/* * 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.gui; import java.awt.Rectangle; import java.io.*; import java.lang.reflect.InvocationTargetException; import java.net.*; import java.util.*; import java.util.Map.Entry; import java.util.jar.*; import javax.swing.*; import org.exolab.castor.xml.*; import uk.ac.vamsas.objects.utils.MapList; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; import jalview.schemes.*; import jalview.structure.StructureSelectionManager; import jalview.util.jarInputStreamProvider; /** * Write out the current jalview desktop state as a Jalview XML stream. * * Note: the vamsas objects referred to here are primitive versions of the * VAMSAS project schema elements - they are not the same and most likely never * will be :) * * @author $author$ * @version $Revision: 1.134 $ */ public class Jalview2XML { /** * create/return unique hash string for sq * * @param sq * @return new or existing unique string for sq */ String seqHash(SequenceI sq) { if (seqsToIds == null) { initSeqRefs(); } if (seqsToIds.containsKey(sq)) { return (String) seqsToIds.get(sq); } else { // create sequential key String key = "sq" + (seqsToIds.size() + 1); key = makeHashCode(sq, key); // check we don't have an external reference // for it already. seqsToIds.put(sq, key); return key; } } void clearSeqRefs() { if (_cleartables) { if (seqRefIds != null) { seqRefIds.clear(); } if (seqsToIds != null) { seqsToIds.clear(); } // seqRefIds = null; // seqsToIds = null; } else { // do nothing warn("clearSeqRefs called when _cleartables was not set. Doing nothing."); // seqRefIds = new Hashtable(); // seqsToIds = new IdentityHashMap(); } } void initSeqRefs() { if (seqsToIds == null) { seqsToIds = new IdentityHashMap(); } if (seqRefIds == null) { seqRefIds = new Hashtable(); } } /** * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps * of sequence objects are created. */ java.util.IdentityHashMap seqsToIds = null; /** * jalview XML Sequence ID to jalview sequence object reference (both dataset * and alignment sequences. Populated as XML reps of sequence objects are * created.) */ java.util.Hashtable seqRefIds = null; // key->SequenceI resolution Vector frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not public Jalview2XML() { } public Jalview2XML(boolean raiseGUI) { this.raiseGUI = raiseGUI; } public void resolveFrefedSequences() { if (frefedSequence.size() > 0) { int r = 0, rSize = frefedSequence.size(); while (r < rSize) { Object[] ref = (Object[]) frefedSequence.elementAt(r); if (ref != null) { String sref = (String) ref[0]; if (seqRefIds.containsKey(sref)) { if (ref[1] instanceof jalview.datamodel.Mapping) { SequenceI seq = (SequenceI) seqRefIds.get(sref); while (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } ((jalview.datamodel.Mapping) ref[1]).setTo(seq); } else { if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame) { SequenceI seq = (SequenceI) seqRefIds.get(sref); while (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } if (ref[2] != null && ref[2] instanceof jalview.datamodel.Mapping) { jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2]; ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap( seq, mp.getTo(), mp.getMap()); } else { System.err .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving " + ref[2].getClass() + " type objects."); } } else { System.err .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " + ref[1].getClass() + " type objects."); } } frefedSequence.remove(r); rSize--; } else { System.err .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string " + ref[0] + " with objecttype " + ref[1].getClass()); r++; } } else { // empty reference frefedSequence.remove(r); rSize--; } } } } /** * This maintains a list of viewports, the key being the seqSetId. Important * to set historyItem and redoList for multiple views */ Hashtable viewportsAdded; Hashtable annotationIds = new Hashtable(); String uniqueSetSuffix = ""; /** * List of pdbfiles added to Jar */ Vector pdbfiles = null; // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE public void SaveState(File statefile) { try { FileOutputStream fos = new FileOutputStream(statefile); JarOutputStream jout = new JarOutputStream(fos); SaveState(jout); } catch (Exception e) { // TODO: inform user of the problem - they need to know if their data was // not saved ! if (errorMessage == null) { errorMessage = "Couldn't write Jalview Archive to output file '" + statefile + "' - See console error log for details"; } else { errorMessage += "(output file was '" + statefile + "')"; } e.printStackTrace(); } reportErrors(); } /** * Writes a jalview project archive to the given Jar output stream. * * @param jout */ public void SaveState(JarOutputStream jout) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { return; } try { // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS // ////////////////////////////////////////////////// // NOTE ALSO new PrintWriter must be used for each new JarEntry PrintWriter out = null; Vector shortNames = new Vector(); // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AlignFrame) { AlignFrame af = (AlignFrame) frames[i]; // skip ? if (skipList != null && skipList.containsKey(af.getViewport() .getSequenceSetId())) { continue; } String shortName = af.getTitle(); if (shortName.indexOf(File.separatorChar) > -1) { shortName = shortName.substring(shortName .lastIndexOf(File.separatorChar) + 1); } int count = 1; while (shortNames.contains(shortName)) { if (shortName.endsWith("_" + (count - 1))) { shortName = shortName .substring(0, shortName.lastIndexOf("_")); } shortName = shortName.concat("_" + count); count++; } shortNames.addElement(shortName); if (!shortName.endsWith(".xml")) { shortName = shortName + ".xml"; } int ap, apSize = af.alignPanels.size(); for (ap = 0; ap < apSize; ap++) { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels .elementAt(ap); String fileName = apSize == 1 ? shortName : ap + shortName; if (!fileName.endsWith(".xml")) { fileName = fileName + ".xml"; } SaveState(apanel, fileName, jout); } } } try { jout.flush(); } catch (Exception foo) { } ; jout.close(); } catch (Exception ex) { // TODO: inform user of the problem - they need to know if their data was // not saved ! if (errorMessage == null) { errorMessage = "Couldn't write Jalview Archive - see error output for details"; } ex.printStackTrace(); } } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW public boolean SaveAlignment(AlignFrame af, String jarFile, String fileName) { try { int ap, apSize = af.alignPanels.size(); FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); for (ap = 0; ap < apSize; ap++) { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels .elementAt(ap); String jfileName = apSize == 1 ? fileName : fileName + ap; if (!jfileName.endsWith(".xml")) { jfileName = jfileName + ".xml"; } SaveState(apanel, jfileName, jout); } try { jout.flush(); } catch (Exception foo) { } ; jout.close(); return true; } catch (Exception ex) { errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details"; ex.printStackTrace(); return false; } } /** * create a JalviewModel from an algnment view and marshall it to a * JarOutputStream * * @param ap * panel to create jalview model for * @param fileName * name of alignment panel written to output stream * @param jout * jar output stream * @param out * jar entry name */ public JalviewModel SaveState(AlignmentPanel ap, String fileName, JarOutputStream jout) { initSeqRefs(); Vector jmolViewIds = new Vector(); // Vector userColours = new Vector(); AlignViewport av = ap.av; JalviewModel object = new JalviewModel(); object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); object.setCreationDate(new java.util.Date(System.currentTimeMillis())); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); jalview.datamodel.AlignmentI jal = av.alignment; if (av.hasHiddenRows) { jal = jal.getHiddenSequences().getFullAlignment(); } SequenceSet vamsasSet = new SequenceSet(); Sequence vamsasSeq; JalviewModelSequence jms = new JalviewModelSequence(); vamsasSet.setGapChar(jal.getGapCharacter() + ""); if (jal.getDataset() != null) { // dataset id is the dataset's hashcode vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset())); } if (jal.getProperties() != null) { Enumeration en = jal.getProperties().keys(); while (en.hasMoreElements()) { String key = en.nextElement().toString(); SequenceSetProperties ssp = new SequenceSetProperties(); ssp.setKey(key); ssp.setValue(jal.getProperties().get(key).toString()); vamsasSet.addSequenceSetProperties(ssp); } } JSeq jseq; // SAVE SEQUENCES String id = ""; jalview.datamodel.SequenceI jds; for (int i = 0; i < jal.getHeight(); i++) { jds = jal.getSequenceAt(i); id = seqHash(jds); if (seqRefIds.get(id) != null) { // This happens for two reasons: 1. multiple views are being serialised. // 2. the hashCode has collided with another sequence's code. This DOES // HAPPEN! (PF00072.15.stk does this) // JBPNote: Uncomment to debug writing out of files that do not read // back in due to ArrayOutOfBoundExceptions. // System.err.println("vamsasSeq backref: "+id+""); // System.err.println(jds.getName()+" // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); // System.err.println("Hashcode: "+seqHash(jds)); // SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); // System.err.println(rsq.getName()+" // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); // System.err.println("Hashcode: "+seqHash(rsq)); } else { vamsasSeq = createVamsasSequence(id, jds); vamsasSet.addSequence(vamsasSeq); seqRefIds.put(id, jds); } jseq = new JSeq(); jseq.setStart(jds.getStart()); jseq.setEnd(jds.getEnd()); jseq.setColour(av.getSequenceColour(jds).getRGB()); jseq.setId(id); // jseq id should be a string not a number if (av.hasHiddenRows) { jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); if (av.hiddenRepSequences != null && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i))) { jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences .get(jal.getSequenceAt(i))).getSequencesInOrder(jal); for (int h = 0; h < reps.length; h++) { if (reps[h] != jal.getSequenceAt(i)) { jseq.addHiddenSequences(jal.findIndex(reps[h])); } } } } if (jds.getDatasetSequence().getSequenceFeatures() != null) { jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence() .getSequenceFeatures(); int index = 0; while (index < sf.length) { Features features = new Features(); features.setBegin(sf[index].getBegin()); features.setEnd(sf[index].getEnd()); features.setDescription(sf[index].getDescription()); features.setType(sf[index].getType()); features.setFeatureGroup(sf[index].getFeatureGroup()); features.setScore(sf[index].getScore()); if (sf[index].links != null) { for (int l = 0; l < sf[index].links.size(); l++) { OtherData keyValue = new OtherData(); keyValue.setKey("LINK_" + l); keyValue.setValue(sf[index].links.elementAt(l).toString()); features.addOtherData(keyValue); } } if (sf[index].otherDetails != null) { String key; Enumeration keys = sf[index].otherDetails.keys(); while (keys.hasMoreElements()) { key = keys.nextElement().toString(); OtherData keyValue = new OtherData(); keyValue.setKey(key); keyValue.setValue(sf[index].otherDetails.get(key).toString()); features.addOtherData(keyValue); } } jseq.addFeatures(features); index++; } } if (jds.getDatasetSequence().getPDBId() != null) { Enumeration en = jds.getDatasetSequence().getPDBId().elements(); while (en.hasMoreElements()) { Pdbids pdb = new Pdbids(); jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en .nextElement(); pdb.setId(entry.getId()); pdb.setType(entry.getType()); AppJmol jmol; // This must have been loaded, is it still visible? JInternalFrame[] frames = Desktop.desktop.getAllFrames(); String matchedFile = null; for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppJmol) { jmol = (AppJmol) frames[f]; for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++) { if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId()) && !(entry.getId().length() > 4 && entry .getId() .toLowerCase() .startsWith( jmol.jmb.pdbentry[peid].getId() .toLowerCase()))) continue; if (matchedFile == null) { matchedFile = jmol.jmb.pdbentry[peid].getFile(); } else if (!matchedFile.equals(jmol.jmb.pdbentry[peid] .getFile())) { Cache.log .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): " + jmol.jmb.pdbentry[peid].getFile()); ; // record the } // file so we // can get at it if the ID // match is ambiguous (e.g. // 1QIP==1qipA) String statestring = jmol.jmb.viewer.getStateInfo(); for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++) { if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1) { StructureState state = new StructureState(); state.setVisible(true); state.setXpos(jmol.getX()); state.setYpos(jmol.getY()); state.setWidth(jmol.getWidth()); state.setHeight(jmol.getHeight()); state.setViewId(jmol.getViewId()); state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap)); state.setColourwithAlignPanel(jmol .isUsedforcolourby(ap)); state.setColourByJmol(jmol.isColouredByJmol()); if (!jmolViewIds.contains(state.getViewId())) { // Make sure we only store a Jmol state once in each XML // document. jmolViewIds.addElement(state.getViewId()); state.setContent(statestring.replaceAll("\n", "")); } else { state.setContent("# duplicate state"); } pdb.addStructureState(state); } } } } } if (matchedFile != null || entry.getFile() != null) { if (entry.getFile() != null) { // use entry's file matchedFile = entry.getFile(); } pdb.setFile(matchedFile); // entry.getFile()); if (pdbfiles == null) { pdbfiles = new Vector(); } if (!pdbfiles.contains(entry.getId())) { pdbfiles.addElement(entry.getId()); try { File file = new File(matchedFile); if (file.exists() && jout != null) { byte[] data = new byte[(int) file.length()]; jout.putNextEntry(new JarEntry(entry.getId())); DataInputStream dis = new DataInputStream( new FileInputStream(file)); dis.readFully(data); DataOutputStream dout = new DataOutputStream(jout); dout.write(data, 0, data.length); dout.flush(); jout.closeEntry(); } } catch (Exception ex) { ex.printStackTrace(); } } } if (entry.getProperty() != null) { PdbentryItem item = new PdbentryItem(); Hashtable properties = entry.getProperty(); Enumeration en2 = properties.keys(); while (en2.hasMoreElements()) { Property prop = new Property(); String key = en2.nextElement().toString(); prop.setName(key); prop.setValue(properties.get(key).toString()); item.addProperty(prop); } pdb.addPdbentryItem(item); } jseq.addPdbids(pdb); } } jms.addJSeq(jseq); } if (av.hasHiddenRows) { jal = av.alignment; } // SAVE MAPPINGS if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0) { jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames(); for (int i = 0; i < jac.length; i++) { AlcodonFrame alc = new AlcodonFrame(); vamsasSet.addAlcodonFrame(alc); for (int p = 0; p < jac[i].aaWidth; p++) { Alcodon cmap = new Alcodon(); if (jac[i].codons[p] != null) { // Null codons indicate a gapped column in the translated peptide // alignment. cmap.setPos1(jac[i].codons[p][0]); cmap.setPos2(jac[i].codons[p][1]); cmap.setPos3(jac[i].codons[p][2]); } alc.addAlcodon(cmap); } if (jac[i].getProtMappings() != null && jac[i].getProtMappings().length > 0) { SequenceI[] dnas = jac[i].getdnaSeqs(); jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings(); for (int m = 0; m < pmaps.length; m++) { AlcodMap alcmap = new AlcodMap(); alcmap.setDnasq(seqHash(dnas[m])); alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, false)); alc.addAlcodMap(alcmap); } } } } // SAVE TREES // ///////////////////////////////// if (av.currentTree != null) { // FIND ANY ASSOCIATED TREES // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT if (Desktop.desktop != null) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int t = 0; t < frames.length; t++) { if (frames[t] instanceof TreePanel) { TreePanel tp = (TreePanel) frames[t]; if (tp.treeCanvas.av.alignment == jal) { Tree tree = new Tree(); tree.setTitle(tp.getTitle()); tree.setCurrentTree((av.currentTree == tp.getTree())); tree.setNewick(tp.getTree().toString()); tree.setThreshold(tp.treeCanvas.threshold); tree.setFitToWindow(tp.fitToWindow.getState()); tree.setFontName(tp.getTreeFont().getName()); tree.setFontSize(tp.getTreeFont().getSize()); tree.setFontStyle(tp.getTreeFont().getStyle()); tree.setMarkUnlinked(tp.placeholdersMenu.getState()); tree.setShowBootstrap(tp.bootstrapMenu.getState()); tree.setShowDistances(tp.distanceMenu.getState()); tree.setHeight(tp.getHeight()); tree.setWidth(tp.getWidth()); tree.setXpos(tp.getX()); tree.setYpos(tp.getY()); tree.setId(makeHashCode(tp, null)); jms.addTree(tree); } } } } } // SAVE ANNOTATIONS /** * store forward refs from an annotationRow to any groups */ IdentityHashMap groupRefs = new IdentityHashMap(); if (jal.getAlignmentAnnotation() != null) { jalview.datamodel.AlignmentAnnotation[] aa = jal .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { Annotation an = new Annotation(); if (aa[i].annotationId != null) { annotationIds.put(aa[i].annotationId, aa[i]); } an.setId(aa[i].annotationId); an.setVisible(aa[i].visible); an.setDescription(aa[i].description); if (aa[i].sequenceRef != null) { // TODO later annotation sequenceRef should be the XML ID of the // sequence rather than its display name an.setSequenceRef(aa[i].sequenceRef.getName()); } if (aa[i].groupRef != null) { Object groupIdr = groupRefs.get(aa[i].groupRef); if (groupIdr == null) { // make a locally unique String groupRefs.put(aa[i].groupRef, groupIdr = ("" + System.currentTimeMillis() + aa[i].groupRef.getName() + groupRefs.size())); } an.setGroupRef(groupIdr.toString()); } // store all visualization attributes for annotation an.setGraphHeight(aa[i].graphHeight); an.setCentreColLabels(aa[i].centreColLabels); an.setScaleColLabels(aa[i].scaleColLabel); an.setShowAllColLabels(aa[i].showAllColLabels); if (aa[i].graph > 0) { an.setGraph(true); an.setGraphType(aa[i].graph); an.setGraphGroup(aa[i].graphGroup); if (aa[i].getThreshold() != null) { ThresholdLine line = new ThresholdLine(); line.setLabel(aa[i].getThreshold().label); line.setValue(aa[i].getThreshold().value); line.setColour(aa[i].getThreshold().colour.getRGB()); an.setThresholdLine(line); } } else { an.setGraph(false); } an.setLabel(aa[i].label); if (aa[i] == av.quality || aa[i] == av.conservation || aa[i] == av.consensus || aa[i].autoCalculated) { // new way of indicating autocalculated annotation - an.setAutoCalculated(aa[i].autoCalculated); } if (aa[i].hasScore()) { an.setScore(aa[i].getScore()); } AnnotationElement ae; if (aa[i].annotations != null) { an.setScoreOnly(false); for (int a = 0; a < aa[i].annotations.length; a++) { if ((aa[i] == null) || (aa[i].annotations[a] == null)) { continue; } ae = new AnnotationElement(); if (aa[i].annotations[a].description != null) ae.setDescription(aa[i].annotations[a].description); if (aa[i].annotations[a].displayCharacter != null) ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); if (!Float.isNaN(aa[i].annotations[a].value)) ae.setValue(aa[i].annotations[a].value); ae.setPosition(a); if (aa[i].annotations[a].secondaryStructure != ' ' && aa[i].annotations[a].secondaryStructure != '\0') ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + ""); if (aa[i].annotations[a].colour != null && aa[i].annotations[a].colour != java.awt.Color.black) { ae.setColour(aa[i].annotations[a].colour.getRGB()); } an.addAnnotationElement(ae); if (aa[i].autoCalculated) { // only write one non-null entry into the annotation row - // sufficient to get the visualization attributes necessary to // display data continue; } } } else { an.setScoreOnly(true); } vamsasSet.addAnnotation(an); } } // SAVE GROUPS if (jal.getGroups() != null) { JGroup[] groups = new JGroup[jal.getGroups().size()]; for (int i = 0; i < groups.length; i++) { groups[i] = new JGroup(); jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal .getGroups().elementAt(i); groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); groups[i].setName(sg.getName()); if (groupRefs.containsKey(sg)) { // group has references so set it's ID field groups[i].setId(groupRefs.get(sg).toString()); } if (sg.cs != null) { if (sg.cs.conservationApplied()) { groups[i].setConsThreshold(sg.cs.getConservationInc()); if (sg.cs instanceof jalview.schemes.UserColourScheme) { groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms)); } else { groups[i] .setColour(ColourSchemeProperty.getColourName(sg.cs)); } } else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) { groups[i] .setColour(ColourSchemeProperty .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs) .getBaseColour())); } else if (sg.cs instanceof jalview.schemes.UserColourScheme) { groups[i] .setColour(SetUserColourScheme(sg.cs, userColours, jms)); } else { groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs)); } groups[i].setPidThreshold(sg.cs.getThreshold()); } groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); groups[i].setDisplayBoxes(sg.getDisplayBoxes()); groups[i].setDisplayText(sg.getDisplayText()); groups[i].setColourText(sg.getColourText()); groups[i].setTextCol1(sg.textColour.getRGB()); groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); groups[i].setShowUnconserved(sg.getShowNonconserved()); groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg .getSequenceAt(s); groups[i].addSeq(seqHash(seq)); } } jms.setJGroup(groups); } // /////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(ap.alignFrame.getTitle()); view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av.getSequenceSetId())); view.setId(av.getViewId()); view.setViewName(av.viewName); view.setGatheredViews(av.gatherViewsHere); if (ap.av.explodedPosition != null) { view.setXpos(av.explodedPosition.x); view.setYpos(av.explodedPosition.y); view.setWidth(av.explodedPosition.width); view.setHeight(av.explodedPosition.height); } else { view.setXpos(ap.alignFrame.getBounds().x); view.setYpos(ap.alignFrame.getBounds().y); view.setWidth(ap.alignFrame.getBounds().width); view.setHeight(ap.alignFrame.getBounds().height); } view.setStartRes(av.startRes); view.setStartSeq(av.startSeq); if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), userColours, jms)); } else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) { jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av .getGlobalColourScheme(); AnnotationColours ac = new AnnotationColours(); ac.setAboveThreshold(acg.getAboveThreshold()); ac.setThreshold(acg.getAnnotationThreshold()); ac.setAnnotation(acg.getAnnotation()); if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) { ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(), userColours, jms)); } else { ac.setColourScheme(ColourSchemeProperty.getColourName(acg .getBaseColour())); } ac.setMaxColour(acg.getMaxColour().getRGB()); ac.setMinColour(acg.getMinColour().getRGB()); view.setAnnotationColours(ac); view.setBgColour("AnnotationColourGradient"); } else { view.setBgColour(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); } ColourSchemeI cs = av.getGlobalColourScheme(); if (cs != null) { if (cs.conservationApplied()) { view.setConsThreshold(cs.getConservationInc()); if (cs instanceof jalview.schemes.UserColourScheme) { view.setBgColour(SetUserColourScheme(cs, userColours, jms)); } } if (cs instanceof ResidueColourScheme) { view.setPidThreshold(cs.getThreshold()); } } view.setConservationSelected(av.getConservationSelected()); view.setPidSelected(av.getAbovePIDThreshold()); view.setFontName(av.font.getName()); view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); view.setRenderGaps(av.renderGaps); view.setShowAnnotation(av.getShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowFullId(av.getShowJVSuffix()); view.setRightAlignIds(av.rightAlignIds); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setShowUnconserved(av.getShowUnconserved()); view.setWrapAlignment(av.getWrapAlignment()); view.setTextCol1(av.textColour.getRGB()); view.setTextCol2(av.textColour2.getRGB()); view.setTextColThreshold(av.thresholdTextColour); view.setShowConsensusHistogram(av.isShowConsensusHistogram()); view.setShowSequenceLogo(av.isShowSequenceLogo()); view.setShowGroupConsensus(av.isShowGroupConsensus()); view.setShowGroupConservation(av.isShowGroupConservation()); view.setShowNPfeatureTooltip(av.isShowNpFeats()); view.setShowDbRefTooltip(av.isShowDbRefs()); view.setFollowHighlight(av.followHighlight); view.setFollowSelection(av.followSelection); view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); if (av.featuresDisplayed != null) { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; Vector settingsAdded = new Vector(); Object gstyle = null; GraduatedColor gcol = null; if (renderOrder != null) { for (int ro = 0; ro < renderOrder.length; ro++) { gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer() .getFeatureStyle(renderOrder[ro]); Setting setting = new Setting(); setting.setType(renderOrder[ro]); if (gstyle instanceof GraduatedColor) { gcol = (GraduatedColor) gstyle; setting.setColour(gcol.getMaxColor().getRGB()); setting.setMincolour(gcol.getMinColor().getRGB()); setting.setMin(gcol.getMin()); setting.setMax(gcol.getMax()); setting.setColourByLabel(gcol.isColourByLabel()); setting.setAutoScale(gcol.isAutoScale()); setting.setThreshold(gcol.getThresh()); setting.setThreshstate(gcol.getThreshType()); } else { setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() .getColour(renderOrder[ro]).getRGB()); } setting.setDisplay(av.featuresDisplayed .containsKey(renderOrder[ro])); float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() .getOrder(renderOrder[ro]); if (rorder > -1) { setting.setOrder(rorder); } fs.addSetting(setting); settingsAdded.addElement(renderOrder[ro]); } } // Make sure we save none displayed feature settings Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours .keys(); while (en.hasMoreElements()) { String key = en.nextElement().toString(); if (settingsAdded.contains(key)) { continue; } Setting setting = new Setting(); setting.setType(key); setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() .getColour(key).getRGB()); setting.setDisplay(false); float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( key); if (rorder > -1) { setting.setOrder(rorder); } fs.addSetting(setting); settingsAdded.addElement(key); } en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys(); Vector groupsAdded = new Vector(); while (en.hasMoreElements()) { String grp = en.nextElement().toString(); if (groupsAdded.contains(grp)) { continue; } Group g = new Group(); g.setName(grp); g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups .get(grp)).booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); } if (av.hasHiddenColumns) { if (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null) { warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); } else { for (int c = 0; c < av.getColumnSelection().getHiddenColumns() .size(); c++) { int[] region = (int[]) av.getColumnSelection().getHiddenColumns() .elementAt(c); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); hc.setEnd(region[1]); view.addHiddenColumns(hc); } } } jms.addViewport(view); object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); if (jout != null && fileName != null) { // We may not want to write the object to disk, // eg we can copy the alignViewport to a new view object // using save and then load try { JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout, "UTF-8")); org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller( pout); marshaller.marshal(object); pout.flush(); jout.closeEntry(); } catch (Exception ex) { // TODO: raise error in GUI if marshalling failed. ex.printStackTrace(); } } return object; } /** * External mapping between jalview objects and objects yielding a valid and * unique object ID string. This is null for normal Jalview project IO, but * non-null when a jalview project is being read or written as part of a * vamsas session. */ IdentityHashMap jv2vobj = null; /** * Construct a unique ID for jvobj using either existing bindings or if none * exist, the result of the hashcode call for the object. * * @param jvobj * jalview data object * @return unique ID for referring to jvobj */ private String makeHashCode(Object jvobj, String altCode) { if (jv2vobj != null) { Object id = jv2vobj.get(jvobj); if (id != null) { return id.toString(); } // check string ID mappings if (jvids2vobj != null && jvobj instanceof String) { id = jvids2vobj.get(jvobj); } if (id != null) { return id.toString(); } // give up and warn that something has gone wrong warn("Cannot find ID for object in external mapping : " + jvobj); } return altCode; } /** * return local jalview object mapped to ID, if it exists * * @param idcode * (may be null) * @return null or object bound to idcode */ private Object retrieveExistingObj(String idcode) { if (idcode != null && vobj2jv != null) { return vobj2jv.get(idcode); } return null; } /** * binding from ID strings from external mapping table to jalview data model * objects. */ private Hashtable vobj2jv; private Sequence createVamsasSequence(String id, SequenceI jds) { return createVamsasSequence(true, id, jds, null); } private Sequence createVamsasSequence(boolean recurse, String id, SequenceI jds, SequenceI parentseq) { Sequence vamsasSeq = new Sequence(); vamsasSeq.setId(id); vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); jalview.datamodel.DBRefEntry[] dbrefs = null; if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); if (jds.getDatasetSequence().getDBRef() != null) { dbrefs = jds.getDatasetSequence().getDBRef(); } } else { vamsasSeq.setDsseqid(id); // so we can tell which sequences really are // dataset sequences only dbrefs = jds.getDBRef(); } if (dbrefs != null) { for (int d = 0; d < dbrefs.length; d++) { DBRef dbref = new DBRef(); dbref.setSource(dbrefs[d].getSource()); dbref.setVersion(dbrefs[d].getVersion()); dbref.setAccessionId(dbrefs[d].getAccessionId()); if (dbrefs[d].hasMap()) { Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } vamsasSeq.addDBRef(dbref); } } return vamsasSeq; } private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp, SequenceI parentseq, SequenceI jds, boolean recurse) { Mapping mp = null; if (jmp.getMap() != null) { mp = new Mapping(); jalview.util.MapList mlst = jmp.getMap(); int r[] = mlst.getFromRanges(); for (int s = 0; s < r.length; s += 2) { MapListFrom mfrom = new MapListFrom(); mfrom.setStart(r[s]); mfrom.setEnd(r[s + 1]); mp.addMapListFrom(mfrom); } r = mlst.getToRanges(); for (int s = 0; s < r.length; s += 2) { MapListTo mto = new MapListTo(); mto.setStart(r[s]); mto.setEnd(r[s + 1]); mp.addMapListTo(mto); } mp.setMapFromUnit(mlst.getFromRatio()); mp.setMapToUnit(mlst.getToRatio()); if (jmp.getTo() != null) { MappingChoice mpc = new MappingChoice(); if (recurse && (parentseq != jmp.getTo() || parentseq .getDatasetSequence() != jmp.getTo())) { mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()), jmp.getTo(), jds)); } else { String jmpid = ""; SequenceI ps = null; if (parentseq != jmp.getTo() && parentseq.getDatasetSequence() != jmp.getTo()) { // chaining dbref rather than a handshaking one jmpid = seqHash(ps = jmp.getTo()); } else { jmpid = seqHash(ps = parentseq); } mpc.setDseqFor(jmpid); if (!seqRefIds.containsKey(mpc.getDseqFor())) { jalview.bin.Cache.log.debug("creatign new DseqFor ID"); seqRefIds.put(mpc.getDseqFor(), ps); } else { jalview.bin.Cache.log.debug("reusing DseqFor ID"); } } mp.setMappingChoice(mpc); } } return mp; } String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, Vector userColours, JalviewModelSequence jms) { String id = null; jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; boolean newucs = false; if (!userColours.contains(ucs)) { userColours.add(ucs); newucs = true; } id = "ucs" + userColours.indexOf(ucs); if (newucs) { // actually create the scheme's entry in the XML model java.awt.Color[] colours = ucs.getColours(); jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); for (int i = 0; i < colours.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(ResidueProperties.aa[i]); col.setRGB(jalview.util.Format.getHexString(colours[i])); jbucs.addColour(col); } if (ucs.getLowerCaseColours() != null) { colours = ucs.getLowerCaseColours(); for (int i = 0; i < colours.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(ResidueProperties.aa[i].toLowerCase()); col.setRGB(jalview.util.Format.getHexString(colours[i])); jbucs.addColour(col); } } uc.setId(id); uc.setUserColourScheme(jbucs); jms.addUserColours(uc); } return id; } jalview.schemes.UserColourScheme GetUserColourScheme( JalviewModelSequence jms, String id) { UserColours[] uc = jms.getUserColours(); UserColours colours = null; for (int i = 0; i < uc.length; i++) { if (uc[i].getId().equals(id)) { colours = uc[i]; break; } } java.awt.Color[] newColours = new java.awt.Color[24]; for (int i = 0; i < 24; i++) { newColours[i] = new java.awt.Color(Integer.parseInt(colours .getUserColourScheme().getColour(i).getRGB(), 16)); } jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( newColours); if (colours.getUserColourScheme().getColourCount() > 24) { newColours = new java.awt.Color[23]; for (int i = 0; i < 23; i++) { newColours[i] = new java.awt.Color(Integer.parseInt(colours .getUserColourScheme().getColour(i + 24).getRGB(), 16)); } ucs.setLowerCaseColours(newColours); } return ucs; } /** * contains last error message (if any) encountered by XML loader. */ String errorMessage = null; /** * flag to control whether the Jalview2XML_V1 parser should be deferred to if * exceptions are raised during project XML parsing */ public boolean attemptversion1parse = true; /** * Load a jalview project archive from a jar file * * @param file * - HTTP URL or filename */ public AlignFrame LoadJalviewAlign(final String file) { jalview.gui.AlignFrame af = null; try { // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING // Workaround is to make sure caller implements the JarInputStreamProvider // interface // so we can re-open the jar input stream for each entry. jarInputStreamProvider jprovider = createjarInputStreamProvider(file); af = LoadJalviewAlign(jprovider); } catch (MalformedURLException e) { errorMessage = "Invalid URL format for '" + file + "'"; reportErrors(); } return af; } private jarInputStreamProvider createjarInputStreamProvider( final String file) throws MalformedURLException { URL url = null; errorMessage = null; uniqueSetSuffix = null; seqRefIds = null; viewportsAdded = null; frefedSequence = null; if (file.startsWith("http://")) { url = new URL(file); } final URL _url = url; return new jarInputStreamProvider() { public JarInputStream getJarInputStream() throws IOException { if (_url != null) { return new JarInputStream(_url.openStream()); } else { return new JarInputStream(new FileInputStream(file)); } } public String getFilename() { return file; } }; } /** * Recover jalview session from a jalview project archive. Caller may * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence * themselves. Any null fields will be initialised with default values, * non-null fields are left alone. * * @param jprovider * @return */ public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider) { errorMessage = null; if (uniqueSetSuffix == null) { uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; } if (seqRefIds == null) { seqRefIds = new Hashtable(); } if (viewportsAdded == null) { viewportsAdded = new Hashtable(); } if (frefedSequence == null) { frefedSequence = new Vector(); } jalview.gui.AlignFrame af = null; Hashtable gatherToThisFrame = new Hashtable(); final String file = jprovider.getFilename(); try { JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; do { jin = jprovider.getJarInputStream(); for (int i = 0; i < entryCount; i++) { jarentry = jin.getNextJarEntry(); } if (jarentry != null && jarentry.getName().endsWith(".xml")) { InputStreamReader in = new InputStreamReader(jin, "UTF-8"); JalviewModel object = new JalviewModel(); Unmarshaller unmar = new Unmarshaller(object); unmar.setValidation(false); object = (JalviewModel) unmar.unmarshal(in); if (true) // !skipViewport(object)) { af = LoadFromObject(object, file, true, jprovider); if (af.viewport.gatherViewsHere) { gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); } } entryCount++; } else if (jarentry != null) { // Some other file here. entryCount++; } } while (jarentry != null); resolveFrefedSequences(); } catch (java.io.FileNotFoundException ex) { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); } catch (java.net.UnknownHostException ex) { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); } catch (Exception ex) { System.err.println("Parsing as Jalview Version 2 file failed."); ex.printStackTrace(System.err); if (attemptversion1parse) { // Is Version 1 Jar file? try { af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); } catch (Exception ex2) { System.err.println("Exception whilst loading as jalviewXMLV1:"); ex2.printStackTrace(); af = null; } } if (Desktop.instance != null) { Desktop.instance.stopLoading(); } if (af != null) { System.out.println("Successfully loaded archive file"); return af; } ex.printStackTrace(); System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); } catch (OutOfMemoryError e) { // Don't use the OOM Window here errorMessage = "Out of memory loading jalview XML file"; System.err.println("Out of memory whilst loading jalview XML file"); e.printStackTrace(); } if (Desktop.instance != null) { Desktop.instance.stopLoading(); } Enumeration en = gatherToThisFrame.elements(); while (en.hasMoreElements()) { Desktop.instance.gatherViews((AlignFrame) en.nextElement()); } if (errorMessage != null) { reportErrors(); } return af; } /** * check errorMessage for a valid error message and raise an error box in the * GUI or write the current errorMessage to stderr and then clear the error * state. */ protected void reportErrors() { reportErrors(false); } protected void reportErrors(final boolean saving) { if (errorMessage != null) { final String finalErrorMessage = errorMessage; if (raiseGUI) { javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, finalErrorMessage, "Error " + (saving ? "saving" : "loading") + " Jalview file", JOptionPane.WARNING_MESSAGE); } }); } else { System.err.println("Problem loading Jalview file: " + errorMessage); } } errorMessage = null; } Hashtable alreadyLoadedPDB; /** * when set, local views will be updated from view stored in JalviewXML * Currently (28th Sep 2008) things will go horribly wrong in vamsas document * sync if this is set to true. */ private boolean updateLocalViews = false; String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) { if (alreadyLoadedPDB == null) alreadyLoadedPDB = new Hashtable(); if (alreadyLoadedPDB.containsKey(pdbId)) return alreadyLoadedPDB.get(pdbId).toString(); try { JarInputStream jin = jprovider.getJarInputStream(); /* * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new * URL(jprovider).openStream()); } else { jin = new JarInputStream(new * FileInputStream(jprovider)); } */ JarEntry entry = null; do { entry = jin.getNextJarEntry(); } while (entry != null && !entry.getName().equals(pdbId)); if (entry != null) { BufferedReader in = new BufferedReader(new InputStreamReader(jin)); File outFile = File.createTempFile("jalview_pdb", ".txt"); outFile.deleteOnExit(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); String data; while ((data = in.readLine()) != null) { out.println(data); } try { out.flush(); } catch (Exception foo) { } ; out.close(); alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); return outFile.getAbsolutePath(); } else { warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId); } } catch (Exception ex) { ex.printStackTrace(); } return null; } private class JvAnnotRow { public JvAnnotRow(int i, AlignmentAnnotation jaa) { order = i; template = jaa; } /** * persisted version of annotation row from which to take vis properties */ public jalview.datamodel.AlignmentAnnotation template; /** * original position of the annotation row in the alignment */ public int order; } /** * Load alignment frame from jalview XML DOM object * * @param object * DOM * @param file * filename source string * @param loadTreesAndStructures * when false only create Viewport * @param jprovider * data source provider * @return alignment frame created from view stored in DOM */ AlignFrame LoadFromObject(JalviewModel object, String file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); Sequence[] vamsasSeq = vamsasSet.getSequence(); JalviewModelSequence jms = object.getJalviewModelSequence(); Viewport view = jms.getViewport(0); // //////////////////////////////// // LOAD SEQUENCES Vector hiddenSeqs = null; jalview.datamodel.Sequence jseq; ArrayList tmpseqs = new ArrayList(); boolean multipleView = false; JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); int vi = 0; // counter in vamsasSeq array for (int i = 0; i < JSEQ.length; i++) { String seqId = JSEQ[i].getId(); if (seqRefIds.get(seqId) != null) { tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId)); multipleView = true; } else { jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), vamsasSeq[vi].getSequence()); jseq.setDescription(vamsasSeq[vi].getDescription()); jseq.setStart(JSEQ[i].getStart()); jseq.setEnd(JSEQ[i].getEnd()); jseq.setVamsasId(uniqueSetSuffix + seqId); seqRefIds.put(vamsasSeq[vi].getId(), jseq); tmpseqs.add(jseq); vi++; } if (JSEQ[i].getHidden()) { if (hiddenSeqs == null) { hiddenSeqs = new Vector(); } hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds .get(seqId)); } } // / // Create the alignment object from the sequence set // /////////////////////////////// jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs .size()]; tmpseqs.toArray(orderedSeqs); jalview.datamodel.Alignment al = new jalview.datamodel.Alignment( orderedSeqs); // / Add the alignment properties for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) { SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); al.setProperty(ssp.getKey(), ssp.getValue()); } // / // SequenceFeatures are added to the DatasetSequence, // so we must create or recover the dataset before loading features // /////////////////////////////// if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") { // older jalview projects do not have a dataset id. al.setDataset(null); } else { recoverDatasetFor(vamsasSet, al); } // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); if (!multipleView) { // load sequence features, database references and any associated PDB // structures for the alignment for (int i = 0; i < vamsasSeq.length; i++) { if (JSEQ[i].getFeaturesCount() > 0) { Features[] features = JSEQ[i].getFeatures(); for (int f = 0; f < features.length; f++) { jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature( features[f].getType(), features[f].getDescription(), features[f].getStatus(), features[f].getBegin(), features[f].getEnd(), features[f].getFeatureGroup()); sf.setScore(features[f].getScore()); for (int od = 0; od < features[f].getOtherDataCount(); od++) { OtherData keyValue = features[f].getOtherData(od); if (keyValue.getKey().startsWith("LINK")) { sf.addLink(keyValue.getValue()); } else { sf.setValue(keyValue.getKey(), keyValue.getValue()); } } al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); } } if (vamsasSeq[i].getDBRefCount() > 0) { addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); } if (JSEQ[i].getPdbidsCount() > 0) { Pdbids[] ids = JSEQ[i].getPdbids(); for (int p = 0; p < ids.length; p++) { jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); entry.setId(ids[p].getId()); entry.setType(ids[p].getType()); if (ids[p].getFile() != null) { if (!pdbloaded.containsKey(ids[p].getFile())) { entry.setFile(loadPDBFile(jprovider, ids[p].getId())); } else { entry.setFile(pdbloaded.get(ids[p].getId()).toString()); } } al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); } } } } // end !multipleview // /////////////////////////////// // LOAD SEQUENCE MAPPINGS if (vamsasSet.getAlcodonFrameCount() > 0) { // TODO Potentially this should only be done once for all views of an // alignment AlcodonFrame[] alc = vamsasSet.getAlcodonFrame(); for (int i = 0; i < alc.length; i++) { jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame( alc[i].getAlcodonCount()); if (alc[i].getAlcodonCount() > 0) { Alcodon[] alcods = alc[i].getAlcodon(); for (int p = 0; p < cf.codons.length; p++) { if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3()) { // translated codons require three valid positions cf.codons[p] = new int[3]; cf.codons[p][0] = (int) alcods[p].getPos1(); cf.codons[p][1] = (int) alcods[p].getPos2(); cf.codons[p][2] = (int) alcods[p].getPos3(); } else { cf.codons[p] = null; } } } if (alc[i].getAlcodMapCount() > 0) { AlcodMap[] maps = alc[i].getAlcodMap(); for (int m = 0; m < maps.length; m++) { SequenceI dnaseq = (SequenceI) seqRefIds .get(maps[m].getDnasq()); // Load Mapping jalview.datamodel.Mapping mapping = null; // attach to dna sequence reference. if (maps[m].getMapping() != null) { mapping = addMapping(maps[m].getMapping()); } if (dnaseq != null) { cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); } else { // defer to later frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, mapping }); } } } al.addCodonFrame(cf); } } // //////////////////////////////// // LOAD ANNOTATIONS ArrayList autoAlan = new ArrayList(); /** * store any annotations which forward reference a group's ID */ Hashtable> groupAnnotRefs = new Hashtable>(); if (vamsasSet.getAnnotationCount() > 0) { Annotation[] an = vamsasSet.getAnnotation(); for (int i = 0; i < an.length; i++) { /** * test if annotation is automatically calculated for this view only */ boolean autoForView = false; if (an[i].getLabel().equals("Quality") || an[i].getLabel().equals("Conservation") || an[i].getLabel().equals("Consensus")) { // Kludge for pre 2.5 projects which lacked the autocalculated flag autoForView = true; if (!an[i].hasAutoCalculated()) { an[i].setAutoCalculated(true); } } if (autoForView || (an[i].hasAutoCalculated() && an[i].isAutoCalculated())) { // remove ID - we don't recover annotation from other views for // view-specific annotation an[i].setId(null); } // set visiblity for other annotation in this view if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) { jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds .get(an[i].getId()); // in principle Visible should always be true for annotation displayed // in multiple views if (an[i].hasVisible()) jda.visible = an[i].getVisible(); al.addAnnotation(jda); continue; } // Construct new annotation from model. AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; if (!an[i].getScoreOnly()) { anot = new jalview.datamodel.Annotation[al.getWidth()]; for (int aa = 0; aa < ae.length && aa < anot.length; aa++) { if (ae[aa].getPosition() >= anot.length) continue; anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa].getSecondaryStructure() == null || ae[aa] .getSecondaryStructure().length() == 0) ? ' ' : ae[aa].getSecondaryStructure().charAt(0), ae[aa].getValue() ); // JBPNote: Consider verifying dataflow for IO of secondary // structure annotation read from Stockholm files // this was added to try to ensure that // if (anot[ae[aa].getPosition()].secondaryStructure>' ') // { // anot[ae[aa].getPosition()].displayCharacter = ""; // } anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour()); } } jalview.datamodel.AlignmentAnnotation jaa = null; if (an[i].getGraph()) { float llim = 0, hlim = 0; // if (autoForView || an[i].isAutoCalculated()) { // hlim=11f; // } jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot, llim, hlim, an[i].getGraphType()); jaa.graphGroup = an[i].getGraphGroup(); if (an[i].getThresholdLine() != null) { jaa.setThreshold(new jalview.datamodel.GraphLine(an[i] .getThresholdLine().getValue(), an[i] .getThresholdLine().getLabel(), new java.awt.Color( an[i].getThresholdLine().getColour()))); } if (autoForView || an[i].isAutoCalculated()) { // Hardwire the symbol display line to ensure that labels for // histograms are displayed jaa.hasText = true; } } else { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } if (autoForView) { // register new annotation if (an[i].getId() != null) { annotationIds.put(an[i].getId(), jaa); jaa.annotationId = an[i].getId(); } // recover sequence association if (an[i].getSequenceRef() != null) { if (al.findName(an[i].getSequenceRef()) != null) { jaa.createSequenceMapping( al.findName(an[i].getSequenceRef()), 1, true); al.findName(an[i].getSequenceRef()).addAlignmentAnnotation( jaa); } } } // and make a note of any group association if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0) { ArrayList aal = groupAnnotRefs .get(an[i].getGroupRef()); if (aal == null) { aal = new ArrayList(); groupAnnotRefs.put(an[i].getGroupRef(), aal); } aal.add(jaa); } if (an[i].hasScore()) { jaa.setScore(an[i].getScore()); } if (an[i].hasVisible()) jaa.visible = an[i].getVisible(); if (an[i].hasCentreColLabels()) jaa.centreColLabels = an[i].getCentreColLabels(); if (an[i].hasScaleColLabels()) { jaa.scaleColLabel = an[i].getScaleColLabels(); } if (an[i].hasAutoCalculated() && an[i].isAutoCalculated()) { // newer files have an 'autoCalculated' flag and store calculation // state in viewport properties jaa.autoCalculated = true; // means annotation will be marked for // update at end of load. } if (an[i].hasGraphHeight()) { jaa.graphHeight = an[i].getGraphHeight(); } if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); } else // if (!autoForView) { // add autocalculated group annotation and any user created annotation // for the view al.addAnnotation(jaa); } } } // /////////////////////// // LOAD GROUPS // Create alignment markup and styles for this view if (jms.getJGroupCount() > 0) { JGroup[] groups = jms.getJGroup(); for (int i = 0; i < groups.length; i++) { ColourSchemeI cs = null; if (groups[i].getColour() != null) { if (groups[i].getColour().startsWith("ucs")) { cs = GetUserColourScheme(jms, groups[i].getColour()); } else { cs = ColourSchemeProperty.getColour(al, groups[i].getColour()); } if (cs != null) { cs.setThreshold(groups[i].getPidThreshold(), true); } } Vector seqs = new Vector(); for (int s = 0; s < groups[i].getSeqCount(); s++) { String seqId = groups[i].getSeq(s) + ""; jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds .get(seqId); if (ts != null) { seqs.addElement(ts); } } if (seqs.size() < 1) { continue; } jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup( seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(), groups[i].getDisplayText(), groups[i].getColourText(), groups[i].getStart(), groups[i].getEnd()); sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour())); sg.textColour = new java.awt.Color(groups[i].getTextCol1()); sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] .isShowUnconserved() : false); sg.thresholdTextColour = groups[i].getTextColThreshold(); if (groups[i].hasShowConsensusHistogram()) { sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); } ; if (groups[i].hasShowSequenceLogo()) { sg.setshowSequenceLogo(groups[i].isShowSequenceLogo()); } if (groups[i].hasIgnoreGapsinConsensus()) { sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus()); } if (groups[i].getConsThreshold() != 0) { jalview.analysis.Conservation c = new jalview.analysis.Conservation( "All", ResidueProperties.propHash, 3, sg.getSequences(null), 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); sg.cs.setConservation(c); } if (groups[i].getId() != null && groupAnnotRefs.size() > 0) { // re-instate unique group/annotation row reference ArrayList jaal = groupAnnotRefs .get(groups[i].getId()); if (jaal != null) { for (jalview.datamodel.AlignmentAnnotation jaa : jaal) { jaa.groupRef = sg; if (jaa.autoCalculated) { // match up and try to set group autocalc alignment row for this // annotation if (jaa.label.startsWith("Consensus for ")) { sg.setConsensus(jaa); } // match up and try to set group autocalc alignment row for this // annotation if (jaa.label.startsWith("Conservation for ")) { sg.setConservationRow(jaa); } } } } } al.addGroup(sg); } } // /////////////////////////////// // LOAD VIEWPORT // If we just load in the same jar file again, the sequenceSetId // will be the same, and we end up with multiple references // to the same sequenceSet. We must modify this id on load // so that each load of the file gives a unique id String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; String viewId = (view.getId() == null ? null : view.getId() + uniqueSetSuffix); AlignFrame af = null; AlignViewport av = null; // now check to see if we really need to create a new viewport. if (multipleView && viewportsAdded.size() == 0) { // We recovered an alignment for which a viewport already exists. // TODO: fix up any settings necessary for overlaying stored state onto // state recovered from another document. (may not be necessary). // we may need a binding from a viewport in memory to one recovered from // XML. // and then recover its containing af to allow the settings to be applied. // TODO: fix for vamsas demo System.err .println("About to recover a viewport for existing alignment: Sequence set ID is " + uniqueSeqSetId); Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); if (seqsetobj != null) { if (seqsetobj instanceof String) { uniqueSeqSetId = (String) seqsetobj; System.err .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + uniqueSeqSetId); } else { System.err .println("Warning : Collision between sequence set ID string and existing jalview object mapping."); } } } AlignmentPanel ap = null; boolean isnewview = true; if (viewId != null) { // Check to see if this alignment already has a view id == viewId jalview.gui.AlignmentPanel views[] = Desktop .getAlignmentPanels(uniqueSeqSetId); if (views != null && views.length > 0) { for (int v = 0; v < views.length; v++) { if (views[v].av.getViewId().equalsIgnoreCase(viewId)) { // recover the existing alignpanel, alignframe, viewport af = views[v].alignFrame; av = views[v].av; ap = views[v]; // TODO: could even skip resetting view settings if we don't want to // change the local settings from other jalview processes isnewview = false; } } } } if (isnewview) { af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view, uniqueSeqSetId, viewId, autoAlan); av = af.viewport; ap = af.alignPanel; } // LOAD TREES // ///////////////////////////////////// if (loadTreesAndStructures && jms.getTreeCount() > 0) { try { for (int t = 0; t < jms.getTreeCount(); t++) { Tree tree = jms.getTree(t); TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { tp = af.ShowNewickTree( new jalview.io.NewickFile(tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos()); if (tree.getId() != null) { // perhaps bind the tree id to something ? } } else { // update local tree attributes ? // TODO: should check if tp has been manipulated by user - if so its // settings shouldn't be modified tp.setTitle(tree.getTitle()); tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree .getWidth(), tree.getHeight())); tp.av = av; // af.viewport; // TODO: verify 'associate with all // views' // works still tp.treeCanvas.av = av; // af.viewport; tp.treeCanvas.ap = ap; // af.alignPanel; } if (tp == null) { warn("There was a problem recovering stored Newick tree: \n" + tree.getNewick()); continue; } tp.fitToWindow.setState(tree.getFitToWindow()); tp.fitToWindow_actionPerformed(null); if (tree.getFontName() != null) { tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree .getFontStyle(), tree.getFontSize())); } else { tp.setTreeFont(new java.awt.Font(view.getFontName(), view .getFontStyle(), tree.getFontSize())); } tp.showPlaceholders(tree.getMarkUnlinked()); tp.showBootstrap(tree.getShowBootstrap()); tp.showDistances(tree.getShowDistances()); tp.treeCanvas.threshold = tree.getThreshold(); if (tree.getCurrentTree()) { af.viewport.setCurrentTree(tp.getTree()); } } } catch (Exception ex) { ex.printStackTrace(); } } // //LOAD STRUCTURES if (loadTreesAndStructures) { // run through all PDB ids on the alignment, and collect mappings between // jmol view ids and all sequences referring to it Hashtable jmolViewIds = new Hashtable(); for (int i = 0; i < JSEQ.length; i++) { if (JSEQ[i].getPdbidsCount() > 0) { Pdbids[] ids = JSEQ[i].getPdbids(); for (int p = 0; p < ids.length; p++) { for (int s = 0; s < ids[p].getStructureStateCount(); s++) { // check to see if we haven't already created this structure view String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null : ids[p].getStructureState(s).getViewId() + uniqueSetSuffix; jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); // Originally : ids[p].getFile() // : TODO: verify external PDB file recovery still works in normal // jalview project load jpdb.setFile(loadPDBFile(jprovider, ids[p].getId())); jpdb.setId(ids[p].getId()); int x = ids[p].getStructureState(s).getXpos(); int y = ids[p].getStructureState(s).getYpos(); int width = ids[p].getStructureState(s).getWidth(); int height = ids[p].getStructureState(s).getHeight(); // Probably don't need to do this anymore... // Desktop.desktop.getComponentAt(x, y); // TODO: NOW: check that this recovers the PDB file correctly. String pdbFile = loadPDBFile(jprovider, ids[p].getId()); jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds .get(JSEQ[i].getId() + ""); if (sviewid == null) { sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + "," + height; } if (!jmolViewIds.containsKey(sviewid)) { jmolViewIds.put(sviewid, new Object[] { new int[] { x, y, width, height }, "", new Hashtable(), new boolean[] { false, false, true } }); // Legacy pre-2.7 conversion JAL-823 : // do not assume any view has to be linked for colour by // sequence } // assemble String[] { pdb files }, String[] { id for each // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { // seqs_file 2}, boolean[] { // linkAlignPanel,superposeWithAlignpanel}} from hash Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid); ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s) .hasAlignwithAlignPanel() ? ids[p].getStructureState( s).getAlignwithAlignPanel() : false; // never colour by linked panel if not specified ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s) .hasColourwithAlignPanel() ? ids[p] .getStructureState(s).getColourwithAlignPanel() : false; // default for pre-2.7 projects is that Jmol colouring is enabled ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s) .hasColourByJmol() ? ids[p].getStructureState(s) .getColourByJmol() : true; if (((String) jmoldat[1]).length() < ids[p] .getStructureState(s).getContent().length()) { { jmoldat[1] = ids[p].getStructureState(s).getContent(); } } if (ids[p].getFile() != null) { Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2]) .get(ids[p].getFile()); if (seqstrmaps == null) { ((Hashtable) jmoldat[2]).put( new File(ids[p].getFile()).toString(), seqstrmaps = new Object[] { pdbFile, ids[p].getId(), new Vector(), new Vector() }); } if (!((Vector) seqstrmaps[2]).contains(seq)) { ((Vector) seqstrmaps[2]).addElement(seq); // ((Vector)seqstrmaps[3]).addElement(n) : // in principle, chains // should be stored here : do we need to // TODO: store and recover seq/pdb_id : // chain mappings } } else { errorMessage = ("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747"); warn(errorMessage); } } } } } { // Instantiate the associated Jmol views for (Entry entry : jmolViewIds.entrySet()) { String sviewid = entry.getKey(); Object[] svattrib = entry.getValue(); int[] geom = (int[]) svattrib[0]; String state = (String) svattrib[1]; Hashtable oldFiles = (Hashtable) svattrib[2]; final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2]; int x = geom[0], y = geom[1], width = geom[2], height = geom[3]; // collate the pdbfile -> sequence mappings from this view Vector pdbfilenames = new Vector(); Vector seqmaps = new Vector(); Vector pdbids = new Vector(); // Search to see if we've already created this Jmol view AppJmol comp = null; JInternalFrame[] frames = null; do { try { frames = Desktop.desktop.getAllFrames(); } catch (ArrayIndexOutOfBoundsException e) { // occasional No such child exceptions are thrown here... frames = null; try { Thread.sleep(10); } catch (Exception f) { } ; } } while (frames == null); // search for any Jmol windows already open from other // alignment views that exactly match the stored structure state for (int f = 0; comp == null && f < frames.length; f++) { if (frames[f] instanceof AppJmol) { if (sviewid != null && ((AppJmol) frames[f]).getViewId().equals(sviewid)) { // post jalview 2.4 schema includes structure view id comp = (AppJmol) frames[f]; } else if (frames[f].getX() == x && frames[f].getY() == y && frames[f].getHeight() == height && frames[f].getWidth() == width) { comp = (AppJmol) frames[f]; } } } if (comp == null) { // create a new Jmol window. // First parse the Jmol state to translate filenames loaded into the // view, and record the order in which files are shown in the Jmol // view, so we can add the sequence mappings in same order. StringBuffer newFileLoc = null; int cp = 0, ncp, ecp; while ((ncp = state.indexOf("load ", cp)) > -1) { if (newFileLoc == null) { newFileLoc = new StringBuffer(); } newFileLoc.append(state.substring(cp, ncp = (state.indexOf("\"", ncp + 1) + 1))); String oldfilenam = state.substring(ncp, ecp = state.indexOf("\"", ncp)); // recover the new mapping data for this old filename // have to normalize filename - since Jmol and jalview do filename // translation differently. Object[] filedat = oldFiles.get(new File(oldfilenam) .toString()); newFileLoc.append(((String) filedat[0])); pdbfilenames.addElement((String) filedat[0]); pdbids.addElement((String) filedat[1]); seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) .toArray(new SequenceI[0])); newFileLoc.append("\""); cp = ecp + 1; // advance beyond last \" and set cursor so we can // look for next file statement. } if (cp > 0) { // just append rest of state newFileLoc.append(state.substring(cp)); } else { System.err .print("Ignoring incomplete Jmol state for PDB ids: "); newFileLoc = new StringBuffer(state); newFileLoc.append("; load append "); for (String id : oldFiles.keySet()) { // add this and any other pdb files that should be present in // the viewer Object[] filedat = oldFiles.get(id); String nfilename; newFileLoc.append(((String) filedat[0])); pdbfilenames.addElement((String) filedat[0]); pdbids.addElement((String) filedat[1]); seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) .toArray(new SequenceI[0])); newFileLoc.append(" \""); newFileLoc.append((String) filedat[0]); newFileLoc.append("\""); } newFileLoc.append(";"); } if (newFileLoc != null) { int histbug = newFileLoc.indexOf("history = "); histbug += 10; int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug); String val = (diff == -1) ? null : newFileLoc.substring( histbug, diff); if (val != null && val.length() >= 4) { if (val.contains("e")) { if (val.trim().equals("true")) { val = "1"; } else { val = "0"; } newFileLoc.replace(histbug, diff, val); } } // TODO: assemble String[] { pdb files }, String[] { id for each // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { // seqs_file 2}} from hash final String[] pdbf = (String[]) pdbfilenames .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids .toArray(new String[pdbids.size()]); final SequenceI[][] sq = (SequenceI[][]) seqmaps .toArray(new SequenceI[seqmaps.size()][]); final String fileloc = newFileLoc.toString(), vid = sviewid; final AlignFrame alf = af; final java.awt.Rectangle rect = new java.awt.Rectangle(x, y, width, height); try { javax.swing.SwingUtilities.invokeAndWait(new Runnable() { public void run() { AppJmol sview = null; try { sview = new AppJmol(pdbf, id, sq, alf.alignPanel, useinJmolsuperpos, usetoColourbyseq, jmolColouring, fileloc, rect, vid); } catch (OutOfMemoryError ex) { new OOMWarning("restoring structure view for PDB id " + id, (OutOfMemoryError) ex.getCause()); if (sview != null && sview.isVisible()) { sview.closeViewer(); sview.setVisible(false); sview.dispose(); } } } }); } catch (InvocationTargetException ex) { warn("Unexpected error when opening Jmol view.", ex); } catch (InterruptedException e) { // e.printStackTrace(); } } } else // if (comp != null) { // NOTE: if the jalview project is part of a shared session then // view synchronization should/could be done here. // add mapping for sequences in this view to an already open Jmol // instance for (String id : oldFiles.keySet()) { // add this and any other pdb files that should be present in the // viewer Object[] filedat = oldFiles.get(id); String pdbFile = (String) filedat[0]; SequenceI[] seq = (SequenceI[]) ((Vector) filedat[2]) .toArray(new SequenceI[0]); ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile, jalview.io.AppletFormatAdapter.FILE); ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq); } // and add the AlignmentPanel's reference to the Jmol view ((AppJmol) comp).addAlignmentPanel(ap); if (useinJmolsuperpos) { ((AppJmol) comp).useAlignmentPanelForSuperposition(ap); } else { ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap); } if (usetoColourbyseq) { ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap, !jmolColouring); } else { ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap); } } } } } // and finally return. return af; } AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs, Alignment al, JalviewModelSequence jms, Viewport view, String uniqueSeqSetId, String viewId, ArrayList autoAlan) { AlignFrame af = null; af = new AlignFrame(al, view.getWidth(), view.getHeight(), uniqueSeqSetId, viewId); af.setFileName(file, "Jalview"); for (int i = 0; i < JSEQ.length; i++) { af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); } af.viewport.gatherViewsHere = view.getGatheredViews(); if (view.getSequenceSetId() != null) { jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded .get(uniqueSeqSetId); af.viewport.sequenceSetID = uniqueSeqSetId; if (av != null) { // propagate shared settings to this new view af.viewport.historyList = av.historyList; af.viewport.redoList = av.redoList; } else { viewportsAdded.put(uniqueSeqSetId, af.viewport); } // TODO: check if this method can be called repeatedly without // side-effects if alignpanel already registered. PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); } // apply Hidden regions to view. if (hiddenSeqs != null) { for (int s = 0; s < JSEQ.length; s++) { jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup(); for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { hidden.addSequence( al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); } af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); } jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs .size()]; for (int s = 0; s < hiddenSeqs.size(); s++) { hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); } af.viewport.hideSequence(hseqs); } // recover view properties and display parameters if (view.getViewName() != null) { af.viewport.viewName = view.getViewName(); af.setInitialTabVisible(); } af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText()); af.viewport.setConservationSelected(view.getConservationSelected()); af.viewport.setShowJVSuffix(view.getShowFullId()); af.viewport.rightAlignIds = view.getRightAlignIds(); af.viewport.setFont(new java.awt.Font(view.getFontName(), view .getFontStyle(), view.getFontSize())); af.alignPanel.fontChanged(); af.viewport.setRenderGaps(view.getRenderGaps()); af.viewport.setWrapAlignment(view.getWrapAlignment()); af.alignPanel.setWrapAlignment(view.getWrapAlignment()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); af.viewport.setShowBoxes(view.getShowBoxes()); af.viewport.setShowText(view.getShowText()); af.viewport.textColour = new java.awt.Color(view.getTextCol1()); af.viewport.textColour2 = new java.awt.Color(view.getTextCol2()); af.viewport.thresholdTextColour = view.getTextColThreshold(); af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view .isShowUnconserved() : false); af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); ColourSchemeI cs = null; // apply colourschemes if (view.getBgColour() != null) { if (view.getBgColour().startsWith("ucs")) { cs = GetUserColourScheme(jms, view.getBgColour()); } else if (view.getBgColour().startsWith("Annotation")) { // int find annotation if (af.viewport.alignment.getAlignmentAnnotation() != null) { for (int i = 0; i < af.viewport.alignment .getAlignmentAnnotation().length; i++) { if (af.viewport.alignment.getAlignmentAnnotation()[i].label .equals(view.getAnnotationColours().getAnnotation())) { if (af.viewport.alignment.getAlignmentAnnotation()[i] .getThreshold() == null) { af.viewport.alignment.getAlignmentAnnotation()[i] .setThreshold(new jalview.datamodel.GraphLine(view .getAnnotationColours().getThreshold(), "Threshold", java.awt.Color.black) ); } if (view.getAnnotationColours().getColourScheme() .equals("None")) { cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], new java.awt.Color(view.getAnnotationColours() .getMinColour()), new java.awt.Color(view .getAnnotationColours().getMaxColour()), view.getAnnotationColours().getAboveThreshold()); } else if (view.getAnnotationColours().getColourScheme() .startsWith("ucs")) { cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], GetUserColourScheme(jms, view .getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); } else { cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], ColourSchemeProperty.getColour(al, view .getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); } // Also use these settings for all the groups if (al.getGroups() != null) { for (int g = 0; g < al.getGroups().size(); g++) { jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al .getGroups().elementAt(g); if (sg.cs == null) { continue; } /* * if * (view.getAnnotationColours().getColourScheme().equals("None" * )) { sg.cs = new AnnotationColourGradient( * af.viewport.alignment.getAlignmentAnnotation()[i], new * java.awt.Color(view.getAnnotationColours(). * getMinColour()), new * java.awt.Color(view.getAnnotationColours(). * getMaxColour()), * view.getAnnotationColours().getAboveThreshold()); } else */ { sg.cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], sg.cs, view.getAnnotationColours() .getAboveThreshold()); } } } break; } } } } else { cs = ColourSchemeProperty.getColour(al, view.getBgColour()); } if (cs != null) { cs.setThreshold(view.getPidThreshold(), true); cs.setConsensus(af.viewport.hconsensus); } } af.viewport.setGlobalColourScheme(cs); af.viewport.setColourAppliesToAllGroups(false); if (view.getConservationSelected() && cs != null) { cs.setConservationInc(view.getConsThreshold()); } af.changeColour(cs); af.viewport.setColourAppliesToAllGroups(true); if (view.getShowSequenceFeatures()) { af.viewport.showSequenceFeatures = true; } if (view.hasCentreColumnLabels()) { af.viewport.setCentreColumnLabels(view.getCentreColumnLabels()); } if (view.hasIgnoreGapsinConsensus()) { af.viewport.ignoreGapsInConsensusCalculation = view .getIgnoreGapsinConsensus(); } if (view.hasFollowHighlight()) { af.viewport.followHighlight = view.getFollowHighlight(); } if (view.hasFollowSelection()) { af.viewport.followSelection = view.getFollowSelection(); } if (view.hasShowConsensusHistogram()) { af.viewport.setShowConsensusHistogram(view .getShowConsensusHistogram()); } else { af.viewport.setShowConsensusHistogram(true); } if (view.hasShowSequenceLogo()) { af.viewport.showSequenceLogo = view.getShowSequenceLogo(); } else { af.viewport.showSequenceLogo = false; } if (view.hasShowDbRefTooltip()) { af.viewport.setShowDbRefs(view.getShowDbRefTooltip()); } if (view.hasShowNPfeatureTooltip()) { af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip()); } if (view.hasShowGroupConsensus()) { af.viewport.setShowGroupConsensus(view.getShowGroupConsensus()); } else { af.viewport.setShowGroupConsensus(false); } if (view.hasShowGroupConservation()) { af.viewport.setShowGroupConservation(view.getShowGroupConservation()); } else { af.viewport.setShowGroupConservation(false); } // recover featre settings if (jms.getFeatureSettings() != null) { af.viewport.featuresDisplayed = new Hashtable(); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); if (setting.hasMincolour()) { GraduatedColor gc = setting.hasMin() ? new GraduatedColor( new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()), setting.getMin(), setting.getMax()) : new GraduatedColor( new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()), 0, 1); if (setting.hasThreshold()) { gc.setThresh(setting.getThreshold()); gc.setThreshType(setting.getThreshstate()); } gc.setAutoScaled(true); // default if (setting.hasAutoScale()) { gc.setAutoScaled(setting.getAutoScale()); } if (setting.hasColourByLabel()) { gc.setColourByLabel(setting.getColourByLabel()); } // and put in the feature colour table. af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( setting.getType(), gc); } else { af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( setting.getType(), new java.awt.Color(setting.getColour())); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( setting.getType(), setting.getOrder()); else af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( setting.getType(), fs / jms.getFeatureSettings().getSettingCount()); if (setting.getDisplay()) { af.viewport.featuresDisplayed.put(setting.getType(), new Integer( setting.getColour())); } } af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; Hashtable fgtable; af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); } } if (view.getHiddenColumnsCount() > 0) { for (int c = 0; c < view.getHiddenColumnsCount(); c++) { af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view .getHiddenColumns(c).getEnd() // +1 ); } } af.setMenusFromViewport(af.viewport); // TODO: we don't need to do this if the viewport is aready visible. Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); af.alignPanel.updateAnnotation(false); // recompute any autoannotation reorderAutoannotation(af, al, autoAlan); return af; } private void reorderAutoannotation(AlignFrame af, Alignment al, ArrayList autoAlan) { // copy over visualization settings for autocalculated annotation in the // view if (al.getAlignmentAnnotation() != null) { /** * Kludge for magic autoannotation names (see JAL-811) */ String[] magicNames = new String[] { "Consensus", "Quality", "Conservation" }; JvAnnotRow nullAnnot = new JvAnnotRow(-1, null); Hashtable visan = new Hashtable(); for (String nm : magicNames) { visan.put(nm, nullAnnot); } for (JvAnnotRow auan : autoAlan) { visan.put(auan.template.label, auan); } int hSize = al.getAlignmentAnnotation().length; ArrayList reorder = new ArrayList(); for (int h = 0; h < hSize; h++) { jalview.datamodel.AlignmentAnnotation jalan = al .getAlignmentAnnotation()[h]; if (jalan.autoCalculated) { JvAnnotRow valan = visan.get(jalan.label); if (valan != null) { // delete the auto calculated row from the alignment al.deleteAnnotation(al.getAlignmentAnnotation()[h], false); hSize--; h--; if (valan != nullAnnot) { if (jalan != valan.template) { // newly created autoannotation row instance // so keep a reference to the visible annotation row // and copy over all relevant attributes if (valan.template.graphHeight >= 0) { jalan.graphHeight = valan.template.graphHeight; } jalan.visible = valan.template.visible; } reorder.add(new JvAnnotRow(valan.order, jalan)); } } } } int s = 0, srt[] = new int[reorder.size()]; JvAnnotRow[] rws = new JvAnnotRow[reorder.size()]; for (JvAnnotRow jvar : reorder) { rws[s] = jvar; srt[s++] = jvar.order; } reorder.clear(); jalview.util.QuickSort.sort(srt, rws); // and re-insert the annotation at its correct position for (JvAnnotRow jvar : rws) { al.addAnnotation(jvar.template, jvar.order); } af.alignPanel.adjustAnnotationHeight(); } } Hashtable skipList = null; /** * TODO remove this method * * @param view * @return AlignFrame bound to sequenceSetId from view, if one exists. private * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) { * throw new Error("Implementation Error. No skipList defined for this * Jalview2XML instance."); } return (AlignFrame) * skipList.get(view.getSequenceSetId()); } */ /** * Check if the Jalview view contained in object should be skipped or not. * * @param object * @return true if view's sequenceSetId is a key in skipList */ private boolean skipViewport(JalviewModel object) { if (skipList == null) { return false; } String id; if (skipList.containsKey(id = object.getJalviewModelSequence() .getViewport()[0].getSequenceSetId())) { if (Cache.log != null && Cache.log.isDebugEnabled()) { Cache.log.debug("Skipping seuqence set id " + id); } return true; } return false; } public void AddToSkipList(AlignFrame af) { if (skipList == null) { skipList = new Hashtable(); } skipList.put(af.getViewport().getSequenceSetId(), af); } public void clearSkipList() { if (skipList != null) { skipList.clear(); skipList = null; } } private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al) { jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId()); Vector dseqs = null; if (ds == null) { // create a list of new dataset sequences dseqs = new Vector(); } for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) { Sequence vamsasSeq = vamsasSet.getSequence(i); ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs); } // create a new dataset if (ds == null) { SequenceI[] dsseqs = new SequenceI[dseqs.size()]; dseqs.copyInto(dsseqs); ds = new jalview.datamodel.Alignment(dsseqs); debug("Created new dataset " + vamsasSet.getDatasetId() + " for alignment " + System.identityHashCode(al)); addDatasetRef(vamsasSet.getDatasetId(), ds); } // set the dataset for the newly imported alignment. if (al.getDataset() == null) { al.setDataset(ds); } } /** * * @param vamsasSeq * sequence definition to create/merge dataset sequence for * @param ds * dataset alignment * @param dseqs * vector to add new dataset sequence to */ private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs) { // JBP TODO: Check this is called for AlCodonFrames to support recovery of // xRef Codon Maps jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds .get(vamsasSeq.getId()); jalview.datamodel.SequenceI dsq = null; if (sq != null && sq.getDatasetSequence() != null) { dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence(); } String sqid = vamsasSeq.getDsseqid(); if (dsq == null) { // need to create or add a new dataset sequence reference to this sequence if (sqid != null) { dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid); } // check again if (dsq == null) { // make a new dataset sequence dsq = sq.createDatasetSequence(); if (sqid == null) { // make up a new dataset reference for this sequence sqid = seqHash(dsq); } dsq.setVamsasId(uniqueSetSuffix + sqid); seqRefIds.put(sqid, dsq); if (ds == null) { if (dseqs != null) { dseqs.addElement(dsq); } } else { ds.addSequence(dsq); } } else { if (sq != dsq) { // make this dataset sequence sq's dataset sequence sq.setDatasetSequence(dsq); } } } // TODO: refactor this as a merge dataset sequence function // now check that sq (the dataset sequence) sequence really is the union of // all references to it // boolean pre = sq.getStart() < dsq.getStart(); // boolean post = sq.getEnd() > dsq.getEnd(); // if (pre || post) if (sq != dsq) { StringBuffer sb = new StringBuffer(); String newres = jalview.analysis.AlignSeq.extractGaps( jalview.util.Comparison.GapChars, sq.getSequenceAsString()); if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length() > dsq.getLength()) { // Update with the longer sequence. synchronized (dsq) { /* * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() - * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) { * sb.append(newres.substring(newres.length() - sq.getEnd() - * dsq.getEnd())); dsq.setEnd(sq.getEnd()); } */ dsq.setSequence(sb.toString()); } // TODO: merges will never happen if we 'know' we have the real dataset // sequence - this should be detected when id==dssid System.err.println("DEBUG Notice: Merged dataset sequence"); // (" // + (pre ? "prepended" : "") + " " // + (post ? "appended" : "")); } } } java.util.Hashtable datasetIds = null; java.util.IdentityHashMap dataset2Ids = null; private Alignment getDatasetFor(String datasetId) { if (datasetIds == null) { datasetIds = new Hashtable(); return null; } if (datasetIds.containsKey(datasetId)) { return (Alignment) datasetIds.get(datasetId); } return null; } private void addDatasetRef(String datasetId, Alignment dataset) { if (datasetIds == null) { datasetIds = new Hashtable(); } datasetIds.put(datasetId, dataset); } /** * make a new dataset ID for this jalview dataset alignment * * @param dataset * @return */ private String getDatasetIdRef(jalview.datamodel.Alignment dataset) { if (dataset.getDataset() != null) { warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment..."); } String datasetId = makeHashCode(dataset, null); if (datasetId == null) { // make a new datasetId and record it if (dataset2Ids == null) { dataset2Ids = new IdentityHashMap(); } else { datasetId = (String) dataset2Ids.get(dataset); } if (datasetId == null) { datasetId = "ds" + dataset2Ids.size() + 1; dataset2Ids.put(dataset, datasetId); } } return datasetId; } private void addDBRefs(SequenceI datasetSequence, Sequence sequence) { for (int d = 0; d < sequence.getDBRefCount(); d++) { DBRef dr = sequence.getDBRef(d); jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( sequence.getDBRef(d).getSource(), sequence.getDBRef(d) .getVersion(), sequence.getDBRef(d).getAccessionId()); if (dr.getMapping() != null) { entry.setMap(addMapping(dr.getMapping())); } datasetSequence.addDBRef(entry); } } private jalview.datamodel.Mapping addMapping(Mapping m) { SequenceI dsto = null; // Mapping m = dr.getMapping(); int fr[] = new int[m.getMapListFromCount() * 2]; Enumeration f = m.enumerateMapListFrom(); for (int _i = 0; f.hasMoreElements(); _i += 2) { MapListFrom mf = (MapListFrom) f.nextElement(); fr[_i] = mf.getStart(); fr[_i + 1] = mf.getEnd(); } int fto[] = new int[m.getMapListToCount() * 2]; f = m.enumerateMapListTo(); for (int _i = 0; f.hasMoreElements(); _i += 2) { MapListTo mf = (MapListTo) f.nextElement(); fto[_i] = mf.getStart(); fto[_i + 1] = mf.getEnd(); } jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit()); if (m.getMappingChoice() != null) { MappingChoice mc = m.getMappingChoice(); if (mc.getDseqFor() != null) { String dsfor = "" + mc.getDseqFor(); if (seqRefIds.containsKey(dsfor)) { /** * recover from hash */ jmap.setTo((SequenceI) seqRefIds.get(dsfor)); } else { frefedSequence.add(new Object[] { dsfor, jmap }); } } else { /** * local sequence definition */ Sequence ms = mc.getSequence(); jalview.datamodel.Sequence djs = null; String sqid = ms.getDsseqid(); if (sqid != null && sqid.length() > 0) { /* * recover dataset sequence */ djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid); } else { System.err .println("Warning - making up dataset sequence id for DbRef sequence map reference"); sqid = ((Object) ms).toString(); // make up a new hascode for // undefined dataset sequence hash // (unlikely to happen) } if (djs == null) { /** * make a new dataset sequence and add it to refIds hash */ djs = new jalview.datamodel.Sequence(ms.getName(), ms.getSequence()); djs.setStart(jmap.getMap().getToLowest()); djs.setEnd(jmap.getMap().getToHighest()); djs.setVamsasId(uniqueSetSuffix + sqid); jmap.setTo(djs); seqRefIds.put(sqid, djs); } jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); addDBRefs(djs, ms); } } return (jmap); } public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs) { initSeqRefs(); jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null, null); if (!keepSeqRefs) { clearSeqRefs(); jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); } else { uniqueSetSuffix = ""; jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't // overwrite the // view we just // copied } if (this.frefedSequence == null) { frefedSequence = new Vector(); } viewportsAdded = new Hashtable(); AlignFrame af = LoadFromObject(jm, null, false, null); af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); /* * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; * i