X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=038ca48f2253af6956017e767f8271637f454cac;hb=4a67afac64ed574a5b79c7d33c97e58e26f60f30;hp=c075bf58bf9f4de18153ea7a346e5ab110ae459d;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index c075bf5..038ca48 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,32 +20,15 @@ */ package jalview.ext.jmol; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.api.SequenceStructureBinding; -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.ArrayList; +import java.util.List; import java.util.Map; +import java.util.StringTokenizer; import java.util.Vector; import org.jmol.adapter.smarter.SmarterJmolAdapter; @@ -53,118 +36,51 @@ 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; +import org.jmol.c.CBK; +import org.jmol.viewer.Viewer; -public abstract class JalviewJmolBinding implements StructureListener, - JmolStatusListener, SequenceStructureBinding, - JmolSelectionListener, ComponentListener, - StructureSelectionManagerProvider +import jalview.api.FeatureRenderer; +import jalview.bin.Cache; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.IProgressIndicator; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; +import jalview.io.StructureFile; +import jalview.structure.AtomSpec; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; +public abstract class JalviewJmolBinding extends AAStructureBindingModel + implements JmolStatusListener, 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; + private String lastMessage; - /** - * 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 - */ - 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; + private Vector atomsPicked = new Vector<>(); - protected JmolPopup jmolpopup; + private String lastCommand; - String lastCommand; + private boolean loadedInline; - String lastMessage; + private StringBuffer resetLastRes = new StringBuffer(); - 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; - - public StructureSelectionManager ssm; - - public JmolViewer viewer; + public Viewer jmolViewer; public JalviewJmolBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { - this.ssm = ssm; - this.sequence = sequenceIs; - this.chains = chains; - this.pdbentry = pdbentry; - this.protocol = protocol; - if (chains == null) - { - this.chains = new String[pdbentry.length][]; - } + super(ssm, pdbentry, sequenceIs, protocol); + setStructureCommands(new JmolCommands()); /* * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), * "jalviewJmol", ap.av.applet .getDocumentBase(), @@ -175,12 +91,14 @@ public abstract class JalviewJmolBinding implements StructureListener, } public JalviewJmolBinding(StructureSelectionManager ssm, - JmolViewer viewer2) + SequenceI[][] seqs, Viewer theViewer) { - this.ssm = ssm; - viewer = viewer2; - viewer.setJmolStatusListener(this); - viewer.addSelectionListener(this); + super(ssm, seqs); + + jmolViewer = theViewer; + jmolViewer.setJmolStatusListener(this); + jmolViewer.addSelectionListener(this); + setStructureCommands(new JmolCommands()); } /** @@ -191,490 +109,35 @@ public abstract class JalviewJmolBinding implements StructureListener, */ 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 - 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; - // 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); + return getViewerTitle("Jmol", true); } - /** - * 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) + private String jmolScript(String script) { - superposeStructures(alignment, refStructure, null); - } + Cache.log.debug(">>Jmol>> " + script); + String s = jmolViewer.scriptWait(script); + Cache.log.debug("< executeCommand(StructureCommandI command, + boolean getReply) { - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - - String[] files = getPdbFile(); - // check to see if we are still waiting for Jmol files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do + if (command == null) { - waiting = false; - for (String file : files) - { - try - { - // HACK - in Jalview 2.8 this call may not be threadsafe so we catch - // every possible exception - StructureMapping[] sm = ssm.getMapping(file); - if (sm == null || sm.length == 0) - { - waiting = true; - } - } catch (Exception x) - { - waiting = true; - } catch (Error q) - { - waiting = true; - } - } - // we wait around for a reasonable time before we give up - } while (waiting - && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime)); - if (waiting) - { - System.err - .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); - return; - } - StringBuffer selectioncom = new StringBuffer(); - // 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) - { - nSeconds = " 0.00001 "; - } - else - { - nSeconds = " " + (2.0 / files.length) + " "; - // if (nSeconds).substring(0,5)+" "; - } - // 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++) - { - 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]); - // RACE CONDITION - getMapping only returns Jmol loaded filenames once - // Jmol callback has completed. - if (mapping == null || mapping.length < 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 (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; - } - } - } - } - - // 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 - { - 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("}"); - } - 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("|"); - } - } - else - { - selcom[pdbfnum] = null; - } - } - } - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - if (pdbfnum == refStructure || selcom[pdbfnum] == null - || selcom[refStructure] == null) - { - continue; - } - 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++) - { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - } - command.append(" ROTATE TRANSLATE;\n"); - } - if (selectioncom.length() > 0) - { - 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()); + return null; } - } - - public void evalStateCommand(String command) - { + String cmd = command.getCommand(); jmolHistory(false); - if (lastCommand == null || !lastCommand.equals(command)) + if (lastCommand == null || !lastCommand.equals(cmd)) { - viewer.evalStringQuiet(command + "\n"); + jmolScript(cmd + "\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 || !loadingFinished) - 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 (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands - .getColourBySequenceCommand(ssm, files, sequence, sr, fr, - alignment)) - for (String cbyseq : cpdbbyseq.commands) - { - evalStateCommand(cbyseq); - } - } - - public boolean isColourBySequence() - { - return colourBySequence; - } - - public void setColourBySequence(boolean colourBySequence) - { - this.colourBySequence = colourBySequence; + lastCommand = cmd; + return null; } public void createImage(String file, String type, int quality) @@ -682,6 +145,7 @@ public abstract class JalviewJmolBinding implements StructureListener, System.out.println("JMOL CREATE IMAGE"); } + @Override public String createImage(String fileName, String type, Object textOrBytes, int quality) { @@ -689,6 +153,7 @@ public abstract class JalviewJmolBinding implements StructureListener, return null; } + @Override public String eval(String strEval) { // System.out.println(strEval); @@ -699,59 +164,20 @@ public abstract class JalviewJmolBinding implements StructureListener, // End StructureListener // ////////////////////////// + @Override public float[][] functionXY(String functionName, int x, int y) { return null; } - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) + @Override + 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 - @@ -759,156 +185,117 @@ public abstract class JalviewJmolBinding implements StructureListener, */ private int _modelFileNameMap[]; - // //////////////////////////////// - // /StructureListener - public synchronized String[] getPdbFile() + @Override + public synchronized String[] getStructureFiles() { - if (viewer == null) + if (jmolViewer == null) { return new String[0]; } + if (modelFileNames == null) { - - String mset[] = new String[viewer.getModelCount()]; - _modelFileNameMap = new int[mset.length]; - int j = 1; - String m = viewer.getModelFileName(0); - if (m != null) - { - try - { - mset[0] = new File(m).getAbsolutePath(); - } catch (AccessControlException x) + int modelCount = jmolViewer.ms.mc; + String filePath = null; + List mset = new ArrayList<>(); + for (int i = 0; i < modelCount; ++i) + { + /* + * defensive check for null as getModelFileName can return null + * even when model count ms.mc is > 0 + */ + filePath = jmolViewer.ms.getModelFileName(i); + if (filePath != null && !mset.contains(filePath)) { - // 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); + mset.add(filePath); } } - for (int i = 1; i < mset.length; i++) + if (!mset.isEmpty()) { - 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] - : (mset[j - 1] == null || !mset[j].equals(mset[j - 1])))) - { - j++; - } + modelFileNames = mset.toArray(new String[mset.size()]); } - modelFileNames = new String[j]; - System.arraycopy(mset, 0, modelFileNames, 0, j); } + return modelFileNames; } /** * map from string to applet */ - public Map getRegistryInfo() + @Override + 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); + // jmolpopup.show(x, y); + // jmolpopup.jpiShow(x, y); } - // jmol/ssm only - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + /** + * Highlight zero, one or more atoms on the structure + */ + @Override + public void highlightAtoms(List atoms) { - if (modelFileNames == null) + if (atoms != null) { - return; + if (resetLastRes.length() > 0) + { + jmolScript(resetLastRes.toString()); + resetLastRes.setLength(0); + } + for (AtomSpec atom : atoms) + { + highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), + atom.getChain(), atom.getPdbFile()); + } } + } - // 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) + // jmol/ssm only + public void highlightAtom(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + String modelId = getModelIdForFile(pdbfile); + if (modelId.isEmpty()) { 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(":"); + StringBuilder selection = new StringBuilder(32); + StringBuilder cmd = new StringBuilder(64); + selection.append("select ").append(String.valueOf(pdbResNum)); + selection.append(":"); if (!chain.equals(" ")) { - eval.append(chain); - resetLastRes.append(chain); - } - { - eval.append(" /" + (mdlNum + 1)); - resetLastRes.append("/" + (mdlNum + 1)); + selection.append(chain); } - eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); + selection.append(" /").append(modelId); - resetLastRes.append(";wireframe 0;" + resetLastRes.toString() - + " and not hetero; spacefill 0;"); + cmd.append(selection).append(";wireframe 100;").append(selection) + .append(" and not hetero;").append("spacefill 200;select none"); - eval.append("spacefill 200;select none"); + resetLastRes.append(selection).append(";wireframe 0;").append(selection) + .append(" and not hetero; spacefill 0;"); - viewer.evalStringQuiet(eval.toString()); + jmolScript(cmd.toString()); jmolHistory(true); - } - boolean debug = true; + private boolean debug = true; private void jmolHistory(boolean enable) { - viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off")); + jmolScript("History " + ((debug || enable) ? "on" : "off")); } public void loadInline(String string) @@ -922,10 +309,10 @@ public abstract class JalviewJmolBinding implements StructureListener, // 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); + jmolViewer.openStringInline(string); } - public void mouseOverStructure(int atomIndex, String strInfo) + protected void mouseOverStructure(int atomIndex, final String strInfo) { int pdbResNum; int alocsep = strInfo.indexOf("^"); @@ -944,64 +331,97 @@ public abstract class JalviewJmolBinding implements StructureListener, // handle insertion codes if (alocsep != -1) { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, alocsep)); + pdbResNum = Integer.parseInt( + strInfo.substring(strInfo.indexOf("]") + 1, alocsep)); } else { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); + 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 + String pdbfilename = modelFileNames[0]; // default is first model if (mdlSep > -1) { if (chainSeparator1 == -1) { chainSeparator1 = strInfo.indexOf(".", mdlSep); } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); + String mdlId = (chainSeparator1 > -1) + ? strInfo.substring(mdlSep + 1, chainSeparator1) + : strInfo.substring(mdlSep + 1); try { // recover PDB filename for the model hovered over. - int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId) - .intValue() - 1; - while (mnumber < _modelFileNameMap[_mp]) + int mnumber = Integer.valueOf(mdlId).intValue() - 1; + if (_modelFileNameMap != null) { - _mp--; + int _mp = _modelFileNameMap.length - 1; + + while (mnumber < _modelFileNameMap[_mp]) + { + _mp--; + } + pdbfilename = modelFileNames[_mp]; } - pdbfilename = modelFileNames[_mp]; - if (pdbfilename == null) + else { - pdbfilename = new File(viewer.getModelFileName(mnumber)) - .getAbsolutePath(); - } + if (mnumber >= 0 && mnumber < modelFileNames.length) + { + pdbfilename = modelFileNames[mnumber]; + } + if (pdbfilename == null) + { + pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber)) + .getAbsolutePath(); + } + } } catch (Exception e) { } - ; } - if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); - lastMessage = strInfo; + /* + * highlight position on alignment(s); if some text is returned, + * show this as a second line on the structure hover tooltip + */ + String label = getSsm().mouseOverStructure(pdbResNum, chainId, + pdbfilename); + if (label != null) + { + // change comma to pipe separator (newline token for Jmol) + label = label.replace(',', '|'); + StringTokenizer toks = new StringTokenizer(strInfo, " "); + StringBuilder sb = new StringBuilder(); + sb.append("select ").append(String.valueOf(pdbResNum)).append(":") + .append(chainId).append("/1"); + sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ") + .append(toks.nextToken()); + sb.append("|").append(label).append("\""); + executeCommand(new StructureCommand(sb.toString()), false); + } } public void notifyAtomHovered(int atomIndex, String strInfo, String data) { + if (strInfo.equals(lastMessage)) + { + return; + } + lastMessage = strInfo; if (data != null) { System.err.println("Ignoring additional hover info: " + data @@ -1016,11 +436,12 @@ public abstract class JalviewJmolBinding implements StructureListener, * } } */ - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) + public void notifyAtomPicked(int atomIndex, String strInfo, + String strData) { /** * this implements the toggle label behaviour copied from the original - * structure viewer, MCView + * structure viewer, mc_view */ if (strData != null) { @@ -1029,13 +450,17 @@ public abstract class JalviewJmolBinding implements StructureListener, 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(".")); + { + picked += strInfo.substring(p, strInfo.indexOf(".")); + } if ((p = strInfo.indexOf("/")) > -1) { @@ -1047,12 +472,12 @@ public abstract class JalviewJmolBinding implements StructureListener, if (!atomsPicked.contains(picked)) { - viewer.evalStringQuiet("select " + picked + ";label %n %r:%c"); + jmolScript("select " + picked + ";label %n %r:%c"); atomsPicked.addElement(picked); } else { - viewer.evalString("select " + picked + ";label off"); + jmolViewer.evalString("select " + picked + ";label off"); atomsPicked.removeElement(picked); } jmolHistory(true); @@ -1067,7 +492,7 @@ public abstract class JalviewJmolBinding implements StructureListener, } @Override - public void notifyCallback(EnumCallback type, Object[] data) + public void notifyCallback(CBK type, Object[] data) { try { @@ -1083,6 +508,7 @@ public abstract class JalviewJmolBinding implements StructureListener, notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); // also highlight in alignment + // deliberate fall through case HOVER: notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); @@ -1095,8 +521,8 @@ public abstract class JalviewJmolBinding implements StructureListener, sendConsoleEcho((String) data[1]); break; case MESSAGE: - sendConsoleMessage((data == null) ? ((String) null) - : (String) data[1]); + sendConsoleMessage( + (data == null) ? ((String) null) : (String) data[1]); break; case ERROR: // System.err.println("Ignoring error callback."); @@ -1109,8 +535,8 @@ public abstract class JalviewJmolBinding implements StructureListener, case CLICK: default: - System.err.println("Unhandled callback " + type + " " - + data[1].toString()); + System.err.println( + "Unhandled callback " + type + " " + data[1].toString()); break; } } catch (Exception e) @@ -1121,7 +547,7 @@ public abstract class JalviewJmolBinding implements StructureListener, } @Override - public boolean notifyEnabled(EnumCallback callbackPick) + public boolean notifyEnabled(CBK callbackPick) { switch (callbackPick) { @@ -1134,13 +560,9 @@ public abstract class JalviewJmolBinding implements StructureListener, case HOVER: case ERROR: return true; - case RESIZE: - case SYNC: - case CLICK: - case ANIMFRAME: - case MINIMIZATION: + default: + return false; } - return false; } // incremented every time a load notification is successfully handled - @@ -1171,10 +593,8 @@ public abstract class JalviewJmolBinding implements StructureListener, fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new Vector(); - chainFile = new Hashtable(); boolean notifyLoaded = false; - String[] modelfilenames = getPdbFile(); + String[] modelfilenames = getStructureFiles(); // first check if we've lost any structures if (oldmodels != null && oldmodels.length > 0) { @@ -1207,7 +627,7 @@ public abstract class JalviewJmolBinding implements StructureListener, } // deregister the Jmol instance for these structures - we'll add // ourselves again at the end for the current structure set. - ssm.removeStructureViewerListener(this, oldmfn); + getSsm().removeStructureViewerListener(this, oldmfn); } } refreshPdbEntries(); @@ -1215,88 +635,79 @@ public abstract class JalviewJmolBinding implements StructureListener, { String fileName = modelfilenames[modelnum]; boolean foundEntry = false; - MCview.PDBfile pdb = null; - String pdbfile = null, pdbfhash = null; + StructureFile pdb = null; + String pdbfile = 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(); + pdbfile = jmolViewer.getData( + "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB"); } - if (pdbentry != null) + // search pdbentries and sequences to find correct pdbentry for this + // model + for (int pe = 0; pe < getPdbCount(); pe++) { - // search pdbentries and sequences to find correct pdbentry for this - // model - for (int pe = 0; pe < pdbentry.length; pe++) + boolean matches = false; + addSequence(pe, getSequence()[pe]); + if (fileName == null) { - boolean matches = false; - if (fileName == null) + if (false) + // see JAL-623 - need method of matching pasted data up { - 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; - } + pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], + pdbfile, DataSourceType.PASTE, getIProgressIndicator()); + getPdbEntry(modelnum).setFile("INLINE" + pdb.getId()); + matches = true; + foundEntry = true; } - else + } + else + { + File fl = new File(getPdbEntry(pe).getFile()); + matches = fl.equals(new File(fileName)); + if (matches) { - 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 + // this + // needs + // to be tested. See mantis bug + // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 + DataSourceType protocol = DataSourceType.URL; + try { - 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 - { - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) + if (fl.exists()) { + protocol = DataSourceType.FILE; } - // Explicitly map to the filename used by Jmol ; - pdb = ssm.setMapping(sequence[pe], chains[pe], fileName, - protocol); - // pdbentry[pe].getFile(), protocol); - - } - } - if (matches) - { - // add an entry for every chain in the model - for (int i = 0; i < pdb.chains.size(); i++) + } catch (Exception e) + { + } catch (Error e) { - String chid = new String(pdb.id + ":" - + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); - chainFile.put(chid, fileName); - chainNames.addElement(chid); } - notifyLoaded = true; + // Explicitly map to the filename used by Jmol ; + pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], + fileName, protocol, getIProgressIndicator()); + // pdbentry[pe].getFile(), protocol); + } } + if (matches) + { + stashFoundChains(pdb, fileName); + 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", + String pdbcontent = jmolViewer.getData("/" + (modelnum + 1) + ".1", "PDB"); // parse pdb file into a chain, etc. // locate best match for pdb in associated views and add mapping to @@ -1308,18 +719,19 @@ public abstract class JalviewJmolBinding implements StructureListener, } // FILE LOADED OK // so finally, update the jmol bits and pieces - if (jmolpopup != null) - { - // potential for deadlock here: - // jmolpopup.updateComputedMenus(); - } + // if (jmolpopup != null) + // { + // // potential for deadlock here: + // // jmolpopup.updateComputedMenus(); + // } if (!isLoadingFromArchive()) { - viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); + jmolScript( + "model *; 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); + getSsm().addStructureViewerListener(this); if (notifyLoaded) { FeatureRenderer fr = getFeatureRenderer(null); @@ -1333,6 +745,11 @@ public abstract class JalviewJmolBinding implements StructureListener, setLoadingFromArchive(false); } + protected IProgressIndicator getIProgressIndicator() + { + return null; + } + public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) { notifyAtomPicked(iatom, strMeasure, null); @@ -1363,6 +780,7 @@ public abstract class JalviewJmolBinding implements StructureListener, */ public abstract void sendConsoleMessage(String strStatus); + @Override public void setCallbackFunction(String callbackType, String callbackFunction) { @@ -1371,40 +789,11 @@ public abstract class JalviewJmolBinding implements StructureListener, } - 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"); + showUrl("http://wiki.jmol.org" + // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/" + , "jmolHelp"); } /** @@ -1415,20 +804,22 @@ public abstract class JalviewJmolBinding implements StructureListener, 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); + public static Viewer getJmolData(JmolParser jmolParser) + { + return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null, + "-x -o -n", jmolParser); + } + /** + * + * + * * @param renderPanel * @param jmolfileio * - when true will initialise jmol's file IO system (should be false @@ -1459,23 +850,36 @@ public abstract class JalviewJmolBinding implements StructureListener, * @param consolePanel * - panel to contain Jmol console * @param buttonsToShow - * - buttons to show on the console, in ordr + * - buttons to show on the console, in order */ public void allocateViewer(Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, String commandOptions, final Container consolePanel, String buttonsToShow) { + + System.err.println("Allocating Jmol Viewer: " + commandOptions); + if (commandOptions == null) { commandOptions = ""; } - viewer = JmolViewer.allocateViewer(renderPanel, - (jmolfileio ? new SmarterJmolAdapter() : null), htmlName - + ((Object) this).toString(), documentBase, codeBase, + jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel, + (jmolfileio ? new SmarterJmolAdapter() : null), + htmlName + ((Object) this).toString(), documentBase, codeBase, commandOptions, this); - console = createJmolConsole(viewer, consolePanel, buttonsToShow); + jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener + + try + { + console = createJmolConsole(consolePanel, buttonsToShow); + } catch (Throwable e) + { + System.err.println("Could not create Jmol application console. " + + e.getMessage()); + e.printStackTrace(); + } if (consolePanel != null) { consolePanel.addComponentListener(this); @@ -1485,217 +889,112 @@ public abstract class JalviewJmolBinding implements StructureListener, } protected abstract JmolAppConsoleInterface createJmolConsole( - JmolViewer viewer2, Container consolePanel, String buttonsToShow); + Container consolePanel, String buttonsToShow); - protected org.jmol.api.JmolAppConsoleInterface console = null; + // BH 2018 -- Jmol console is not working due to problems with styled + // documents. - public void componentResized(ComponentEvent e) - { - - } - - public void componentMoved(ComponentEvent e) - { - - } + protected org.jmol.api.JmolAppConsoleInterface console = null; - public void componentShown(ComponentEvent e) + @Override + public int[] resizeInnerPanel(String data) { - showConsole(true); + // Jalview doesn't honour resize panel requests + return null; } - public void componentHidden(ComponentEvent e) + /** + * + */ + protected void closeConsole() { - showConsole(false); + if (console != null) + { + try + { + console.setVisible(false); + } catch (Error e) + { + } catch (Exception x) + { + } + ; + console = null; + } } - public void setLoadingFromArchive(boolean loadingFromArchive) + /** + * ComponentListener method + */ + @Override + public void componentMoved(ComponentEvent e) { - this.loadingFromArchive = loadingFromArchive; } /** - * - * @return true if Jmol is still restoring state or loading is still going on - * (see setFinsihedLoadingFromArchive) + * ComponentListener method */ - public boolean isLoadingFromArchive() + @Override + public void componentResized(ComponentEvent e) { - return loadingFromArchive && !loadingFinished; } /** - * modify flag which controls if sequence colouring events are honoured by the - * binding. Should be true for normal operation - * - * @param finishedLoading + * ComponentListener method */ - public void setFinishedLoadingFromArchive(boolean finishedLoading) + @Override + public void componentShown(ComponentEvent e) { - loadingFinished = finishedLoading; + showConsole(true); } - public void setBackgroundColour(java.awt.Color col) + /** + * ComponentListener method + */ + @Override + public void componentHidden(ComponentEvent e) { - jmolHistory(false); - viewer.evalStringQuiet("background [" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - jmolHistory(true); + showConsole(false); } - /** - * 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) + @Override + protected String getModelIdForFile(String pdbFile) { - int pe = -1; - Vector v = new Vector(); - Vector rtn = new Vector(); - for (int i = 0; i < pdbentry.length; i++) + if (modelFileNames == null) { - v.addElement(pdbentry[i]); + return ""; } - for (int i = 0; i < pdbe.length; i++) + for (int i = 0; i < modelFileNames.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 + if (modelFileNames[i].equalsIgnoreCase(pdbFile)) { - // just make sure the sequence/chain entries are all up to date - addSequenceAndChain(r, seq[i], chns[i]); + return String.valueOf(i + 1); } } - 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; + return ""; } - public void addSequence(int pe, SequenceI[] seq) + @Override + protected ViewerType getViewerType() { - // add sequences to the pe'th pdbentry's seuqence set. - addSequenceAndChain(pe, seq, null); + return ViewerType.JMOL; } - private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) + @Override + protected String getModelId(int pdbfnum, String file) { - 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; - } + return String.valueOf(pdbfnum + 1); } /** + * Returns ".spt" - the Jmol session file extension * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences + * @return + * @see https://chemapps.stolaf.edu/jmol/docs/#writemodel */ - public String printMapping(String pdbfile) - { - return ssm.printMapping(pdbfile); - } - @Override - public void resizeInnerPanel(String data) + public String getSessionFileExtension() { - // Jalview doesn't honour resize panel requests - + return ".spt"; } }