, int modelParts) + { + if (errorMsg != null) + { + fileLoadingError = errorMsg; + refreshGUI(); + return; + } + // TODO: deal sensibly with models loaded inLine: + // modelName will be null, as will fullPathName. + + // the rest of this routine ignores the arguments, and simply interrogates + // the Jmol view to find out what structures it contains, and adds them to + // the structure selection manager. + fileLoadingError = null; + 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) + { + int oldm = 0; + for (int i = 0; i < oldmodels.length; i++) + { + for (int n = 0; n < modelfilenames.length; n++) + { + if (modelfilenames[n] == oldmodels[i]) + { + oldmodels[i] = null; + break; + } + } + if (oldmodels[i] != null) + { + oldm++; + } + } + if (oldm > 0) + { + String[] oldmfn = new String[oldm]; + oldm = 0; + for (int i = 0; i < oldmodels.length; i++) + { + if (oldmodels[i] != null) + { + oldmfn[oldm++] = oldmodels[i]; + } + } + // deregister the Jmol instance for these structures - we'll add + // ourselves again at the end for the current structure set. + ssm.removeStructureViewerListener(this, oldmfn); + } + } + refreshPdbEntries(); + for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) + { + String fileName = modelfilenames[modelnum]; + boolean foundEntry = false; + MCview.PDBfile pdb = null; + String pdbfile = null, pdbfhash = null; + // model was probably loaded inline - so check the pdb file hashcode + if (loadedInline) + { + // calculate essential attributes for the pdb data imported inline. + // prolly need to resolve modelnumber properly - for now just use our + // 'best guess' + pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum]) + + ".0", "PDB"); + pdbfhash = "" + pdbfile.hashCode(); + } + if (pdbentry != null) + { + // search pdbentries and sequences to find correct pdbentry for this + // model + for (int pe = 0; pe < pdbentry.length; pe++) + { + boolean matches = false; + if (fileName == null) + { + if (false) + // see JAL-623 - need method of matching pasted data up + { + pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile, + AppletFormatAdapter.PASTE); + pdbentry[modelnum].setFile("INLINE" + pdb.id); + matches = true; + foundEntry = true; + } + } + else + { + if (matches = pdbentry[pe].getFile().equals(fileName)) + { + foundEntry = true; + // TODO: Jmol can in principle retrieve from CLASSLOADER but + // this + // needs + // to be tested. See mantis bug + // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 + String protocol = AppletFormatAdapter.URL; + try + { + File fl = new java.io.File(pdbentry[pe].getFile()); + if (fl.exists()) + { + protocol = AppletFormatAdapter.FILE; + } + } catch (Exception e) + { + } catch (Error e) + { + } + ; + pdb = ssm.setMapping(sequence[pe], chains[pe], + 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()); + chainNames.addElement(chid); + } + notifyLoaded = true; + } + } + } + if (!foundEntry && associateNewStructs) + { + // this is a foreign pdb file that jalview doesn't know about - add + // it to the dataset and try to find a home - either on a matching + // sequence or as a new sequence. + String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1", + "PDB"); + // parse pdb file into a chain, etc. + // locate best match for pdb in associated views and add mapping to + // ssm + // if properly registered then + notifyLoaded = true; + + } + } + // FILE LOADED OK + // so finally, update the jmol bits and pieces + if (jmolpopup != null) + { + // potential for deadlock here: + // jmolpopup.updateComputedMenus(); + } + if (!isLoadingFromArchive()) + { + viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); + } + // register ourselves as a listener and notify the gui that it needs to + // update itself. + ssm.addStructureViewerListener(this); + if (notifyLoaded) + { + FeatureRenderer fr = getFeatureRenderer(null); + if (fr != null) + { + fr.featuresAdded(); + } + refreshGUI(); + loadNotifiesHandled++; + } + setLoadingFromArchive(false); + } + + public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) + { + notifyAtomPicked(iatom, strMeasure, null); + } + + public abstract void notifyScriptTermination(String strStatus, + int msWalltime); + + /** + * display a message echoed from the jmol viewer + * + * @param strEcho + */ + public abstract void sendConsoleEcho(String strEcho); /* + * { showConsole(true); + * + * history.append("\n" + + * strEcho); } + */ + + // /End JmolStatusListener + // ///////////////////////////// + + /** + * @param strStatus + * status message - usually the response received after a script + * executed + */ + public abstract void sendConsoleMessage(String strStatus); + + public void setCallbackFunction(String callbackType, + String callbackFunction) + { + System.err.println("Ignoring set-callback request to associate " + + callbackType + " with function " + callbackFunction); + + } + + public void setJalviewColourScheme(ColourSchemeI cs) + { + colourBySequence = false; + + if (cs == null) + return; + + String res; + int index; + Color col; + jmolHistory(false); + // TODO: Switch between nucleotide or aa selection expressions + Enumeration en = ResidueProperties.aa3Hash.keys(); + StringBuffer command = new StringBuffer("select *;color white;"); + while (en.hasMoreElements()) + { + res = en.nextElement().toString(); + index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); + if (index > 20) + continue; + + col = cs.findColour(ResidueProperties.aa[index].charAt(0)); + + command.append("select " + res + ";color[" + col.getRed() + "," + + col.getGreen() + "," + col.getBlue() + "];"); + } + + evalStateCommand(command.toString()); + jmolHistory(true); + } + + public void showHelp() + { + showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp"); + } + + /** + * open the URL somehow + * + * @param target + */ + public abstract void showUrl(String url, String target); + + /** + * called when the binding thinks the UI needs to be refreshed after a Jmol + * state change. this could be because structures were loaded, or because an + * error has occured. + */ + public abstract void refreshGUI(); + + /** + * called to show or hide the associated console window container. + * + * @param show + */ + public abstract void showConsole(boolean show); + + /** + * @param renderPanel + * @param jmolfileio + * - when true will initialise jmol's file IO system (should be false + * in applet context) + * @param htmlName + * @param documentBase + * @param codeBase + * @param commandOptions + */ + public void allocateViewer(Container renderPanel, boolean jmolfileio, + String htmlName, URL documentBase, URL codeBase, + String commandOptions) + { + allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, + codeBase, commandOptions, null, null); + } + + /** + * + * @param renderPanel + * @param jmolfileio + * - when true will initialise jmol's file IO system (should be false + * in applet context) + * @param htmlName + * @param documentBase + * @param codeBase + * @param commandOptions + * @param consolePanel + * - panel to contain Jmol console + * @param buttonsToShow + * - buttons to show on the console, in ordr + */ + 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, - commandOptions, this); - - console = createJmolConsole(viewer, consolePanel, buttonsToShow); - if (consolePanel != null) - { - consolePanel.addComponentListener(this); - - } - - } - - protected abstract JmolAppConsoleInterface createJmolConsole( - JmolViewer viewer2, Container consolePanel, String buttonsToShow); - - protected org.jmol.api.JmolAppConsoleInterface console = null; - - public void componentResized(ComponentEvent e) - { - - } - - public void componentMoved(ComponentEvent e) - { - - } - - public void componentShown(ComponentEvent e) - { - showConsole(true); - } - - public void componentHidden(ComponentEvent e) - { - showConsole(false); - } - - public void setLoadingFromArchive(boolean loadingFromArchive) - { - this.loadingFromArchive = loadingFromArchive; - } - - public boolean isLoadingFromArchive() - { - return loadingFromArchive; - } - - public void setBackgroundColour(java.awt.Color col) - { - jmolHistory(false); - viewer.evalStringQuiet("background [" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - jmolHistory(true); - } - - /** - * add structures and any known sequence associations - * - * @returns the pdb entries added to the current set. - */ - public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, - SequenceI[][] seq, String[][] chns) - { - int pe = -1; - Vector v = new Vector(); - Vector rtn = new Vector(); - for (int i = 0; i < pdbentry.length; i++) - { - v.addElement(pdbentry[i]); - } - for (int i = 0; i < pdbe.length; i++) - { - int r = v.indexOf(pdbe[i]); - if (r == -1 || r >= pdbentry.length) - { - rtn.addElement(new int[] - { v.size(), i }); - v.addElement(pdbe[i]); - } - else - { - // just make sure the sequence/chain entries are all up to date - addSequenceAndChain(r, seq[i], chns[i]); - } - } - pdbe = new PDBEntry[v.size()]; - v.copyInto(pdbe); - pdbentry = pdbe; - if (rtn.size() > 0) - { - // expand the tied seuqence[] and string[] arrays - SequenceI[][] sqs = new SequenceI[pdbentry.length][]; - String[][] sch = new String[pdbentry.length][]; - System.arraycopy(sequence, 0, sqs, 0, sequence.length); - System.arraycopy(chains, 0, sch, 0, this.chains.length); - sequence = sqs; - chains = sch; - pdbe = new PDBEntry[rtn.size()]; - for (int r = 0; r < pdbe.length; r++) - { - int[] stri = ((int[]) rtn.elementAt(r)); - // record the pdb file as a new addition - pdbe[r] = pdbentry[stri[0]]; - // and add the new sequence/chain entries - addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); - } - } - else - { - pdbe = null; - } - return pdbe; - } - - public void addSequence(int pe, SequenceI[] seq) - { - // add sequences to the pe'th pdbentry's seuqence set. - addSequenceAndChain(pe, seq, null); - } - - private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) - { - if (pe < 0 || pe >= pdbentry.length) - { - throw new Error( - "Implementation error - no corresponding pdbentry (for index " - + pe + ") to add sequences mappings to"); - } - final String nullChain = "TheNullChain"; - Vector s = new Vector(); - Vector c = new Vector(); - if (chains == null) - { - chains = new String[pdbentry.length][]; - } - if (sequence[pe] != null) - { - for (int i = 0; i < sequence[pe].length; i++) - { - s.addElement(sequence[pe][i]); - if (chains[pe] != null) - { - if (i < chains[pe].length) - { - c.addElement(chains[pe][i]); - } - else - { - c.addElement(nullChain); - } - } - else - { - if (tchain != null && tchain.length > 0) - { - c.addElement(nullChain); - } - } - } - } - for (int i = 0; i < seq.length; i++) - { - if (!s.contains(seq[i])) - { - s.addElement(seq[i]); - if (tchain != null && i < tchain.length) - { - c.addElement(tchain[i] == null ? nullChain : tchain[i]); - } - } - } - SequenceI[] tmp = new SequenceI[s.size()]; - s.copyInto(tmp); - sequence[pe] = tmp; - if (c.size() > 0) - { - String[] tch = new String[c.size()]; - c.copyInto(tch); - for (int i = 0; i < tch.length; i++) - { - if (tch[i] == nullChain) - { - tch[i] = null; - } - } - chains[pe] = tch; - } - else - { - chains[pe] = null; - } - } -} + viewer = JmolViewer.allocateViewer(renderPanel, + (jmolfileio ? new SmarterJmolAdapter() : null), htmlName + + ((Object) this).toString(), documentBase, codeBase, + commandOptions, this); + + console = createJmolConsole(viewer, consolePanel, buttonsToShow); + if (consolePanel != null) + { + consolePanel.addComponentListener(this); + + } + + } + + protected abstract JmolAppConsoleInterface createJmolConsole( + JmolViewer viewer2, Container consolePanel, String buttonsToShow); + + protected org.jmol.api.JmolAppConsoleInterface console = null; + + public void componentResized(ComponentEvent e) + { + + } + + public void componentMoved(ComponentEvent e) + { + + } + + public void componentShown(ComponentEvent e) + { + showConsole(true); + } + + public void componentHidden(ComponentEvent e) + { + showConsole(false); + } + + public void setLoadingFromArchive(boolean loadingFromArchive) + { + this.loadingFromArchive = loadingFromArchive; + } + + public boolean isLoadingFromArchive() + { + return loadingFromArchive; + } + + public void setBackgroundColour(java.awt.Color col) + { + jmolHistory(false); + viewer.evalStringQuiet("background [" + col.getRed() + "," + + col.getGreen() + "," + col.getBlue() + "];"); + jmolHistory(true); + } + + /** + * add structures and any known sequence associations + * + * @returns the pdb entries added to the current set. + */ + public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, + SequenceI[][] seq, String[][] chns) + { + int pe = -1; + Vector v = new Vector(); + Vector rtn = new Vector(); + for (int i = 0; i < pdbentry.length; i++) + { + v.addElement(pdbentry[i]); + } + for (int i = 0; i < pdbe.length; i++) + { + int r = v.indexOf(pdbe[i]); + if (r == -1 || r >= pdbentry.length) + { + rtn.addElement(new int[] + { v.size(), i }); + v.addElement(pdbe[i]); + } + else + { + // just make sure the sequence/chain entries are all up to date + addSequenceAndChain(r, seq[i], chns[i]); + } + } + pdbe = new PDBEntry[v.size()]; + v.copyInto(pdbe); + pdbentry = pdbe; + if (rtn.size() > 0) + { + // expand the tied seuqence[] and string[] arrays + SequenceI[][] sqs = new SequenceI[pdbentry.length][]; + String[][] sch = new String[pdbentry.length][]; + System.arraycopy(sequence, 0, sqs, 0, sequence.length); + System.arraycopy(chains, 0, sch, 0, this.chains.length); + sequence = sqs; + chains = sch; + pdbe = new PDBEntry[rtn.size()]; + for (int r = 0; r < pdbe.length; r++) + { + int[] stri = ((int[]) rtn.elementAt(r)); + // record the pdb file as a new addition + pdbe[r] = pdbentry[stri[0]]; + // and add the new sequence/chain entries + addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); + } + } + else + { + pdbe = null; + } + return pdbe; + } + + public void addSequence(int pe, SequenceI[] seq) + { + // add sequences to the pe'th pdbentry's seuqence set. + addSequenceAndChain(pe, seq, null); + } + + private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) + { + if (pe < 0 || pe >= pdbentry.length) + { + throw new Error( + "Implementation error - no corresponding pdbentry (for index " + + pe + ") to add sequences mappings to"); + } + final String nullChain = "TheNullChain"; + Vector s = new Vector(); + Vector c = new Vector(); + if (chains == null) + { + chains = new String[pdbentry.length][]; + } + if (sequence[pe] != null) + { + for (int i = 0; i < sequence[pe].length; i++) + { + s.addElement(sequence[pe][i]); + if (chains[pe] != null) + { + if (i < chains[pe].length) + { + c.addElement(chains[pe][i]); + } + else + { + c.addElement(nullChain); + } + } + else + { + if (tchain != null && tchain.length > 0) + { + c.addElement(nullChain); + } + } + } + } + for (int i = 0; i < seq.length; i++) + { + if (!s.contains(seq[i])) + { + s.addElement(seq[i]); + if (tchain != null && i < tchain.length) + { + c.addElement(tchain[i] == null ? nullChain : tchain[i]); + } + } + } + SequenceI[] tmp = new SequenceI[s.size()]; + s.copyInto(tmp); + sequence[pe] = tmp; + if (c.size() > 0) + { + String[] tch = new String[c.size()]; + c.copyInto(tch); + for (int i = 0; i < tch.length; i++) + { + if (tch[i] == nullChain) + { + tch[i] = null; + } + } + chains[pe] = tch; + } + else + { + chains[pe] = null; + } + } +} diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java new file mode 100644 index 0000000..acf27f6 --- /dev/null +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -0,0 +1,135 @@ +/** + * + */ +package jalview.ext.jmol; + +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; + +import java.awt.Color; +import java.util.ArrayList; + +/** + * Routines for generating Jmol commands for Jalview/Jmol binding + * @author JimP + * + */ +public class JmolCommands +{ + + /** + * Jmol utility which constructs the commands to colour chains by the given alignment + * + */ + public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) + { + ArrayList str = new ArrayList(); + 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 (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 (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.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom)) + { + command = JmolCommands.condenseCommand(command, pos); + continue; + } + // TODO: deal with case when buffer is too large for Jmol to parse + // - execute command and flush + + command.append(";"); + if (command.length()>51200) + { + // add another chunk + str.add(command.toString()); + command.setLength(0); + } + command.append("select " + pos); + command.append(newSelcom); + } + break; + } + } + } + } + return str.toArray(new String[str.size()]); + } + + public static StringBuffer condenseCommand(StringBuffer command, int pos) + { + + // work back to last 'select' + int p=command.length(),q=p; + do { + p-=6; + if (p<1) { p=0; }; + } while ((q=command.indexOf("select",p))==-1 && p>0); + + StringBuffer sb = new StringBuffer(command.substring(0,q+7)); + + command = command.delete(0,q+7); + + 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; + } + +} -- 1.7.10.2