/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program 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 2 * of the License, or (at your option) any later version. * * This program 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 this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import java.io.*; import java.net.*; import java.util.*; import java.util.jar.*; import javax.swing.*; import org.exolab.castor.xml.*; import jalview.schemabinding.version2.*; import jalview.schemes.*; import jalview.structure.StructureSelectionManager; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class Jalview2XML { Hashtable seqRefIds; /** * 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) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { return; } try { FileOutputStream fos = new FileOutputStream(statefile); JarOutputStream jout = new JarOutputStream(fos); //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS //////////////////////////////////////////////////// PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8")); 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]; 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); SaveState(apanel, apSize == 1 ? shortName : ap + shortName, jout, out); } } } out.close(); jout.close(); } catch (Exception ex) { 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); PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8")); for (ap = 0; ap < apSize; ap++) { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap); SaveState(apanel, apSize == 1 ? fileName : fileName + ap, jout, out); } out.close(); jout.close(); return true; } catch (Exception ex) { ex.printStackTrace(); return false; } } /** * DOCUMENT ME! * * @param af DOCUMENT ME! * @param timeStamp DOCUMENT ME! * @param fileName DOCUMENT ME! * @param jout DOCUMENT ME! * @param out DOCUMENT ME! */ public JalviewModel SaveState(AlignmentPanel ap, String fileName, JarOutputStream jout, PrintWriter out) { if (seqRefIds == null) { seqRefIds = new Hashtable(); } 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() + ""); JSeq jseq; //SAVE SEQUENCES int id = 0; jalview.datamodel.SequenceI jds; for (int i = 0; i < jal.getHeight(); i++) { jds = jal.getSequenceAt(i); id = jds.hashCode(); if (seqRefIds.get(id + "") != null) { } else { vamsasSeq = new Sequence(); vamsasSeq.setId(id + ""); vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); if (jds.getDatasetSequence().getDBRef() != null) { jalview.datamodel.DBRefEntry[] dbrefs = jds.getDatasetSequence().getDBRef(); 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()); vamsasSeq.addDBRef(dbref); } } vamsasSet.addSequence(vamsasSeq); seqRefIds.put(id + "", jal.getSequenceAt(i)); } jseq = new JSeq(); jseq.setStart(jds.getStart()); jseq.setEnd(jds.getEnd()); jseq.setColour(av.getSequenceColour(jds).getRGB()); jseq.setId(id); 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(); for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppJMol) { jmol = (AppJMol) frames[f]; if (!jmol.pdbentry.getId().equals(entry.getId())) continue; StructureState state = new StructureState(); state.setVisible(true); state.setXpos(jmol.getX()); state.setYpos(jmol.getY()); state.setWidth(jmol.getWidth()); state.setHeight(jmol.getHeight()); state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", "")); for (int s = 0; s < jmol.sequence.length; s++) { if (jal.findIndex(jmol.sequence[s]) > -1) { pdb.addStructureState(state); } } } } if (entry.getFile() != null) { pdb.setFile(entry.getFile()); if (pdbfiles == null) { pdbfiles = new Vector(); } if (!pdbfiles.contains(entry.getId())) { pdbfiles.addElement(entry.getId()); try { File file = new File(entry.getFile()); 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); 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 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()); jms.addTree(tree); } } } } } //SAVE ANNOTATIONS 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); if (aa[i] == av.quality || aa[i] == av.conservation || aa[i] == av.consensus) { an.setLabel(aa[i].label); an.setGraph(true); vamsasSet.addAnnotation(an); continue; } an.setDescription(aa[i].description); if (aa[i].sequenceRef != null) { an.setSequenceRef(aa[i].sequenceRef.getName()); } 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].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(); ae.setDescription(aa[i].annotations[a].description); ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); ae.setValue(aa[i].annotations[a].value); ae.setPosition(a); ae .setSecondaryStructure(aa[i].annotations[a].secondaryStructure + ""); if (aa[i].annotations[a].colour != java.awt.Color.black) { ae.setColour(aa[i].annotations[a].colour.getRGB()); } an.addAnnotationElement(ae); } } 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 (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); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s); groups[i].addSeq(seq.hashCode()); } } jms.setJGroup(groups); } ///////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(ap.alignFrame.getTitle()); view.setSequenceSetId(av.getSequenceSetId()); 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.setWrapAlignment(av.getWrapAlignment()); view.setTextCol1(av.textColour.getRGB()); view.setTextCol2(av.textColour2.getRGB()); view.setTextColThreshold(av.thresholdTextColour); 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(); for (int ro = 0; ro < renderOrder.length; ro++) { Setting setting = new Setting(); setting.setType(renderOrder[ro]); 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) { 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 (out != null) { //We may not want to right the object to disk, //eg we can copy the alignViewport to a new view object //using save and then load try { if (!fileName.endsWith(".xml")) { fileName = fileName + ".xml"; } JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); object.marshal(out); } catch (Exception ex) { ex.printStackTrace(); } } return object; } String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, Vector userColours, JalviewModelSequence jms) { String id = null; jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; if (!userColours.contains(ucs)) { userColours.add(ucs); 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); } } id = "ucs" + userColours.indexOf(ucs); 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; } /** * DOCUMENT ME! * * @param file DOCUMENT ME! */ public AlignFrame LoadJalviewAlign(final String file) { uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; jalview.gui.AlignFrame af = null; seqRefIds = new Hashtable(); viewportsAdded = new Hashtable(); Hashtable gatherToThisFrame = new Hashtable(); try { //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING URL url = null; if (file.startsWith("http://")) { url = new URL(file); } JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; do { if (url != null) { jin = new JarInputStream(url.openStream()); } else { jin = new JarInputStream(new FileInputStream(file)); } 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); af = LoadFromObject(object, file, true); if (af.viewport.gatherViewsHere) { gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); } entryCount++; } else if (jarentry != null) { //Some other file here. entryCount++; } } while (jarentry != null); } catch (java.net.UnknownHostException ex) { ex.printStackTrace(); System.err.println("Couldn't locate Jalview XML file : " + ex + "\n"); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't locate " + file, "URL not found", JOptionPane.WARNING_MESSAGE); } }); } catch (Exception ex) { //Is Version 1 Jar file? af = new Jalview2XML_V1().LoadJalviewAlign(file); 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"); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Error loading " + file, "Error loading Jalview file", JOptionPane.WARNING_MESSAGE); } }); } if (Desktop.instance != null) { Desktop.instance.stopLoading(); } Enumeration en = gatherToThisFrame.elements(); while(en.hasMoreElements()) { Desktop.instance.gatherViews( (AlignFrame) en.nextElement()); } return af; } Hashtable alreadyLoadedPDB; String loadPDBFile(String file, String pdbId) { if (alreadyLoadedPDB == null) alreadyLoadedPDB = new Hashtable(); if (alreadyLoadedPDB.containsKey(pdbId)) return alreadyLoadedPDB.get(pdbId).toString(); try { JarInputStream jin = null; if (file.startsWith("http://")) { jin = new JarInputStream(new URL(file).openStream()); } else { jin = new JarInputStream(new FileInputStream(file)); } JarEntry entry = null; do { entry = jin.getNextJarEntry(); } while (!entry.getName().equals(pdbId)); 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); } out.close(); alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); return outFile.getAbsolutePath(); } catch (Exception ex) { ex.printStackTrace(); } return null; } AlignFrame LoadFromObject(JalviewModel object, String file, boolean loadTreesAndStructures) { 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(); 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[i].getName(), vamsasSeq[i].getSequence()); jseq.setDescription(vamsasSeq[i].getDescription()); jseq.setStart(JSEQ[i].getStart()); jseq.setEnd(JSEQ[i].getEnd()); seqRefIds.put(vamsasSeq[i].getId(), jseq); tmpseqs.add(jseq); } if (JSEQ[i].getHidden()) { if (hiddenSeqs == null) { hiddenSeqs = new Vector(); } hiddenSeqs.addElement( (jalview.datamodel.Sequence) seqRefIds.get(seqId)); } } ///SequenceFeatures are added to the DatasetSequence, // so we must create the dataset before loading features ///////////////////////////////// jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[ tmpseqs.size()]; tmpseqs.toArray(orderedSeqs); jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(orderedSeqs); al.setDataset(null); ///////////////////////////////// Hashtable pdbloaded = new Hashtable(); if (!multipleView) { 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 (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(file, ids[p].getId())); } else { entry.setFile(pdbloaded.get(ids[p].getId()).toString()); } } al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); } } if (vamsasSeq[i].getDBRefCount() > 0) { for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++) { jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( vamsasSeq[i].getDBRef(d).getSource(), vamsasSeq[i].getDBRef(d).getVersion(), vamsasSeq[i].getDBRef(d).getAccessionId() ); al.getSequenceAt(i).getDatasetSequence().addDBRef(entry); } } } } ///////////////////////////////// ////////////////////////////////// //LOAD ANNOTATIONS boolean hideQuality = true, hideConservation = true, hideConsensus = true; if (vamsasSet.getAnnotationCount() > 0) { Annotation[] an = vamsasSet.getAnnotation(); for (int i = 0; i < an.length; i++) { if (an[i].getLabel().equals("Quality")) { hideQuality = false; continue; } else if (an[i].getLabel().equals("Conservation")) { hideConservation = false; continue; } else if (an[i].getLabel().equals("Consensus")) { hideConsensus = false; continue; } if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) { al.addAnnotation( (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i]. getId()) ); continue; } 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++) { anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa]. getDisplayCharacter(), ae[aa].getDescription(), ae[aa].getSecondaryStructure().length() == 0 ? ' ' : ae[aa].getSecondaryStructure().charAt(0), ae[aa].getValue()); anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]. getColour()); } } jalview.datamodel.AlignmentAnnotation jaa = null; if (an[i].getGraph()) { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot, 0, 0, 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())) ); } } else { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } if (an[i].getId() != null) { annotationIds.put(an[i].getId(), jaa); jaa.annotationId = an[i].getId(); } if (an[i].getSequenceRef() != null) { jaa.createSequenceMapping( al.findName(an[i].getSequenceRef()), 1, true ); al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); } if (an[i].hasScore()) { jaa.setScore(an[i].getScore()); } al.addAnnotation(jaa); } } ///////////////////////// //LOAD GROUPS 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.thresholdTextColour = groups[i].getTextColThreshold(); 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); } al.addGroup(sg); } } ///////////////////////////////// // LOAD VIEWPORT AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); 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())); } //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; 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) { af.viewport.historyList = av.historyList; af.viewport.redoList = av.redoList; } else { viewportsAdded.put(uniqueSeqSetId, af.viewport); } PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); } 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); } if ( (hideConsensus || hideQuality || hideConservation) && al.getAlignmentAnnotation() != null) { int hSize = al.getAlignmentAnnotation().length; for (int h = 0; h < hSize; h++) { if ( (hideConsensus && al.getAlignmentAnnotation()[h].label.equals("Consensus")) || (hideQuality && al.getAlignmentAnnotation()[h].label.equals("Quality")) || (hideConservation && al.getAlignmentAnnotation()[h].label.equals("Conservation"))) { al.deleteAnnotation(al.getAlignmentAnnotation()[h]); hSize--; h--; } } af.alignPanel.adjustAnnotationHeight(); } 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.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); ColourSchemeI cs = null; if (view.getBgColour() != null) { if (view.getBgColour().startsWith("ucs")) { cs = GetUserColourScheme(jms, view.getBgColour()); } else if (view.getBgColour().startsWith("Annotation")) { //int find annotation 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 (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); 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 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); Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); //LOAD TREES /////////////////////////////////////// if (loadTreesAndStructures && jms.getTreeCount() > 0) { try { for (int t = 0; t < jms.getTreeCount(); t++) { Tree tree = jms.getTree(t); TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile( tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos()); 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) { 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++) { jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); jpdb.setFile(loadPDBFile(ids[p].getFile(), 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(); java.awt.Component comp = Desktop.desktop.getComponentAt(x, y); String pdbFile = loadPDBFile(file, ids[p].getId()); jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[] { al.getSequenceAt(i)}; if (comp == null || (comp.getWidth() != width && comp.getHeight() != height)) { String state = ids[p].getStructureState(s).getContent(); StringBuffer newFileLoc = new StringBuffer(state.substring(0, state.indexOf("\"", state.indexOf("load")) + 1)); newFileLoc.append(jpdb.getFile()); newFileLoc.append(state.substring( state.indexOf("\"", state.indexOf("load \"") + 6))); new AppJMol(pdbFile, ids[p].getId(), seq, af.alignPanel, newFileLoc.toString(), new java.awt.Rectangle(x, y, width, height)); } else if(comp!=null) { StructureSelectionManager.getStructureSelectionManager() .setMapping(seq, pdbFile, jalview.io.AppletFormatAdapter.FILE); ( (AppJMol) comp).addSequence(seq); } } } } } } return af; } public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs) { jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null, null, null); if (!keepSeqRefs) { seqRefIds.clear(); jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); } else { uniqueSetSuffix = ""; } viewportsAdded = new Hashtable(); AlignFrame af = LoadFromObject(jm, null, false); af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); /* if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i