X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=8497df7361a1323b223abc686fd7886b834b68b6;hb=4e1cb9b8b058d9b633af223b1cdb7b220d5d2ccd;hp=7d6d519dca2cbbd6c0514e417851997092e9e9b0;hpb=fbd0380f6ba13c335225197177c416009e786a5b;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 7d6d519..8497df7 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,1736 +1,3303 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 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.schemes.*; - +import java.awt.Rectangle; import java.io.*; - import java.net.*; - import java.util.*; - 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.AlignmentI; +import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; - - - +import jalview.schemes.*; +import jalview.structure.StructureSelectionManager; +import jalview.util.jarInputStreamProvider; /** - * DOCUMENT ME! - * + * 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 $Revision$ */ 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 + * create/return unique hash string for sq + * + * @param sq + * @return new or existing unique string for sq */ - Hashtable viewportsAdded; + 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; + } + } - Hashtable annotationIds = new Hashtable(); + 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(); + } + } - String uniqueSetSuffix = ""; + 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; - // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE - public void SaveState(File statefile) - { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + /** + * 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 - if (frames == null) - { - return; - } + Vector frefedSequence = null; - try - { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); + boolean raiseGUI = true; // whether errors are raised in dialog boxes or not - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); + public Jalview2XML() + { + } - Vector shortNames = new Vector(); + public Jalview2XML(boolean raiseGUI) + { + this.raiseGUI = raiseGUI; + } - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + 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) { - if (frames[i] instanceof AlignFrame) + 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) { - 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); - } + 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."); + } } - - out.close(); - jout.close(); + frefedSequence.remove(r); + rSize--; + } + else + { + System.err + .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string " + + ref[0] + + " with objecttype " + + ref[1].getClass()); + r++; + } } - catch (Exception ex) + else { - ex.printStackTrace(); + // empty reference + frefedSequence.remove(r); + rSize--; } + } } + } - // 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 -1; i--) + { + if (frames[i] instanceof AlignFrame) { - jal = jal.getHiddenSequences().getFullAlignment(); - } - - SequenceSet vamsasSet = new SequenceSet(); - Sequence vamsasSeq; - JalviewModelSequence jms = new JalviewModelSequence(); + AlignFrame af = (AlignFrame) frames[i]; + // skip ? + if (skipList != null + && skipList.containsKey(af.getViewport() + .getSequenceSetId())) + { + continue; + } - vamsasSet.setGapChar(jal.getGapCharacter() + ""); + String shortName = af.getTitle(); - JSeq jseq; - Vector pdbfiles = null; + if (shortName.indexOf(File.separatorChar) > -1) + { + shortName = shortName.substring(shortName + .lastIndexOf(File.separatorChar) + 1); + } - //SAVE SEQUENCES - int id = 0; - jalview.datamodel.SequenceI jds; - for (int i = 0; i < jal.getHeight(); i++) - { - jds = jal.getSequenceAt(i); - id = jds.hashCode(); + int count = 1; - if(seqRefIds.get(id+"")!=null) + while (shortNames.contains(shortName)) + { + if (shortName.endsWith("_" + (count - 1))) { - + shortName = shortName + .substring(0, shortName.lastIndexOf("_")); } - 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(); + shortName = shortName.concat("_" + count); + count++; + } - 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); - } - } + shortNames.addElement(shortName); + + if (!shortName.endsWith(".xml")) + { + shortName = shortName + ".xml"; + } - vamsasSet.addSequence(vamsasSeq); - seqRefIds.put(id+"", jal.getSequenceAt(i)); + 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"; } - jseq = new JSeq(); - jseq.setStart(jds.getStart()); - jseq.setEnd(jds.getEnd()); - jseq.setColour( av.getSequenceColour(jds).getRGB()); + 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(); + } + } - jseq.setId(id); + // 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); + } - if (av.hasHiddenRows) - { - jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); + 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; + } + } - 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); + /** + * 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(); - for(int h=0; h -1; f--) + { + if (frames[f] instanceof AppJmol) + { + jmol = (AppJmol) frames[f]; + if (!jmol.pdbentry.getId().equals(entry.getId()) + && !(entry.getId().length()>4 + && entry.getId().toLowerCase().startsWith(jmol.pdbentry.getId().toLowerCase()))) + continue; + matchedFile = jmol.pdbentry.getFile(); // record the file so we can get at it if the ID match is ambiguous (e.g. 1QIP==1qipA) + 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()); + String statestring = jmol.viewer.getStateInfo(); + if (state != null) + { + state.setContent(statestring.replaceAll("\n", "")); + } + for (int s = 0; s < jmol.sequence.length; s++) + { + if (jal.findIndex(jmol.sequence[s]) > -1) { - an.setLabel(aa[i].label); - an.setGraph(true); - vamsasSet.addAnnotation(an); - continue; + 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(); + } - an.setDescription(aa[i].description); - - if(aa[i].sequenceRef!=null) - { - an.setSequenceRef(aa[i].sequenceRef.getName()); - } - - if(aa[i].graph>0) + if (!pdbfiles.contains(entry.getId())) + { + pdbfiles.addElement(entry.getId()); + try + { + File file = new File(matchedFile); + if (file.exists() && jout != null) { - 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); - } + 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(); } - else - an.setGraph(false); - - an.setLabel(aa[i].label); - - AnnotationElement ae; + } catch (Exception ex) + { + ex.printStackTrace(); + } - 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); - } + } + } - vamsasSet.addAnnotation(an); + 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); } + } - //SAVE GROUPS - if (jal.getGroups() != null) - { - JGroup[] groups = new JGroup[jal.getGroups().size()]; + jms.addJSeq(jseq); + } - 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)); - } + 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); + } + } + } + } - groups[i].setPidThreshold(sg.cs.getThreshold()); - } + // 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(); - 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 t = 0; t < frames.length; t++) + { + if (frames[t] instanceof TreePanel) + { + TreePanel tp = (TreePanel) frames[t]; - for (int s = 0; s < sg.getSize(); s++) - { - jalview.datamodel.Sequence seq = - (jalview.datamodel.Sequence) sg.getSequenceAt(s); - groups[i].addSeq(seq.hashCode()); - } + 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); } - - jms.setJGroup(groups); + } } + } + } + // SAVE ANNOTATIONS + if (jal.getAlignmentAnnotation() != null) + { + jalview.datamodel.AlignmentAnnotation[] aa = jal + .getAlignmentAnnotation(); - ///////////SAVE VIEWPORT - Viewport view = new Viewport(); - view.setTitle(ap.alignFrame.getTitle()); - view.setSequenceSetId(av.getSequenceSetId()); - view.setViewName(av.viewName); - view.setGatheredViews(av.gatherViewsHere); - + for (int i = 0; i < aa.length; i++) + { + Annotation an = new Annotation(); - 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 + if (aa[i].annotationId != null) { - view.setXpos(ap.alignFrame.getBounds().x); - view.setYpos(ap.alignFrame.getBounds().y); - view.setWidth(ap.alignFrame.getBounds().width); - view.setHeight(ap.alignFrame.getBounds().height); + annotationIds.put(aa[i].annotationId, aa[i]); } - view.setStartRes(av.startRes); - view.setStartSeq(av.startSeq); + an.setId(aa[i].annotationId); - if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) + if (aa[i] == av.quality || aa[i] == av.conservation + || aa[i] == av.consensus) { - view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), - userColours, jms)); + an.setLabel(aa[i].label); + an.setGraph(true); + vamsasSet.addAnnotation(an); + continue; } - 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())); + an.setVisible(aa[i].visible); - ac.setMaxColour(acg.getMaxColour().getRGB()); - ac.setMinColour(acg.getMinColour().getRGB()); - view.setAnnotationColours(ac); - view.setBgColour("AnnotationColourGradient"); - } - else + an.setDescription(aa[i].description); + + if (aa[i].sequenceRef != null) { - view.setBgColour(ColourSchemeProperty.getColourName( - av.getGlobalColourScheme())); + // TODO later annotation sequenceRef should be the XML ID of the + // sequence rather than its display name + an.setSequenceRef(aa[i].sequenceRef.getName()); } - ColourSchemeI cs = av.getGlobalColourScheme(); - - if(cs!=null) + if (aa[i].graph > 0) { - if (cs.conservationApplied()) - { - view.setConsThreshold(cs.getConservationInc()); - if (cs instanceof jalview.schemes.UserColourScheme) - view.setBgColour(SetUserColourScheme(cs, userColours, jms)); - } - - if (cs instanceof ResidueColourScheme) + an.setGraph(true); + an.setGraphType(aa[i].graph); + an.setGraphGroup(aa[i].graphGroup); + if (aa[i].getThreshold() != null) { - view.setPidThreshold(cs.getThreshold()); + 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); } } - - 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) + else { - 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 24) + 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.getShowunconserved()); + for (int s = 0; s < sg.getSize(); s++) { - 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); + jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg + .getSequenceAt(s); + groups[i].addSeq(seqHash(seq)); } + } - return ucs; + 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); - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - */ - public AlignFrame LoadJalviewAlign(final String file) + if (ap.av.explodedPosition != null) { - uniqueSetSuffix = System.currentTimeMillis()%100000 +""; - - jalview.gui.AlignFrame af = null; - - seqRefIds = new Hashtable(); - viewportsAdded = new Hashtable(); - - Vector gatherToThisFrame= new Vector(); - - 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.add(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); + 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); + } - if(af!=null) - { - System.out.println("Successfully loaded archive file"); - return af; - } - ex.printStackTrace(); + view.setStartRes(av.startRes); + view.setStartSeq(av.startSeq); - System.err.println("Exception whilst loading jalview XML file : " + - ex + "\n"); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { + 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())); + } - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Error loading " + file, - "Error loading Jalview file", - JOptionPane.WARNING_MESSAGE); - }}); - } + ac.setMaxColour(acg.getMaxColour().getRGB()); + ac.setMinColour(acg.getMinColour().getRGB()); + view.setAnnotationColours(ac); + view.setBgColour("AnnotationColourGradient"); + } + else + { + view.setBgColour(ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); + } - if (Desktop.instance != null) - Desktop.instance.stopLoading(); + ColourSchemeI cs = av.getGlobalColourScheme(); - for (int i = 0; i < gatherToThisFrame.size(); i++) + if (cs != null) + { + if (cs.conservationApplied()) + { + view.setConsThreshold(cs.getConservationInc()); + if (cs instanceof jalview.schemes.UserColourScheme) { - Desktop.instance.gatherViews( - (AlignFrame) gatherToThisFrame.elementAt(i)); + view.setBgColour(SetUserColourScheme(cs, userColours, jms)); } + } - return af; + if (cs instanceof ResidueColourScheme) + { + view.setPidThreshold(cs.getThreshold()); + } } - String loadPDBFile(String file, String pdbId) + 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); + + if (av.featuresDisplayed != null) { - System.out.println(file +" "+pdbId); - try - { - JarInputStream jin = null; + jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - if (file.startsWith("http://")) - { - jin = new JarInputStream(new URL(file).openStream()); - } - else + 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) { - jin = new JarInputStream(new FileInputStream(file)); + setting.setOrder(rorder); } + fs.addSetting(setting); + settingsAdded.addElement(renderOrder[ro]); + } - JarEntry entry = null; - do + // 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)) { - entry = jin.getNextJarEntry(); + continue; } - 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; + Setting setting = new Setting(); + setting.setType(key); + setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + .getColour(key).getRGB()); - while ( (data = in.readLine()) != null) + setting.setDisplay(false); + float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( + key); + if (rorder > -1) { - out.println(data); + setting.setOrder(rorder); } - out.close(); - return outFile.getAbsolutePath(); - + fs.addSetting(setting); + settingsAdded.addElement(key); } - catch (Exception ex) + en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys(); + Vector groupsAdded = new Vector(); + while (en.hasMoreElements()) { - ex.printStackTrace(); + 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); - return null; } - - AlignFrame LoadFromObject(JalviewModel object, - String file, - boolean loadTrees ) + if (av.hasHiddenColumns) { - SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); - Sequence[] vamsasSeq = vamsasSet.getSequence(); + 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); + } + } - JalviewModelSequence jms = object.getJalviewModelSequence(); + jms.addViewport(view); - Viewport view = jms.getViewport(0); + object.setJalviewModelSequence(jms); + object.getVamsasModel().addSequenceSet(vamsasSet); - ////////////////////////////////// - //LOAD SEQUENCES + 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; + } - Vector hiddenSeqs = null; - jalview.datamodel.Sequence jseq; + /** + * 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; - ArrayList tmpseqs = new ArrayList(); + /** + * 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; + } - boolean multipleView = false; + /** + * 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; + } - JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); - for (int i = 0; i < JSEQ.length; i++) + /** + * 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()) { - String seqId = JSEQ[i].getId() + ""; + 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(); - if (seqRefIds.get(seqId) != null) + 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()) { - tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId)); - multipleView = true; + // chaining dbref rather than a handshaking one + jmpid = seqHash(ps = jmp.getTo()); } 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 ); + jmpid = seqHash(ps = parentseq); } - - - - if (JSEQ[i].getHidden()) + mpc.setDseqFor(jmpid); + if (!seqRefIds.containsKey(mpc.getDseqFor())) { - if (hiddenSeqs == null) - hiddenSeqs = new Vector(); + 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; - hiddenSeqs.addElement( - (jalview.datamodel.Sequence) seqRefIds.get(seqId)); - } + 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); } + } - ///SequenceFeatures are added to the DatasetSequence, - // so we must create the dataset before loading features - ///////////////////////////////// + id = "ucs" + userColours.indexOf(ucs); + uc.setId(id); + uc.setUserColourScheme(jbucs); + jms.addUserColours(uc); + } + return id; + } - jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[ - tmpseqs.size()]; + jalview.schemes.UserColourScheme GetUserColourScheme( + JalviewModelSequence jms, String id) + { + UserColours[] uc = jms.getUserColours(); + UserColours colours = null; - tmpseqs.toArray(orderedSeqs) ; + for (int i = 0; i < uc.length; i++) + { + if (uc[i].getId().equals(id)) + { + colours = uc[i]; + break; + } + } - jalview.datamodel.Alignment al = - new jalview.datamodel.Alignment(orderedSeqs); + java.awt.Color[] newColours = new java.awt.Color[24]; - al.setDataset(null); - ///////////////////////////////// + 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); - 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()); + 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; + } - 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())) - { - String tmppdb = loadPDBFile(file, ids[p].getId()); - entry.setFile(tmppdb); - pdbloaded.put(ids[p].getId(), tmppdb); - } - else - entry.setFile(pdbloaded.get(ids[p].getId()).toString()); - } + /** + * contains last error message (if any) encountered by XML loader. + */ + String errorMessage = null; - 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); - } + /** + * 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; - ///////////////////////////////// - ////////////////////////////////// - //LOAD ANNOTATIONS - boolean hideQuality = true, - hideConservation = true, - hideConsensus = true; + do + { + jin = jprovider.getJarInputStream(); + for (int i = 0; i < entryCount; i++) + { + jarentry = jin.getNextJarEntry(); + } - if (vamsasSet.getAnnotationCount()>0) + if (jarentry != null && jarentry.getName().endsWith(".xml")) { - Annotation[] an = vamsasSet.getAnnotation(); + InputStreamReader in = new InputStreamReader(jin, "UTF-8"); + JalviewModel object = new JalviewModel(); - for (int i = 0; i < an.length; i++) + 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) { - 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 = new jalview.datamodel.Annotation[al.getWidth()]; + 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(); - for (int aa = 0; aa < ae.length && aa 0) + try { - JGroup[] groups = jms.getJGroup(); + out.flush(); + } catch (Exception foo) + { + } + ; + out.close(); - for (int i = 0; i < groups.length; i++) - { - ColourSchemeI cs = null; + 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(); + } - 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); - } + return null; + } - Vector seqs = new Vector(); + /** + * 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(); - 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); + JalviewModelSequence jms = object.getJalviewModelSequence(); - if (ts != null) - seqs.addElement(ts); - } + Viewport view = jms.getViewport(0); + // //////////////////////////////// + // LOAD SEQUENCES - if(seqs.size()<1) - continue; + Vector hiddenSeqs = null; + jalview.datamodel.Sequence jseq; - 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()); + ArrayList tmpseqs = new ArrayList(); - sg.setOutlineColour(new java.awt.Color( - groups[i].getOutlineColour())); + boolean multipleView = false; - sg.textColour = new java.awt.Color(groups[i].getTextCol1()); - sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); - sg.thresholdTextColour = groups[i].getTextColThreshold(); + 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 (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 (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++; + } - al.addGroup(sg); - } + if (JSEQ[i].getHidden()) + { + if (hiddenSeqs == null) + { + hiddenSeqs = new Vector(); } + hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds + .get(seqId)); + } - ///////////////////////////////// - // LOAD VIEWPORT + } - AlignFrame af = new AlignFrame(al, - view.getWidth(), - view.getHeight() ); + // / + // Create the alignment object from the sequence set + // /////////////////////////////// + jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs + .size()]; - af.setFileName(file, "Jalview"); + tmpseqs.toArray(orderedSeqs); - for (int i = 0; i < JSEQ.length; i++) - { - af.viewport.setSequenceColour( - af.viewport.alignment.getSequenceAt(i), - new java.awt.Color( - JSEQ[i].getColour())); - } + jalview.datamodel.Alignment al = new jalview.datamodel.Alignment( + orderedSeqs); - //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; + // / Add the alignment properties + for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) + { + SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); + al.setProperty(ssp.getKey(), ssp.getValue()); + } - af.viewport.gatherViewsHere = view.getGatheredViews(); + // / + // 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); + } + // /////////////////////////////// - if (view.getSequenceSetId() != null) + 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) { - jalview.gui.AlignViewport av = - (jalview.gui.AlignViewport) - viewportsAdded.get(uniqueSeqSetId); - - af.viewport.sequenceSetID = uniqueSeqSetId; - if(av!=null) + 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()); - af.viewport.historyList = av.historyList; - af.viewport.redoList = av.redoList; - } - else - { - viewportsAdded.put(uniqueSeqSetId, af.viewport); - } + 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()); + } + + } - PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); + al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + } + } + if (vamsasSeq[i].getDBRefCount() > 0) + { + addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); } - if(hiddenSeqs!=null) + if (JSEQ[i].getPdbidsCount() > 0) { - for(int s=0; s