/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 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 jalview.io.*; import jalview.schemes.*; import java.io.*; import java.net.*; import java.util.*; import java.util.jar.*; import javax.swing.*; import jalview.binding.*; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class Jalview2XML { // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE public static void SaveState(File statefile) { long creation = System.currentTimeMillis(); 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"; } SaveState(af, creation, shortName, jout, out); } } out.close(); jout.close(); } catch (Exception ex) { ex.printStackTrace(); } } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW public static void SaveAlignment(AlignFrame af, String jarFile, String fileName) { try { FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS //////////////////////////////////////////////////// PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8")); SaveState(af, System.currentTimeMillis(), fileName, jout, out); out.close(); jout.close(); } catch (Exception ex) { ex.printStackTrace(); } } /** * DOCUMENT ME! * * @param af DOCUMENT ME! * @param timeStamp DOCUMENT ME! * @param fileName DOCUMENT ME! * @param jout DOCUMENT ME! * @param out DOCUMENT ME! */ public static void SaveState(AlignFrame af, long timeStamp, String fileName, JarOutputStream jout, PrintWriter out) { Vector seqids = new Vector(); Vector userColours = new Vector(); AlignViewport av = af.viewport; JalviewModel object = new JalviewModel(); object.setVamsasModel(new jalview.binding.VamsasModel()); object.setCreationDate(new java.util.Date(timeStamp)); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); jalview.datamodel.AlignmentI jal = af.viewport.alignment; SequenceSet vamsasSet = new SequenceSet(); Sequence vamsasSeq; JalviewModelSequence jms = new JalviewModelSequence(); vamsasSet.setGapChar(jal.getGapCharacter() + ""); JSeq jseq; //SAVE SEQUENCES int id = 0; for (int i = 0; i < jal.getHeight(); i++) { seqids.add(jal.getSequenceAt(i)); vamsasSeq = new Sequence(); vamsasSeq.setId(id + ""); vamsasSeq.setName(jal.getSequenceAt(i).getName()); vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); jseq = new JSeq(); jseq.setStart(jal.getSequenceAt(i).getStart()); jseq.setEnd(jal.getSequenceAt(i).getEnd()); jseq.setColour(jal.getSequenceAt(i).getColor().getRGB()); jseq.setId(id); jms.addJSeq(jseq); vamsasSet.addSequence(vamsasSeq); id++; } //SAVE TREES /////////////////////////////////// if (af.viewport.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( (af.viewport.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++) { if (aa[i].label.equals("Quality") || aa[i].label.equals("Conservation") || aa[i].label.equals("Consensus")) { continue; } Annotation an = new Annotation(); an.setDescription(aa[i].description); an.setGraph(aa[i].isGraph); an.setLabel(aa[i].label); AnnotationElement ae; 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 + ""); an.addAnnotationElement(ae); } 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.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()); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s); int index = seqids.indexOf(seq); groups[i].addSeq(index); } } jms.setJGroup(groups); } ///////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(af.getTitle()); view.setXpos(af.getX()); view.setYpos(af.getY()); view.setWidth(af.getWidth()); view.setHeight(af.getHeight()); view.setStartRes(av.startRes); view.setStartSeq(av.startSeq); if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), userColours, jms)); } 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.setShowConservation(av.showConservation); view.setShowFullId(av.getShowFullId()); view.setShowIdentity(av.showIdentity); view.setShowQuality(av.showQuality); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setWrapAlignment(av.getWrapAlignment()); jms.addViewport(view); object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); try { if (!fileName.endsWith(".xml")) { fileName = fileName + ".xml"; } JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); object.marshal(out); } catch (Exception ex) { ex.printStackTrace(); } } static 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.binding.UserColours uc = new jalview.binding.UserColours(); jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme(); for (int i = 0; i < colours.length; i++) { jalview.binding.Colour col = new jalview.binding.Colour(); 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; } static 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; } } int csize = colours.getUserColourScheme().getColourCount(); java.awt.Color[] newColours = new java.awt.Color[csize]; for (int i = 0; i < csize; i++) { newColours[i] = new java.awt.Color(Integer.parseInt( colours.getUserColourScheme().getColour(i).getRGB(), 16)); } return new jalview.schemes.UserColourScheme(newColours); } /** * DOCUMENT ME! * * @param file DOCUMENT ME! */ public static AlignFrame LoadJalviewAlign(String file) { JalviewModel object = new JalviewModel(); jalview.gui.AlignFrame af = null; 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) { InputStreamReader in = new InputStreamReader(jin, "UTF-8"); object = (JalviewModel) object.unmarshal(in); af = LoadFromObject(object); entryCount++; } } while (jarentry != null); } catch(java.net.UnknownHostException ex) { ex.printStackTrace(); System.err.println("Couldn't locate Jalview XML file : " + ex + "\n"); JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't locate " + file, "URL not found", JOptionPane.WARNING_MESSAGE); } catch (Exception ex) { ex.printStackTrace(); System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); JOptionPane.showInternalMessageDialog(Desktop.desktop, "Error loading " + file, "Error loading Jalview file", JOptionPane.WARNING_MESSAGE); } return af; } static AlignFrame LoadFromObject(JalviewModel object) { Vector seqids = new Vector(); SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); Sequence[] vamsasSeq = vamsasSet.getSequence(); JalviewModelSequence jms = object.getJalviewModelSequence(); ////////////////////////////////// //LOAD SEQUENCES jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length]; JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); for (int i = 0; i < vamsasSeq.length; i++) { jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), vamsasSeq[i].getSequence()); jseqs[i].setStart(JSEQ[i].getStart()); jseqs[i].setEnd(JSEQ[i].getEnd()); jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour())); seqids.add(jseqs[i]); } ///////////////////////////////// jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); ///////////////////////////////// ////////////////////////////////// //LOAD ANNOTATIONS if (vamsasSet.getAnnotation() != null) { Annotation[] an = vamsasSet.getAnnotation(); for (int i = 0; i < an.length; i++) { AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()]; for (int aa = 0; aa < ae.length; aa++) { anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(), ae[aa].getDescription(), ae[aa].getSecondaryStructure().charAt(0), ae[aa].getValue()); } jalview.datamodel.AlignmentAnnotation jaa = null; if (an[i].getGraph()) { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot, 0, 0, 1); } else { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } al.addAnnotation(jaa); } } ///////////////////////////////// // LOAD VIEWPORT Viewport[] views = jms.getViewport(); Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER AlignFrame af = new AlignFrame(al); // af.changeColour() ); ///////////////////////// //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()); } cs.setThreshold(groups[i].getPidThreshold(), true); } Vector seqs = new Vector(); int[] ids = groups[i].getSeq(); for (int s = 0; s < ids.length; s++) { seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt( ids[s])); } 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())); if (groups[i].getConsThreshold() != 0) { jalview.analysis.Conservation c = new jalview.analysis.Conservation("All", ResidueProperties.propHash, 3, sg.sequences, 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); sg.cs.setConservation(c); } al.addGroup(sg); } } af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight()); af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); af.viewport.showConservation = view.getShowConservation(); af.viewport.showQuality = view.getShowQuality(); af.viewport.showIdentity = view.getShowIdentity(); af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.abovePIDThreshold.setSelected(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText()); af.colourTextMenuItem.setSelected(view.getShowColourText()); af.viewport.setConservationSelected(view.getConservationSelected()); af.conservationMenuItem.setSelected(view.getConservationSelected()); af.viewport.setShowFullId(view.getShowFullId()); af.fullSeqId.setSelected(view.getShowFullId()); af.viewport.setFont(new java.awt.Font(view.getFontName(), view.getFontStyle(), view.getFontSize())); af.alignPanel.fontChanged(); af.viewport.setRenderGaps(view.getRenderGaps()); af.renderGapsMenuItem.setSelected(view.getRenderGaps()); af.viewport.setWrapAlignment(view.getWrapAlignment()); af.wrapMenuItem.setSelected(view.getWrapAlignment()); if (view.getWrapAlignment()) { af.alignPanel.setWrapAlignment(view.getWrapAlignment()); } else { af.annotationPanelMenuItem.setState(view.getShowAnnotation()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); } af.viewport.setShowBoxes(view.getShowBoxes()); af.viewBoxesMenuItem.setSelected(view.getShowBoxes()); af.viewport.setShowText(view.getShowText()); af.viewTextMenuItem.setSelected(view.getShowText()); ColourSchemeI cs = null; if (view.getBgColour() != null) { if (view.getBgColour().startsWith("ucs")) { cs = GetUserColourScheme(jms, view.getBgColour()); } else { cs = ColourSchemeProperty.getColour(al, view.getBgColour()); } if(cs!=null) { cs.setThreshold(view.getPidThreshold(), true); cs.setConsensus(af.viewport.vconsensus); } } af.setColourSelected(view.getBgColour()); af.viewport.setGlobalColourScheme(cs); af.viewport.setColourAppliesToAllGroups(false); af.changeColour(cs); if (view.getConservationSelected() && cs!=null) { cs.setConservationInc(view.getConsThreshold()); } af.viewport.setColourAppliesToAllGroups(true); if (view.getShowSequenceFeatures()) { af.viewport.showSequenceFeatures = true; af.sequenceFeatures.setSelected(true); new SequenceFeatureFetcher(al, af.alignPanel); al.featuresAdded = true; } Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); //LOAD TREES /////////////////////////////////////// if (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(); } } return af; } }