X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b28ed0e3d9d20bdd348ad79210f1cd5cc5681105;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=e6191deb0f3e5f9a26791ab7169c448f7de2e7ce;hpb=24caafeb32f8531894aeead29c1932a57348c1d9;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index e6191de..b28ed0e 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,1679 +1,3723 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; - -import jalview.schemes.*; - -import jalview.gui.*; - +import java.awt.Rectangle; import java.io.*; - +import java.lang.reflect.InvocationTargetException; import java.net.*; - import java.util.*; - +import java.util.Map.Entry; import java.util.jar.*; import javax.swing.*; import org.exolab.castor.xml.*; +import uk.ac.vamsas.objects.utils.MapList; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.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 { + /** + * create/return unique hash string for sq + * + * @param sq + * @return new or existing unique string for sq + */ + String seqHash(SequenceI sq) + { + if (seqsToIds == null) + { + initSeqRefs(); + } + if (seqsToIds.containsKey(sq)) + { + return (String) seqsToIds.get(sq); + } + else + { + // create sequential key + String key = "sq" + (seqsToIds.size() + 1); + key = makeHashCode(sq, key); // check we don't have an external reference + // for it already. + seqsToIds.put(sq, key); + return key; + } + } + + void clearSeqRefs() + { + if (_cleartables) + { + if (seqRefIds != null) + { + seqRefIds.clear(); + } + if (seqsToIds != null) + { + seqsToIds.clear(); + } + // seqRefIds = null; + // seqsToIds = null; + } + else + { + // do nothing + warn("clearSeqRefs called when _cleartables was not set. Doing nothing."); + // seqRefIds = new Hashtable(); + // seqsToIds = new IdentityHashMap(); + } + } + + void initSeqRefs() + { + if (seqsToIds == null) + { + seqsToIds = new IdentityHashMap(); + } + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + } - Hashtable seqRefIds; + /** + * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps + * of sequence objects are created. + */ + java.util.IdentityHashMap seqsToIds = null; /** - * This maintains a list of viewports, the key being the - * seqSetId. Important to set historyItem and redoList - * for multiple views + * jalview XML Sequence ID to jalview sequence object reference (both dataset + * and alignment sequences. Populated as XML reps of sequence objects are + * created.) */ - Hashtable viewportsAdded; + java.util.Hashtable seqRefIds = null; // key->SequenceI resolution - String uniqueSetSuffix = ""; + Vector frefedSequence = null; + boolean raiseGUI = true; // whether errors are raised in dialog boxes or not - // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE - public void SaveState(File statefile) - { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + public Jalview2XML() + { + } - if (frames == null) + public Jalview2XML(boolean raiseGUI) + { + this.raiseGUI = raiseGUI; + } + + public void resolveFrefedSequences() + { + if (frefedSequence.size() > 0) + { + int r = 0, rSize = frefedSequence.size(); + while (r < rSize) + { + Object[] ref = (Object[]) frefedSequence.elementAt(r); + if (ref != null) { - return; + String sref = (String) ref[0]; + if (seqRefIds.containsKey(sref)) + { + if (ref[1] instanceof jalview.datamodel.Mapping) + { + SequenceI seq = (SequenceI) seqRefIds.get(sref); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + ((jalview.datamodel.Mapping) ref[1]).setTo(seq); + } + else + { + if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame) + { + SequenceI seq = (SequenceI) seqRefIds.get(sref); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + if (ref[2] != null + && ref[2] instanceof jalview.datamodel.Mapping) + { + jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2]; + ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap( + seq, mp.getTo(), mp.getMap()); + } + else + { + System.err + .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving " + + ref[2].getClass() + " type objects."); + } + } + else + { + System.err + .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " + + ref[1].getClass() + " type objects."); + } + } + frefedSequence.remove(r); + rSize--; + } + else + { + System.err + .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string " + + ref[0] + + " with objecttype " + + ref[1].getClass()); + r++; + } } - - try + else { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); + // empty reference + frefedSequence.remove(r); + rSize--; + } + } + } + } - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); + /** + * This maintains a list of viewports, the key being the seqSetId. Important + * to set historyItem and redoList for multiple views + */ + Hashtable viewportsAdded; - Vector shortNames = new Vector(); + Hashtable annotationIds = new Hashtable(); - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) - { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; + String uniqueSetSuffix = ""; - String shortName = af.getTitle(); + /** + * List of pdbfiles added to Jar + */ + Vector pdbfiles = null; - if (shortName.indexOf(File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - File.separatorChar) + 1); - } + // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE + public void SaveState(File statefile) + { + try + { + FileOutputStream fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); + SaveState(jout); - int count = 1; + } catch (Exception e) + { + // TODO: inform user of the problem - they need to know if their data was + // not saved ! + if (errorMessage == null) + { + errorMessage = "Couldn't write Jalview Archive to output file '" + + statefile + "' - See console error log for details"; + } + else + { + errorMessage += "(output file was '" + statefile + "')"; + } + e.printStackTrace(); + } + reportErrors(); + } - while (shortNames.contains(shortName)) - { - if (shortName.endsWith("_" + (count - 1))) - { - shortName = shortName.substring(0, - shortName.lastIndexOf("_")); - } - - shortName = shortName.concat("_" + count); - count++; - } + /** + * Writes a jalview project archive to the given Jar output stream. + * + * @param jout + */ + public void SaveState(JarOutputStream jout) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - shortNames.addElement(shortName); + if (frames == null) + { + return; + } - if (!shortName.endsWith(".xml")) - { - shortName = shortName + ".xml"; - } + try + { - int ap, apSize= af.alignPanels.size(); - for (ap = 0; ap < apSize; ap++) - { - AlignmentPanel apanel = (AlignmentPanel) af.alignPanels. - elementAt(ap); + // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS + // ////////////////////////////////////////////////// + // NOTE ALSO new PrintWriter must be used for each new JarEntry + PrintWriter out = null; - SaveState(apanel, - apSize == 1 ? shortName : ap+shortName, - jout, out); - } - } - } + Vector shortNames = new Vector(); - out.close(); - jout.close(); - } - catch (Exception ex) + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) { - ex.printStackTrace(); - } - } + AlignFrame af = (AlignFrame) frames[i]; + // skip ? + if (skipList != null + && skipList.containsKey(af.getViewport() + .getSequenceSetId())) + { + continue; + } - // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public void 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) + { + shortName = shortName.substring(shortName + .lastIndexOf(File.separatorChar) + 1); + } + + int count = 1; + + while (shortNames.contains(shortName)) { - AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap); + if (shortName.endsWith("_" + (count - 1))) + { + shortName = shortName + .substring(0, shortName.lastIndexOf("_")); + } - SaveState(apanel, - apSize==1?fileName:fileName+ap, - jout, out); + shortName = shortName.concat("_" + count); + count++; } - out.close(); - jout.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); + shortNames.addElement(shortName); + + if (!shortName.endsWith(".xml")) + { + shortName = shortName + ".xml"; + } + + int ap, apSize = af.alignPanels.size(); + for (ap = 0; ap < apSize; ap++) + { + AlignmentPanel apanel = (AlignmentPanel) af.alignPanels + .elementAt(ap); + String fileName = apSize == 1 ? shortName : ap + shortName; + if (!fileName.endsWith(".xml")) + { + fileName = fileName + ".xml"; + } + + SaveState(apanel, fileName, jout); + } } + } + try + { + jout.flush(); + } catch (Exception foo) + { + } + ; + jout.close(); + } catch (Exception ex) + { + // TODO: inform user of the problem - they need to know if their data was + // not saved ! + if (errorMessage == null) + { + errorMessage = "Couldn't write Jalview Archive - see error output for details"; + } + ex.printStackTrace(); } + } - /** - * 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) + // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW + public boolean SaveAlignment(AlignFrame af, String jarFile, + String fileName) + { + try { - if (seqRefIds == null) - seqRefIds = new Hashtable(); + 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); + } - Vector userColours = new Vector(); + 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; + } + } - AlignViewport av = ap.av; + /** + * create a JalviewModel from an algnment view and marshall it to a + * JarOutputStream + * + * @param ap + * panel to create jalview model for + * @param fileName + * name of alignment panel written to output stream + * @param jout + * jar output stream + * @param out + * jar entry name + */ + public JalviewModel SaveState(AlignmentPanel ap, String fileName, + JarOutputStream jout) + { + initSeqRefs(); + Vector jmolViewIds = new Vector(); // + Vector userColours = new Vector(); - JalviewModel object = new JalviewModel(); - object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); + AlignViewport av = ap.av; - object.setCreationDate(new java.util.Date(System.currentTimeMillis())); - object.setVersion(jalview.bin.Cache.getProperty("VERSION")); + JalviewModel object = new JalviewModel(); + object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); - jalview.datamodel.AlignmentI jal = av.alignment; + object.setCreationDate(new java.util.Date(System.currentTimeMillis())); + object.setVersion(jalview.bin.Cache.getProperty("VERSION")); - if(av.hasHiddenRows) - { - jal = jal.getHiddenSequences().getFullAlignment(); - } + jalview.datamodel.AlignmentI jal = av.alignment; - SequenceSet vamsasSet = new SequenceSet(); - Sequence vamsasSeq; - JalviewModelSequence jms = new JalviewModelSequence(); + if (av.hasHiddenRows) + { + jal = jal.getHiddenSequences().getFullAlignment(); + } - vamsasSet.setGapChar(jal.getGapCharacter() + ""); + SequenceSet vamsasSet = new SequenceSet(); + Sequence vamsasSeq; + JalviewModelSequence jms = new JalviewModelSequence(); - JSeq jseq; - Vector pdbfiles = null; + vamsasSet.setGapChar(jal.getGapCharacter() + ""); - //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 (jal.getDataset() != null) + { + // dataset id is the dataset's hashcode + vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset())); + } + if (jal.getProperties() != null) + { + Enumeration en = jal.getProperties().keys(); + while (en.hasMoreElements()) + { + String key = en.nextElement().toString(); + SequenceSetProperties ssp = new SequenceSetProperties(); + ssp.setKey(key); + ssp.setValue(jal.getProperties().get(key).toString()); + vamsasSet.addSequenceSetProperties(ssp); + } + } - if(seqRefIds.get(id+"")!=null) - { + JSeq jseq; - } - else - { - vamsasSeq = new Sequence(); - vamsasSeq.setId(id + ""); - vamsasSeq.setName(jds.getName()); - vamsasSeq.setSequence(jds.getSequence()); - vamsasSeq.setDescription(jds.getDescription()); + // SAVE SEQUENCES + String id = ""; + jalview.datamodel.SequenceI jds; + for (int i = 0; i < jal.getHeight(); i++) + { + jds = jal.getSequenceAt(i); + id = seqHash(jds); - if (jds.getDatasetSequence().getDBRef() != null) - { - jalview.datamodel.DBRefEntry[] dbrefs = - jds.getDatasetSequence().getDBRef(); + if (seqRefIds.get(id) != null) + { + // This happens for two reasons: 1. multiple views are being serialised. + // 2. the hashCode has collided with another sequence's code. This DOES + // HAPPEN! (PF00072.15.stk does this) + // JBPNote: Uncomment to debug writing out of files that do not read + // back in due to ArrayOutOfBoundExceptions. + // System.err.println("vamsasSeq backref: "+id+""); + // System.err.println(jds.getName()+" + // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); + // System.err.println("Hashcode: "+seqHash(jds)); + // SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); + // System.err.println(rsq.getName()+" + // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); + // System.err.println("Hashcode: "+seqHash(rsq)); + } + else + { + vamsasSeq = createVamsasSequence(id, jds); + vamsasSet.addSequence(vamsasSeq); + seqRefIds.put(id, jds); + } - 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); - } - } + jseq = new JSeq(); + jseq.setStart(jds.getStart()); + jseq.setEnd(jds.getEnd()); + jseq.setColour(av.getSequenceColour(jds).getRGB()); - vamsasSet.addSequence(vamsasSeq); - seqRefIds.put(id+"", jal.getSequenceAt(i)); - } + jseq.setId(id); // jseq id should be a string not a number - jseq = new JSeq(); - jseq.setStart(jds.getStart()); - jseq.setEnd(jds.getEnd()); - jseq.setColour( av.getSequenceColour(jds).getRGB()); + if (av.hasHiddenRows) + { + jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); - jseq.setId(id); + 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); - if (av.hasHiddenRows) + for (int h = 0; h < reps.length; h++) + { + if (reps[h] != jal.getSequenceAt(i)) { - jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); - - if(jal.getSequenceAt(i).getHiddenSequences()!=null) - { - jalview.datamodel.SequenceI [] reps = - jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal); + jseq.addHiddenSequences(jal.findIndex(reps[h])); + } + } + } + } - for(int h=0; h -1; f--) + { + if (frames[f] instanceof AppJmol) { - jalview.datamodel.SequenceFeature[] sf - = jds.getDatasetSequence().getSequenceFeatures(); - int index = 0; - while(index < sf.length) + // TODO: revise schema to allow many:one PDB id binding to viewer + jmol = (AppJmol) frames[f]; + for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++) { - 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) + if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId()) + && !(entry.getId().length() > 4 && entry + .getId() + .toLowerCase() + .startsWith( + jmol.jmb.pdbentry[peid].getId() + .toLowerCase()))) + continue; + if (matchedFile == null) { - for(int l=0; l -1) { - pdbfiles.addElement(entry.getId()); - try + 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()); + if (!jmolViewIds.contains(state.getViewId())) { - File file = new File(entry.getFile()); - if(file.exists()) - { - 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(); - } + // Make sure we only store a Jmol state once in each XML + // document. + jmolViewIds.addElement(state.getViewId()); + state.setContent(statestring.replaceAll("\n", "")); } - catch (Exception ex) + else { - ex.printStackTrace(); + state.setContent("# duplicate state"); } + pdb.addStructureState(state); } } - - - 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) + if (matchedFile != null || entry.getFile() != null) { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + if (entry.getFile() != null) + { + // use entry's file + matchedFile = entry.getFile(); + } + pdb.setFile(matchedFile); // entry.getFile()); + if (pdbfiles == null) + { + pdbfiles = new Vector(); + } - for (int t = 0; t < frames.length; t++) + if (!pdbfiles.contains(entry.getId())) { - if (frames[t] instanceof TreePanel) + pdbfiles.addElement(entry.getId()); + try { - TreePanel tp = (TreePanel) frames[t]; - - if (tp.treeCanvas.av.alignment == jal) + File file = new File(matchedFile); + if (file.exists() && jout != null) { - 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); + byte[] data = new byte[(int) file.length()]; + jout.putNextEntry(new JarEntry(entry.getId())); + DataInputStream dis = new DataInputStream( + new FileInputStream(file)); + dis.readFully(data); + + DataOutputStream dout = new DataOutputStream(jout); + dout.write(data, 0, data.length); + dout.flush(); + jout.closeEntry(); } + } catch (Exception ex) + { + ex.printStackTrace(); } + } } - } - - //SAVE ANNOTATIONS - if (jal.getAlignmentAnnotation() != null) - { - jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); - for (int i = 0; i < aa.length; i++) + if (entry.getProperty() != null) + { + PdbentryItem item = new PdbentryItem(); + Hashtable properties = entry.getProperty(); + Enumeration en2 = properties.keys(); + while (en2.hasMoreElements()) { - Annotation an = new Annotation(); + Property prop = new Property(); + String key = en2.nextElement().toString(); + prop.setName(key); + prop.setValue(properties.get(key).toString()); + item.addProperty(prop); + } + pdb.addPdbentryItem(item); + } - if (aa[i].label.equals("Quality") || - aa[i].label.equals("Conservation") || - aa[i].label.equals("Consensus")) - { - an.setLabel(aa[i].label); - an.setGraph(true); - vamsasSet.addAnnotation(an); - continue; - } + jseq.addPdbids(pdb); + } + } + jms.addJSeq(jseq); + } - 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); - - 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 + - ""); - - 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 (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); } - - //SAVE GROUPS - if (jal.getGroups() != null) + if (jac[i].getProtMappings() != null + && jac[i].getProtMappings().length > 0) { - 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)); - } + 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(false); 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 + /** + * store forward refs from an annotationRow to any groups + */ + IdentityHashMap groupRefs = new IdentityHashMap(); + 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) + if (aa[i].annotationId != 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); + 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) - { - view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), - userColours, jms)); - } - else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) - { - jalview.schemes.AnnotationColourGradient acg - = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme(); + an.setVisible(aa[i].visible); - 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.setDescription(aa[i].description); - ac.setMaxColour(acg.getMaxColour().getRGB()); - ac.setMinColour(acg.getMinColour().getRGB()); - view.setAnnotationColours(ac); - view.setBgColour("AnnotationColourGradient"); - } - else + 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].groupRef != null) { - if (cs.conservationApplied()) - { - view.setConsThreshold(cs.getConservationInc()); - if (cs instanceof jalview.schemes.UserColourScheme) - view.setBgColour(SetUserColourScheme(cs, userColours, jms)); - } - - if (cs instanceof ResidueColourScheme) + Object groupIdr = groupRefs.get(aa[i].groupRef); + if (groupIdr == null) { - view.setPidThreshold(cs.getThreshold()); + // make a locally unique String + groupRefs.put(aa[i].groupRef, + groupIdr = ("" + System.currentTimeMillis() + + aa[i].groupRef.getName() + groupRefs.size())); } + an.setGroupRef(groupIdr.toString()); } - - 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) + if (aa[i] == av.quality || aa[i] == av.conservation + || aa[i] == av.consensus || aa[i].autoCalculated) { - 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 0) + { + an.setGraph(true); + an.setGraphType(aa[i].graph); + an.setGraphGroup(aa[i].graphGroup); + if (aa[i].getThreshold() != null) { - 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); - - fs.addSetting(setting); - settingsAdded.addElement(key); + 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); } - - jms.setFeatureSettings(fs); - + } + else + { + an.setGraph(false); } - if(av.hasHiddenColumns) + an.setLabel(aa[i].label); + if (aa[i].hasScore()) { - for(int c=0; c 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); - } + // /////////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); - return ucs; + 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); - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - */ - public AlignFrame LoadJalviewAlign(final String file) + if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { - uniqueSetSuffix = System.currentTimeMillis()%100000 +""; - - jalview.gui.AlignFrame af = null; + 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())); + } - seqRefIds = new Hashtable(); - viewportsAdded = new Hashtable(); + ac.setMaxColour(acg.getMaxColour().getRGB()); + ac.setMinColour(acg.getMinColour().getRGB()); + view.setAnnotationColours(ac); + view.setBgColour("AnnotationColourGradient"); + } + else + { + view.setBgColour(ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); + } - Vector gatherToThisFrame= new Vector(); + ColourSchemeI cs = av.getGlobalColourScheme(); - try + if (cs != null) + { + if (cs.conservationApplied()) + { + view.setConsThreshold(cs.getConservationInc()); + if (cs instanceof jalview.schemes.UserColourScheme) { - //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)); - } + view.setBgColour(SetUserColourScheme(cs, userColours, jms)); + } + } - for (int i = 0; i < entryCount; i++) - { - jarentry = jin.getNextJarEntry(); - } + if (cs instanceof ResidueColourScheme) + { + view.setPidThreshold(cs.getThreshold()); + } + } - if (jarentry != null && jarentry.getName().endsWith(".xml")) - { - InputStreamReader in = new InputStreamReader(jin, "UTF-8"); - JalviewModel object = new JalviewModel(); + view.setConservationSelected(av.getConservationSelected()); + view.setPidSelected(av.getAbovePIDThreshold()); + view.setFontName(av.font.getName()); + view.setFontSize(av.font.getSize()); + view.setFontStyle(av.font.getStyle()); + view.setRenderGaps(av.renderGaps); + view.setShowAnnotation(av.getShowAnnotation()); + view.setShowBoxes(av.getShowBoxes()); + view.setShowColourText(av.getColourText()); + view.setShowFullId(av.getShowJVSuffix()); + view.setRightAlignIds(av.rightAlignIds); + view.setShowSequenceFeatures(av.showSequenceFeatures); + view.setShowText(av.getShowText()); + view.setShowUnconserved(av.getShowUnconserved()); + view.setWrapAlignment(av.getWrapAlignment()); + view.setTextCol1(av.textColour.getRGB()); + view.setTextCol2(av.textColour2.getRGB()); + view.setTextColThreshold(av.thresholdTextColour); + view.setShowConsensusHistogram(av.isShowConsensusHistogram()); + view.setShowSequenceLogo(av.isShowSequenceLogo()); + view.setShowGroupConsensus(av.isShowGroupConsensus()); + view.setShowGroupConservation(av.isShowGroupConservation()); + view.setShowNPfeatureTooltip(av.isShowNpFeats()); + view.setShowDbRefTooltip(av.isShowDbRefs()); + view.setFollowHighlight(av.followHighlight); + view.setFollowSelection(av.followSelection); + view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); + if (av.featuresDisplayed != null) + { + jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal( in ); + String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; - 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) + Vector settingsAdded = new Vector(); + Object gstyle = null; + GraduatedColor gcol = null; + for (int ro = 0; ro < renderOrder.length; ro++) + { + gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getFeatureStyle(renderOrder[ro]); + Setting setting = new Setting(); + setting.setType(renderOrder[ro]); + if (gstyle instanceof GraduatedColor) { - 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); - } - }); + gcol = (GraduatedColor) gstyle; + setting.setColour(gcol.getMaxColor().getRGB()); + setting.setMincolour(gcol.getMinColor().getRGB()); + setting.setMin(gcol.getMin()); + setting.setMax(gcol.getMax()); + setting.setColourByLabel(gcol.isColourByLabel()); + setting.setAutoScale(gcol.isAutoScale()); + setting.setThreshold(gcol.getThresh()); + setting.setThreshstate(gcol.getThreshType()); } - catch (Exception ex) + else { - //Is Version 1 Jar file? - af = new Jalview2XML_V1().LoadJalviewAlign(file); - - if(af!=null) - { - System.out.println("Successfully loaded archive file"); - return af; - } - - 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); - }}); + setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + .getColour(renderOrder[ro]).getRGB()); } - if (Desktop.instance != null) - Desktop.instance.stopLoading(); - - for (int i = 0; i < gatherToThisFrame.size(); i++) + setting.setDisplay(av.featuresDisplayed + .containsKey(renderOrder[ro])); + float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( + renderOrder[ro]); + if (rorder > -1) { - Desktop.instance.gatherViews( - (AlignFrame) gatherToThisFrame.elementAt(i)); + setting.setOrder(rorder); } + fs.addSetting(setting); + settingsAdded.addElement(renderOrder[ro]); + } - return af; - } - - String loadPDBFile(String file, String pdbId) - { - try + // Make sure we save none displayed feature settings + Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours + .keys(); + while (en.hasMoreElements()) { - JarInputStream jin = null; - - if (file.startsWith("http://")) + String key = en.nextElement().toString(); + if (settingsAdded.contains(key)) { - jin = new JarInputStream(new URL(file).openStream()); + continue; } - else + + 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) { - jin = new JarInputStream(new FileInputStream(file)); + setting.setOrder(rorder); } - - JarEntry entry = null; - do + 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)) { - entry = jin.getNextJarEntry(); + continue; } - while (!entry.getName().equals(pdbId)); + 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); - 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) + if (av.hasHiddenColumns) + { + if (av.getColumnSelection() == null + || av.getColumnSelection().getHiddenColumns() == null) + { + warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); + } + else + { + for (int c = 0; c < av.getColumnSelection().getHiddenColumns() + .size(); c++) { - out.println(data); + int[] region = (int[]) av.getColumnSelection().getHiddenColumns() + .elementAt(c); + HiddenColumns hc = new HiddenColumns(); + hc.setStart(region[0]); + hc.setEnd(region[1]); + view.addHiddenColumns(hc); } - out.close(); - return outFile.getAbsolutePath(); - } - catch (Exception ex) + } + + jms.addViewport(view); + + object.setJalviewModelSequence(jms); + object.getVamsasModel().addSequenceSet(vamsasSet); + + if (jout != null && fileName != null) + { + // We may not want to write the object to disk, + // eg we can copy the alignViewport to a new view object + // using save and then load + try + { + JarEntry entry = new JarEntry(fileName); + jout.putNextEntry(entry); + PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout, + "UTF-8")); + org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller( + pout); + marshaller.marshal(object); + pout.flush(); + jout.closeEntry(); + } catch (Exception ex) { + // TODO: raise error in GUI if marshalling failed. ex.printStackTrace(); } - - return null; } + return object; + } + /** + * External mapping between jalview objects and objects yielding a valid and + * unique object ID string. This is null for normal Jalview project IO, but + * non-null when a jalview project is being read or written as part of a + * vamsas session. + */ + IdentityHashMap jv2vobj = null; - AlignFrame LoadFromObject(JalviewModel object, - String file, - boolean loadTrees ) + /** + * 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) { - 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(); + 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(); - - - hiddenSeqs.addElement( - (jalview.datamodel.Sequence) seqRefIds.get(seqId)); + jalview.bin.Cache.log.debug("creatign new DseqFor ID"); + seqRefIds.put(mpc.getDseqFor(), ps); + } + else + { + jalview.bin.Cache.log.debug("reusing DseqFor ID"); } + } + mp.setMappingChoice(mpc); + } + } + return mp; + } + + String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, + Vector userColours, JalviewModelSequence jms) + { + String id = null; + jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; + boolean newucs = false; + if (!userColours.contains(ucs)) + { + userColours.add(ucs); + newucs = true; + } + id = "ucs" + userColours.indexOf(ucs); + if (newucs) + { + // actually create the scheme's entry in the XML model + java.awt.Color[] colours = ucs.getColours(); + jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); + jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); + for (int i = 0; i < colours.length; i++) + { + jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); + col.setName(ResidueProperties.aa[i]); + col.setRGB(jalview.util.Format.getHexString(colours[i])); + jbucs.addColour(col); + } + if (ucs.getLowerCaseColours() != null) + { + colours = ucs.getLowerCaseColours(); + for (int i = 0; i < colours.length; i++) + { + jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); + col.setName(ResidueProperties.aa[i].toLowerCase()); + col.setRGB(jalview.util.Format.getHexString(colours[i])); + jbucs.addColour(col); } + } - ///SequenceFeatures are added to the DatasetSequence, - // so we must create the dataset before loading features - ///////////////////////////////// + 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; - ///////////////////////////////// - ////////////////////////////////// - //LOAD ANNOTATIONS - boolean hideQuality = true, - hideConservation = true, - hideConsensus = true; + 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() + { - if (vamsasSet.getAnnotationCount()>0) + public JarInputStream getJarInputStream() throws IOException + { + if (_url != null) { - 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; - } - - 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().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())) - ); + return new JarInputStream(_url.openStream()); + } + else + { + return new JarInputStream(new FileInputStream(file)); + } + } - } + public String getFilename() + { + return file; + } + }; + } - } - else - { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot); - } + /** + * 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(); + } - if(an[i].getSequenceRef()!=null) - { - jaa.createSequenceMapping( - al.findName(an[i].getSequenceRef()), 1, true - ); - al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); - } + jalview.gui.AlignFrame af = null; + Hashtable gatherToThisFrame = new Hashtable(); + final String file = jprovider.getFilename(); + try + { + JarInputStream jin = null; + JarEntry jarentry = null; + int entryCount = 1; - al.addAnnotation(jaa); - } + do + { + jin = jprovider.getJarInputStream(); + for (int i = 0; i < entryCount; i++) + { + jarentry = jin.getNextJarEntry(); } - ///////////////////////// - //LOAD GROUPS - if (jms.getJGroupCount() > 0) + if (jarentry != null && jarentry.getName().endsWith(".xml")) { - JGroup[] groups = jms.getJGroup(); + InputStreamReader in = new InputStreamReader(jin, "UTF-8"); + JalviewModel object = new JalviewModel(); - for (int i = 0; i < groups.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) { - 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)+""; - seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId)); - } - - 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(false), 0, - sg.getWidth() - 1); - c.calculate(); - c.verdict(false, 25); - sg.cs.setConservation(c); - } - - al.addGroup(sg); + gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); } + } + entryCount++; } - - - ///////////////////////////////// - // LOAD VIEWPORT - - AlignFrame af = new AlignFrame(al, - view.getWidth(), - view.getHeight() ); - - af.setFileName(file, "Jalview"); - - for (int i = 0; i < JSEQ.length; i++) + else if (jarentry != null) { - af.viewport.setSequenceColour( - af.viewport.alignment.getSequenceAt(i), - new java.awt.Color( - JSEQ[i].getColour())); + // Some other file here. + entryCount++; } - - //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) + } 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 { - jalview.gui.AlignViewport av = - (jalview.gui.AlignViewport) - viewportsAdded.get(uniqueSeqSetId); + 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(); - af.viewport.sequenceSetID = uniqueSeqSetId; - if(av!=null) - { + System.err.println("Exception whilst loading jalview XML file : " + + ex + "\n"); + } catch (OutOfMemoryError e) + { + // Don't use the OOM Window here + errorMessage = "Out of memory loading jalview XML file"; + System.err.println("Out of memory whilst loading jalview XML file"); + e.printStackTrace(); + } - af.viewport.historyList = av.historyList; - af.viewport.redoList = av.redoList; - } - else - { - viewportsAdded.put(uniqueSeqSetId, af.viewport); - } + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } - PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); - } - if(hiddenSeqs!=null) + Enumeration en = gatherToThisFrame.elements(); + while (en.hasMoreElements()) + { + Desktop.instance.gatherViews((AlignFrame) en.nextElement()); + } + if (errorMessage != null) + { + reportErrors(); + } + return af; + } + + /** + * check errorMessage for a valid error message and raise an error box in the + * GUI or write the current errorMessage to stderr and then clear the error + * state. + */ + protected void reportErrors() + { + reportErrors(false); + } + + protected void reportErrors(final boolean saving) + { + if (errorMessage != null) + { + final String finalErrorMessage = errorMessage; + if (raiseGUI) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() { - for(int s=0; s 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()); } + } - else + + al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + } + } + if (vamsasSeq[i].getDBRefCount() > 0) + { + addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); + } + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); + entry.setId(ids[p].getId()); + entry.setType(ids[p].getType()); + if (ids[p].getFile() != null) { - cs = ColourSchemeProperty.getColour(al, view.getBgColour()); + if (!pdbloaded.containsKey(ids[p].getFile())) + { + entry.setFile(loadPDBFile(jprovider, ids[p].getId())); + } + else + { + entry.setFile(pdbloaded.get(ids[p].getId()).toString()); + } } - if(cs!=null) + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + } + } + } // end !multipleview + + // /////////////////////////////// + // LOAD SEQUENCE MAPPINGS + + if (vamsasSet.getAlcodonFrameCount() > 0) + { + // TODO Potentially this should only be done once for all views of an + // alignment + AlcodonFrame[] alc = vamsasSet.getAlcodonFrame(); + for (int i = 0; i < alc.length; i++) + { + jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame( + alc[i].getAlcodonCount()); + if (alc[i].getAlcodonCount() > 0) + { + Alcodon[] alcods = alc[i].getAlcodon(); + for (int p = 0; p < cf.codons.length; p++) + { + if (alcods[p].hasPos1() && alcods[p].hasPos2() + && alcods[p].hasPos3()) + { + // translated codons require three valid positions + cf.codons[p] = new int[3]; + cf.codons[p][0] = (int) alcods[p].getPos1(); + cf.codons[p][1] = (int) alcods[p].getPos2(); + cf.codons[p][2] = (int) alcods[p].getPos3(); + } + else + { + cf.codons[p] = null; + } + } + } + if (alc[i].getAlcodMapCount() > 0) + { + AlcodMap[] maps = alc[i].getAlcodMap(); + for (int m = 0; m < maps.length; m++) + { + SequenceI dnaseq = (SequenceI) seqRefIds + .get(maps[m].getDnasq()); + // Load Mapping + jalview.datamodel.Mapping mapping = null; + // attach to dna sequence reference. + if (maps[m].getMapping() != null) + { + mapping = addMapping(maps[m].getMapping()); + } + if (dnaseq != null) + { + cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); + } + else { - cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.hconsensus); + // defer to later + frefedSequence.add(new Object[] + { maps[m].getDnasq(), cf, mapping }); } + } } + al.addCodonFrame(cf); + } + + } + // //////////////////////////////// + // LOAD ANNOTATIONS + boolean hideQuality = true, hideConservation = true, hideConsensus = true; + /** + * store any annotations which forward reference a group's ID + */ + Hashtable groupAnnotRefs = new Hashtable(); - af.viewport.setGlobalColourScheme(cs); - af.viewport.setColourAppliesToAllGroups(false); + if (vamsasSet.getAnnotationCount() > 0) + { + Annotation[] an = vamsasSet.getAnnotation(); - if (view.getConservationSelected() && cs!=null) + for (int i = 0; i < an.length; i++) + { + // set visibility for automatic annotation for this view + if (an[i].getLabel().equals("Quality")) { - cs.setConservationInc(view.getConsThreshold()); + hideQuality = false; + continue; } + else if (an[i].getLabel().equals("Conservation")) + { + hideConservation = false; + continue; + } + else if (an[i].getLabel().equals("Consensus")) + { + hideConsensus = false; + continue; + } + // set visiblity for other annotation in this view + if (an[i].getId() != null + && annotationIds.containsKey(an[i].getId())) + { + jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds + .get(an[i].getId()); + // in principle Visible should always be true for annotation displayed + // in multiple views + if (an[i].hasVisible()) + jda.visible = an[i].getVisible(); - af.changeColour(cs); + al.addAnnotation(jda); - af.viewport.setColourAppliesToAllGroups(true); + continue; + } + // Construct new annotation from model. + AnnotationElement[] ae = an[i].getAnnotationElement(); + jalview.datamodel.Annotation[] anot = null; + if (!an[i].getScoreOnly()) + { + anot = new jalview.datamodel.Annotation[al.getWidth()]; + for (int aa = 0; aa < ae.length && aa < anot.length; aa++) + { + if (ae[aa].getPosition() >= anot.length) + continue; - if (view.getShowSequenceFeatures()) - { - af.viewport.showSequenceFeatures = true; + anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( + + ae[aa].getDisplayCharacter(), ae[aa].getDescription(), + (ae[aa].getSecondaryStructure() == null || ae[aa] + .getSecondaryStructure().length() == 0) ? ' ' + : ae[aa].getSecondaryStructure().charAt(0), + ae[aa].getValue() + + ); + // JBPNote: Consider verifying dataflow for IO of secondary + // structure annotation read from Stockholm files + // this was added to try to ensure that + // if (anot[ae[aa].getPosition()].secondaryStructure>' ') + // { + // anot[ae[aa].getPosition()].displayCharacter = ""; + // } + anot[ae[aa].getPosition()].colour = new java.awt.Color( + ae[aa].getColour()); + } } + jalview.datamodel.AlignmentAnnotation jaa = null; - if(jms.getFeatureSettings()!=null) + if (an[i].getGraph()) { - af.viewport.featuresDisplayed = new Hashtable(); - String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()]; - for(int fs=0; fs 0) + else { - for (int c = 0; c < view.getHiddenColumnsCount(); c++) + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot); + } + // register new annotation + if (an[i].getId() != null) + { + annotationIds.put(an[i].getId(), jaa); + jaa.annotationId = an[i].getId(); + } + // recover sequence association + if (an[i].getSequenceRef() != null) + { + if (al.findName(an[i].getSequenceRef()) != null) { - af.viewport.hideColumns( - view.getHiddenColumns(c).getStart(), - view.getHiddenColumns(c).getEnd() //+1 - ); + jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()), + 1, true); + al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); } } + // and make a note of any group association + if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0) + { + groupAnnotRefs.put(an[i].getGroupRef(), jaa); + } + + if (an[i].hasScore()) + { + jaa.setScore(an[i].getScore()); + } + if (an[i].hasVisible()) + jaa.visible = an[i].getVisible(); - af.setMenusFromViewport(af.viewport); + if (an[i].hasCentreColLabels()) + jaa.centreColLabels = an[i].getCentreColLabels(); + + if (an[i].hasScaleColLabels()) + { + jaa.scaleColLabel = an[i].getScaleColLabels(); + } + if (an[i].hasAutoCalculated() && an[i].isAutoCalculated()) + { + // newer files have an 'autoCalculated' flag and store calculation + // state in viewport properties + jaa.autoCalculated = true; // means annotation will be marked for + // update at end of load. + } + al.addAnnotation(jaa); + } + } + // /////////////////////// + // LOAD GROUPS + // Create alignment markup and styles for this view + if (jms.getJGroupCount() > 0) + { + JGroup[] groups = jms.getJGroup(); - Desktop.addInternalFrame(af, view.getTitle(), - view.getWidth(), view.getHeight()); + for (int i = 0; i < groups.length; i++) + { + ColourSchemeI cs = null; - //LOAD TREES - /////////////////////////////////////// - if (loadTrees && jms.getTreeCount() > 0) + if (groups[i].getColour() != null) { - try - { - for (int t = 0; t < jms.getTreeCount(); t++) - { + if (groups[i].getColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, groups[i].getColour()); + } + else + { + cs = ColourSchemeProperty.getColour(al, groups[i].getColour()); + } - Tree tree = jms.getTree(t); + if (cs != null) + { + cs.setThreshold(groups[i].getPidThreshold(), true); + } + } - TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile( - tree.getNewick()), tree.getTitle(), - tree.getWidth(), tree.getHeight(), - tree.getXpos(), tree.getYpos()); + Vector seqs = new Vector(); - tp.fitToWindow.setState(tree.getFitToWindow()); - tp.fitToWindow_actionPerformed(null); + 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(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())); + if (ts != null) + { + seqs.addElement(ts); + } + } - tp.showPlaceholders(tree.getMarkUnlinked()); - tp.showBootstrap(tree.getShowBootstrap()); - tp.showDistances(tree.getShowDistances()); + if (seqs.size() < 1) + { + continue; + } - tp.treeCanvas.threshold = tree.getThreshold(); + 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()); - if (tree.getCurrentTree()) - af.viewport.setCurrentTree(tp.getTree()); - } + sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour())); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + sg.textColour = new java.awt.Color(groups[i].getTextCol1()); + sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); + sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] + .isShowUnconserved() : false); + sg.thresholdTextColour = groups[i].getTextColThreshold(); + if (groups[i].hasShowConsensusHistogram()) + { + sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); + } + ; + if (groups[i].hasShowSequenceLogo()) + { + sg.setshowSequenceLogo(groups[i].isShowSequenceLogo()); + } + if (groups[i].hasIgnoreGapsinConsensus()) + { + sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus()); + } + if (groups[i].getConsThreshold() != 0) + { + jalview.analysis.Conservation c = new jalview.analysis.Conservation( + "All", ResidueProperties.propHash, 3, + sg.getSequences(null), 0, sg.getWidth() - 1); + c.calculate(); + c.verdict(false, 25); + sg.cs.setConservation(c); + } + if (groups[i].getId() != null && groupAnnotRefs.size() > 0) + { + // re-instate unique group/annotation row reference + jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs + .get(groups[i].getId()); + if (jaa != null) + { + jaa.groupRef = sg; + } } + al.addGroup(sg); - return af; + } } - public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs ) + // /////////////////////////////// + // LOAD VIEWPORT + + // If we just load in the same jar file again, the sequenceSetId + // will be the same, and we end up with multiple references + // to the same sequenceSet. We must modify this id on load + // so that each load of the file gives a unique id + String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; + String viewId = (view.getId() == null ? null : view.getId() + + uniqueSetSuffix); + AlignFrame af = null; + AlignViewport av = null; + // now check to see if we really need to create a new viewport. + if (multipleView && viewportsAdded.size() == 0) { - jalview.schemabinding.version2.JalviewModel jm - = SaveState(ap, null, null, null); + // We recovered an alignment for which a viewport already exists. + // TODO: fix up any settings necessary for overlaying stored state onto + // state recovered from another document. (may not be necessary). + // we may need a binding from a viewport in memory to one recovered from + // XML. + // and then recover its containing af to allow the settings to be applied. + // TODO: fix for vamsas demo + System.err + .println("About to recover a viewport for existing alignment: Sequence set ID is " + + uniqueSeqSetId); + Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); + if (seqsetobj != null) + { + if (seqsetobj instanceof String) + { + uniqueSeqSetId = (String) seqsetobj; + System.err + .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + + uniqueSeqSetId); + } + else + { + System.err + .println("Warning : Collision between sequence set ID string and existing jalview object mapping."); + } - if (!keepSeqRefs) + } + } + AlignmentPanel ap = null; + boolean isnewview = true; + if (viewId != null) + { + // Check to see if this alignment already has a view id == viewId + jalview.gui.AlignmentPanel views[] = Desktop + .getAlignmentPanels(uniqueSeqSetId); + if (views != null && views.length > 0) { - seqRefIds.clear(); - jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); + for (int v = 0; v < views.length; v++) + { + if (views[v].av.getViewId().equalsIgnoreCase(viewId)) + { + // recover the existing alignpanel, alignframe, viewport + af = views[v].alignFrame; + av = views[v].av; + ap = views[v]; + // TODO: could even skip resetting view settings if we don't want to + // change the local settings from other jalview processes + isnewview = false; + } + } } - else - uniqueSetSuffix = ""; + } - viewportsAdded = new Hashtable(); + if (isnewview) + { + af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus, + hideQuality, hideConservation, jms, view, uniqueSeqSetId, + viewId); + av = af.viewport; + ap = af.alignPanel; + } + // LOAD TREES + // ///////////////////////////////////// + if (loadTreesAndStructures && jms.getTreeCount() > 0) + { + try + { + for (int t = 0; t < jms.getTreeCount(); t++) + { + + Tree tree = jms.getTree(t); + + TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); + if (tp == null) + { + tp = af.ShowNewickTree( + new jalview.io.NewickFile(tree.getNewick()), + tree.getTitle(), tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); + if (tree.getId() != null) + { + // perhaps bind the tree id to something ? + } + } + else + { + // update local tree attributes ? + // TODO: should check if tp has been manipulated by user - if so its + // settings shouldn't be modified + tp.setTitle(tree.getTitle()); + tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree + .getWidth(), tree.getHeight())); + tp.av = av; // af.viewport; // TODO: verify 'associate with all + // views' + // works still + tp.treeCanvas.av = av; // af.viewport; + tp.treeCanvas.ap = ap; // af.alignPanel; + + } + if (tp == null) + { + warn("There was a problem recovering stored Newick tree: \n" + + tree.getNewick()); + continue; + } + + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_actionPerformed(null); + + if (tree.getFontName() != null) + { + tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree + .getFontStyle(), tree.getFontSize())); + } + else + { + tp.setTreeFont(new java.awt.Font(view.getFontName(), view + .getFontStyle(), tree.getFontSize())); + } + + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); + + tp.treeCanvas.threshold = tree.getThreshold(); - AlignFrame af = LoadFromObject(jm, null, false); - af.alignPanels.clear(); - af.closeMenuItem_actionPerformed(true); + if (tree.getCurrentTree()) + { + af.viewport.setCurrentTree(tp.getTree()); + } + } - return af.alignPanel; + } catch (Exception ex) + { + ex.printStackTrace(); + } } -} + // //LOAD STRUCTURES + if (loadTreesAndStructures) + { + // run through all PDB ids on the alignment, and collect mappings between + // jmol view ids and all sequences referring to it + Hashtable jmolViewIds = new Hashtable(); + + for (int i = 0; i < JSEQ.length; i++) + { + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + for (int s = 0; s < ids[p].getStructureStateCount(); s++) + { + // check to see if we haven't already created this structure view + String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null + : ids[p].getStructureState(s).getViewId() + + uniqueSetSuffix; + jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); + // Originally : ids[p].getFile() + // : TODO: verify external PDB file recovery still works in normal + // jalview project load + jpdb.setFile(loadPDBFile(jprovider, ids[p].getId())); + jpdb.setId(ids[p].getId()); + + int x = ids[p].getStructureState(s).getXpos(); + int y = ids[p].getStructureState(s).getYpos(); + int width = ids[p].getStructureState(s).getWidth(); + int height = ids[p].getStructureState(s).getHeight(); + + // Probably don't need to do this anymore... + // Desktop.desktop.getComponentAt(x, y); + // TODO: NOW: check that this recovers the PDB file correctly. + String pdbFile = loadPDBFile(jprovider, ids[p].getId()); + jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds + .get(JSEQ[i].getId() + ""); + if (sviewid == null) + { + sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + + "," + height; + } + if (!jmolViewIds.containsKey(sviewid)) + { + jmolViewIds.put(sviewid, new Object[] + { new int[] + { x, y, width, height }, "", + new Hashtable() }); + } + // TODO: assemble String[] { pdb files }, String[] { id for each + // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { + // seqs_file 2}} from hash + Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid); + if (((String) jmoldat[1]).length() < ids[p] + .getStructureState(s).getContent().length()) + { + { + jmoldat[1] = ids[p].getStructureState(s).getContent(); + } + } + Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2]) + .get(ids[p].getFile()); + if (seqstrmaps == null) + { + ((Hashtable) jmoldat[2]).put( + new File(ids[p].getFile()).toString(), + seqstrmaps = new Object[] + { pdbFile, ids[p].getId(), new Vector(), + new Vector() }); + } + if (!((Vector) seqstrmaps[2]).contains(seq)) + { + ((Vector) seqstrmaps[2]).addElement(seq); + // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains + // should be stored here : do we need to + // TODO: store and recover seq/pdb_id : chain mappings + } + } + } + } + } + { + + // Instantiate the associated Jmol views + for (Entry entry : jmolViewIds.entrySet()) + { + String sviewid = entry.getKey(); + Object[] svattrib = entry.getValue(); + int[] geom = (int[]) svattrib[0]; + String state = (String) svattrib[1]; + Hashtable oldFiles = (Hashtable) svattrib[2]; + + int x = geom[0], y = geom[1], width = geom[2], height = geom[3]; + // collate the pdbfile -> sequence mappings from this view + Vector pdbfilenames = new Vector(); + Vector seqmaps = new Vector(); + Vector pdbids = new Vector(); + + // Search to see if we've already created this Jmol view + AppJmol comp = null; + JInternalFrame[] frames = null; + do + { + try + { + frames = Desktop.desktop.getAllFrames(); + } catch (ArrayIndexOutOfBoundsException e) + { + // occasional No such child exceptions are thrown here... + frames = null; + try + { + Thread.sleep(10); + } catch (Exception f) + { + } + ; + } + } while (frames == null); + // search for any Jmol windows already open from other + // alignment views that exactly match the stored structure state + for (int f = 0; comp == null && f < frames.length; f++) + { + if (frames[f] instanceof AppJmol) + { + if (sviewid != null + && ((AppJmol) frames[f]).getViewId().equals(sviewid)) + { + // post jalview 2.4 schema includes structure view id + comp = (AppJmol) frames[f]; + } + else if (frames[f].getX() == x && frames[f].getY() == y + && frames[f].getHeight() == height + && frames[f].getWidth() == width) + { + comp = (AppJmol) frames[f]; + } + } + } + + if (comp == null) + { + // create a new Jmol window. + // First parse the Jmol state to translate filenames loaded into the + // view, and record the order in which files are shown in the Jmol + // view, so we can add the sequence mappings in same order. + StringBuffer newFileLoc = null; + int cp = 0, ncp, ecp; + while ((ncp = state.indexOf("load ", cp)) > -1) + { + if (newFileLoc == null) + { + newFileLoc = new StringBuffer(); + } + newFileLoc.append(state.substring(cp, + ncp = (state.indexOf("\"", ncp + 1) + 1))); + String oldfilenam = state.substring(ncp, + ecp = state.indexOf("\"", ncp)); + // recover the new mapping data for this old filename + // have to normalize filename - since Jmol and jalview do filename + // translation differently. + Object[] filedat = oldFiles.get(new File(oldfilenam) + .toString()); + newFileLoc.append(((String) filedat[0])); + pdbfilenames.addElement((String) filedat[0]); + pdbids.addElement((String) filedat[1]); + seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) + .toArray(new SequenceI[0])); + newFileLoc.append("\""); + cp = ecp + 1; // advance beyond last \" and set cursor so we can + // look for next file statement. + } + if (cp > 0) + { + // just append rest of state + newFileLoc.append(state.substring(cp)); + } + else + { + System.err + .print("Ignoring incomplete Jmol state for PDB ids: "); + newFileLoc = new StringBuffer(state); + newFileLoc.append("; load append "); + for (String id : oldFiles.keySet()) + { + // add this and any other pdb files that should be present in + // the viewer + Object[] filedat = oldFiles.get(id); + String nfilename; + newFileLoc.append(((String) filedat[0])); + pdbfilenames.addElement((String) filedat[0]); + pdbids.addElement((String) filedat[1]); + seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) + .toArray(new SequenceI[0])); + newFileLoc.append(" \""); + newFileLoc.append((String) filedat[0]); + newFileLoc.append("\""); + + } + newFileLoc.append(";"); + } + + if (newFileLoc != null) + { + int histbug = newFileLoc.indexOf("history = "); + histbug += 10; + int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", + histbug); + String val = (diff == -1) ? null : newFileLoc.substring( + histbug, diff); + if (val != null && val.length() >= 4) + { + if (val.contains("e")) + { + if (val.trim().equals("true")) + { + val = "1"; + } + else + { + val = "0"; + } + newFileLoc.replace(histbug, diff, val); + } + } + // TODO: assemble String[] { pdb files }, String[] { id for each + // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { + // seqs_file 2}} from hash + final String[] pdbf = (String[]) pdbfilenames + .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids + .toArray(new String[pdbids.size()]); + final SequenceI[][] sq = (SequenceI[][]) seqmaps + .toArray(new SequenceI[seqmaps.size()][]); + final String fileloc = newFileLoc.toString(), vid = sviewid; + final AlignFrame alf = af; + final java.awt.Rectangle rect = new java.awt.Rectangle(x, y, + width, height); + try + { + javax.swing.SwingUtilities.invokeAndWait(new Runnable() + { + public void run() + { + AppJmol sview=null; + try { + sview=new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc, + + rect, vid); + } + catch (OutOfMemoryError ex) + { + new OOMWarning("restoring structure view for PDB id "+id,(OutOfMemoryError) ex.getCause()); + if (sview!=null && sview.isVisible()) + { + sview.closeViewer(); + sview.setVisible(false); + sview.dispose(); + } + } + } + }); + } catch (InvocationTargetException ex) + { + warn("Unexpected error when opening Jmol view.",ex); + + } catch (InterruptedException e) + { + // e.printStackTrace(); + } + } + + } + else + // if (comp != null) + { + // NOTE: if the jalview project is part of a shared session then + // view synchronization should/could be done here. + + // add mapping for sequences in this view to an already open Jmol + // instance + for (String id : oldFiles.keySet()) + { + // add this and any other pdb files that should be present in the + // viewer + Object[] filedat = oldFiles.get(id); + String pdbFile = (String) filedat[0]; + SequenceI[] seq = (SequenceI[]) ((Vector) filedat[2]) + .toArray(new SequenceI[0]); + StructureSelectionManager.getStructureSelectionManager() + .setMapping(seq, null, pdbFile, + jalview.io.AppletFormatAdapter.FILE); + ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq); + } + } + } + } + } + // and finally return. + return af; + } + + AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs, + Alignment al, boolean hideConsensus, boolean hideQuality, + boolean hideConservation, JalviewModelSequence jms, + Viewport view, String uniqueSeqSetId, String viewId) + { + AlignFrame af = null; + af = new AlignFrame(al, view.getWidth(), view.getHeight(), + uniqueSeqSetId, viewId); + + af.setFileName(file, "Jalview"); + + for (int i = 0; i < JSEQ.length; i++) + { + af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i), + new java.awt.Color(JSEQ[i].getColour())); + } + + af.viewport.gatherViewsHere = view.getGatheredViews(); + + if (view.getSequenceSetId() != null) + { + jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded + .get(uniqueSeqSetId); + + af.viewport.sequenceSetID = uniqueSeqSetId; + if (av != null) + { + // propagate shared settings to this new view + af.viewport.historyList = av.historyList; + af.viewport.redoList = av.redoList; + } + else + { + viewportsAdded.put(uniqueSeqSetId, af.viewport); + } + // TODO: check if this method can be called repeatedly without + // side-effects if alignpanel already registered. + PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); + } + // apply Hidden regions to view. + if (hiddenSeqs != null) + { + for (int s = 0; s < JSEQ.length; s++) + { + jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup(); + + for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) + { + hidden.addSequence( + al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); + } + af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); + } + + jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs + .size()]; + + for (int s = 0; s < hiddenSeqs.size(); s++) + { + hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); + } + + af.viewport.hideSequence(hseqs); + + } + // set visibility of annotation in view + 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(); + } + // recover view properties and display parameters + if (view.getViewName() != null) + { + af.viewport.viewName = view.getViewName(); + af.setInitialTabVisible(); + } + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), + view.getHeight()); + + af.viewport.setShowAnnotation(view.getShowAnnotation()); + af.viewport.setAbovePIDThreshold(view.getPidSelected()); + + af.viewport.setColourText(view.getShowColourText()); + + af.viewport.setConservationSelected(view.getConservationSelected()); + af.viewport.setShowJVSuffix(view.getShowFullId()); + af.viewport.rightAlignIds = view.getRightAlignIds(); + af.viewport.setFont(new java.awt.Font(view.getFontName(), view + .getFontStyle(), view.getFontSize())); + af.alignPanel.fontChanged(); + af.viewport.setRenderGaps(view.getRenderGaps()); + af.viewport.setWrapAlignment(view.getWrapAlignment()); + af.alignPanel.setWrapAlignment(view.getWrapAlignment()); + af.viewport.setShowAnnotation(view.getShowAnnotation()); + af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); + + af.viewport.setShowBoxes(view.getShowBoxes()); + + af.viewport.setShowText(view.getShowText()); + + af.viewport.textColour = new java.awt.Color(view.getTextCol1()); + af.viewport.textColour2 = new java.awt.Color(view.getTextCol2()); + af.viewport.thresholdTextColour = view.getTextColThreshold(); + af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view + .isShowUnconserved() : false); + af.viewport.setStartRes(view.getStartRes()); + af.viewport.setStartSeq(view.getStartSeq()); + + ColourSchemeI cs = null; + // apply colourschemes + if (view.getBgColour() != null) + { + if (view.getBgColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, view.getBgColour()); + } + else if (view.getBgColour().startsWith("Annotation")) + { + // int find annotation + if (af.viewport.alignment.getAlignmentAnnotation() != null) + { + for (int i = 0; i < af.viewport.alignment + .getAlignmentAnnotation().length; i++) + { + if (af.viewport.alignment.getAlignmentAnnotation()[i].label + .equals(view.getAnnotationColours().getAnnotation())) + { + if (af.viewport.alignment.getAlignmentAnnotation()[i] + .getThreshold() == null) + { + af.viewport.alignment.getAlignmentAnnotation()[i] + .setThreshold(new jalview.datamodel.GraphLine(view + .getAnnotationColours().getThreshold(), + "Threshold", java.awt.Color.black) + + ); + } + + if (view.getAnnotationColours().getColourScheme() + .equals("None")) + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + new java.awt.Color(view.getAnnotationColours() + .getMinColour()), new java.awt.Color(view + .getAnnotationColours().getMaxColour()), + view.getAnnotationColours().getAboveThreshold()); + } + else if (view.getAnnotationColours().getColourScheme() + .startsWith("ucs")) + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + GetUserColourScheme(jms, view + .getAnnotationColours().getColourScheme()), + view.getAnnotationColours().getAboveThreshold()); + } + else + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + ColourSchemeProperty.getColour(al, view + .getAnnotationColours().getColourScheme()), + view.getAnnotationColours().getAboveThreshold()); + } + + // Also use these settings for all the groups + if (al.getGroups() != null) + { + for (int g = 0; g < al.getGroups().size(); g++) + { + jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al + .getGroups().elementAt(g); + + if (sg.cs == null) + { + continue; + } + + /* + * if + * (view.getAnnotationColours().getColourScheme().equals("None" + * )) { sg.cs = new AnnotationColourGradient( + * af.viewport.alignment.getAlignmentAnnotation()[i], new + * java.awt.Color(view.getAnnotationColours(). + * getMinColour()), new + * java.awt.Color(view.getAnnotationColours(). + * getMaxColour()), + * view.getAnnotationColours().getAboveThreshold()); } else + */ + { + sg.cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + sg.cs, view.getAnnotationColours() + .getAboveThreshold()); + } + + } + } + + break; + } + + } + } + } + else + { + cs = ColourSchemeProperty.getColour(al, view.getBgColour()); + } + + if (cs != null) + { + cs.setThreshold(view.getPidThreshold(), true); + cs.setConsensus(af.viewport.hconsensus); + } + } + + af.viewport.setGlobalColourScheme(cs); + af.viewport.setColourAppliesToAllGroups(false); + + if (view.getConservationSelected() && cs != null) + { + cs.setConservationInc(view.getConsThreshold()); + } + + af.changeColour(cs); + + af.viewport.setColourAppliesToAllGroups(true); + + if (view.getShowSequenceFeatures()) + { + af.viewport.showSequenceFeatures = true; + } + if (view.hasCentreColumnLabels()) + { + af.viewport.setCentreColumnLabels(view.getCentreColumnLabels()); + } + if (view.hasIgnoreGapsinConsensus()) + { + af.viewport.ignoreGapsInConsensusCalculation = view + .getIgnoreGapsinConsensus(); + } + if (view.hasFollowHighlight()) + { + af.viewport.followHighlight = view.getFollowHighlight(); + } + if (view.hasFollowSelection()) + { + af.viewport.followSelection = view.getFollowSelection(); + } + if (view.hasShowConsensusHistogram()) + { + af.viewport.setShowConsensusHistogram(view + .getShowConsensusHistogram()); + } + else + { + af.viewport.setShowConsensusHistogram(true); + } + if (view.hasShowSequenceLogo()) + { + af.viewport.showSequenceLogo = view.getShowSequenceLogo(); + } + else + { + af.viewport.showSequenceLogo = false; + } + if (view.hasShowDbRefTooltip()) + { + af.viewport.setShowDbRefs(view.getShowDbRefTooltip()); + } + if (view.hasShowNPfeatureTooltip()) + { + af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip()); + } + if (view.hasShowGroupConsensus()) + { + af.viewport.setShowGroupConsensus(view.getShowGroupConsensus()); + } + else + { + af.viewport.setShowGroupConsensus(false); + } + if (view.hasShowGroupConservation()) + { + af.viewport.setShowGroupConservation(view.getShowGroupConservation()); + } + else + { + af.viewport.setShowGroupConservation(false); + } + + // recover featre settings + if (jms.getFeatureSettings() != null) + { + af.viewport.featuresDisplayed = new Hashtable(); + String[] renderOrder = new String[jms.getFeatureSettings() + .getSettingCount()]; + for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) + { + Setting setting = jms.getFeatureSettings().getSetting(fs); + if (setting.hasMincolour()) + { + GraduatedColor gc = setting.hasMin() ? new GraduatedColor( + new java.awt.Color(setting.getMincolour()), + new java.awt.Color(setting.getColour()), + setting.getMin(), setting.getMax()) : new GraduatedColor( + new java.awt.Color(setting.getMincolour()), + new java.awt.Color(setting.getColour()), 0, 1); + if (setting.hasThreshold()) + { + gc.setThresh(setting.getThreshold()); + gc.setThreshType(setting.getThreshstate()); + } + gc.setAutoScaled(true); // default + if (setting.hasAutoScale()) + { + gc.setAutoScaled(setting.getAutoScale()); + } + if (setting.hasColourByLabel()) + { + gc.setColourByLabel(setting.getColourByLabel()); + } + // and put in the feature colour table. + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + setting.getType(), gc); + } + else + { + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + setting.getType(), + new java.awt.Color(setting.getColour())); + } + renderOrder[fs] = setting.getType(); + if (setting.hasOrder()) + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( + setting.getType(), setting.getOrder()); + else + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( + setting.getType(), + fs / jms.getFeatureSettings().getSettingCount()); + if (setting.getDisplay()) + { + af.viewport.featuresDisplayed.put(setting.getType(), new Integer( + setting.getColour())); + } + } + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; + Hashtable fgtable; + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); + for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) + { + Group grp = jms.getFeatureSettings().getGroup(gs); + fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); + } + } + + if (view.getHiddenColumnsCount() > 0) + { + for (int c = 0; c < view.getHiddenColumnsCount(); c++) + { + af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view + .getHiddenColumns(c).getEnd() // +1 + ); + } + } + + af.setMenusFromViewport(af.viewport); + // TODO: we don't need to do this if the viewport is aready visible. + Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), + view.getHeight()); + af.alignPanel.updateAnnotation(false); // recompute any autoannotation + return af; + } + + Hashtable skipList = null; + + /** + * TODO remove this method + * + * @param view + * @return AlignFrame bound to sequenceSetId from view, if one exists. private + * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) { + * throw new Error("Implementation Error. No skipList defined for this + * Jalview2XML instance."); } return (AlignFrame) + * skipList.get(view.getSequenceSetId()); } + */ + + /** + * Check if the Jalview view contained in object should be skipped or not. + * + * @param object + * @return true if view's sequenceSetId is a key in skipList + */ + private boolean skipViewport(JalviewModel object) + { + if (skipList == null) + { + return false; + } + String id; + if (skipList.containsKey(id = object.getJalviewModelSequence() + .getViewport()[0].getSequenceSetId())) + { + if (Cache.log != null && Cache.log.isDebugEnabled()) + { + Cache.log.debug("Skipping seuqence set id " + id); + } + return true; + } + return false; + } + + public void AddToSkipList(AlignFrame af) + { + if (skipList == null) + { + skipList = new Hashtable(); + } + skipList.put(af.getViewport().getSequenceSetId(), af); + } + + public void clearSkipList() + { + if (skipList != null) + { + skipList.clear(); + skipList = null; + } + } + + private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al) + { + jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId()); + Vector dseqs = null; + if (ds == null) + { + // create a list of new dataset sequences + dseqs = new Vector(); + } + for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) + { + Sequence vamsasSeq = vamsasSet.getSequence(i); + ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs); + } + // create a new dataset + if (ds == null) + { + SequenceI[] dsseqs = new SequenceI[dseqs.size()]; + dseqs.copyInto(dsseqs); + ds = new jalview.datamodel.Alignment(dsseqs); + debug("Created new dataset " + vamsasSet.getDatasetId() + + " for alignment " + System.identityHashCode(al)); + addDatasetRef(vamsasSet.getDatasetId(), ds); + } + // set the dataset for the newly imported alignment. + if (al.getDataset() == null) + { + al.setDataset(ds); + } + } + + /** + * + * @param vamsasSeq + * sequence definition to create/merge dataset sequence for + * @param ds + * dataset alignment + * @param dseqs + * vector to add new dataset sequence to + */ + private void ensureJalviewDatasetSequence(Sequence vamsasSeq, + AlignmentI ds, Vector dseqs) + { + // JBP TODO: Check this is called for AlCodonFrames to support recovery of + // xRef Codon Maps + jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds + .get(vamsasSeq.getId()); + jalview.datamodel.SequenceI dsq = null; + if (sq != null && sq.getDatasetSequence() != null) + { + dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence(); + } + + String sqid = vamsasSeq.getDsseqid(); + if (dsq == null) + { + // need to create or add a new dataset sequence reference to this sequence + if (sqid != null) + { + dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid); + } + // check again + if (dsq == null) + { + // make a new dataset sequence + dsq = sq.createDatasetSequence(); + if (sqid == null) + { + // make up a new dataset reference for this sequence + sqid = seqHash(dsq); + } + dsq.setVamsasId(uniqueSetSuffix + sqid); + seqRefIds.put(sqid, dsq); + if (ds == null) + { + if (dseqs != null) + { + dseqs.addElement(dsq); + } + } + else + { + ds.addSequence(dsq); + } + } + else + { + if (sq != dsq) + { // make this dataset sequence sq's dataset sequence + sq.setDatasetSequence(dsq); + } + } + } + // TODO: refactor this as a merge dataset sequence function + // now check that sq (the dataset sequence) sequence really is the union of + // all references to it + // boolean pre = sq.getStart() < dsq.getStart(); + // boolean post = sq.getEnd() > dsq.getEnd(); + // if (pre || post) + if (sq != dsq) + { + StringBuffer sb = new StringBuffer(); + String newres = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, sq.getSequenceAsString()); + if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) + && newres.length() > dsq.getLength()) + { + // Update with the longer sequence. + synchronized (dsq) + { + /* + * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() - + * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) { + * sb.append(newres.substring(newres.length() - sq.getEnd() - + * dsq.getEnd())); dsq.setEnd(sq.getEnd()); } + */ + dsq.setSequence(sb.toString()); + } + // TODO: merges will never happen if we 'know' we have the real dataset + // sequence - this should be detected when id==dssid + System.err.println("DEBUG Notice: Merged dataset sequence"); // (" + // + (pre ? "prepended" : "") + " " + // + (post ? "appended" : "")); + } + } + } + + java.util.Hashtable datasetIds = null; + + java.util.IdentityHashMap dataset2Ids = null; + + private Alignment getDatasetFor(String datasetId) + { + if (datasetIds == null) + { + datasetIds = new Hashtable(); + return null; + } + if (datasetIds.containsKey(datasetId)) + { + return (Alignment) datasetIds.get(datasetId); + } + return null; + } + + private void addDatasetRef(String datasetId, Alignment dataset) + { + if (datasetIds == null) + { + datasetIds = new Hashtable(); + } + datasetIds.put(datasetId, dataset); + } + + /** + * make a new dataset ID for this jalview dataset alignment + * + * @param dataset + * @return + */ + private String getDatasetIdRef(jalview.datamodel.Alignment dataset) + { + if (dataset.getDataset() != null) + { + warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment..."); + } + String datasetId = makeHashCode(dataset, null); + if (datasetId == null) + { + // make a new datasetId and record it + if (dataset2Ids == null) + { + dataset2Ids = new IdentityHashMap(); + } + else + { + datasetId = (String) dataset2Ids.get(dataset); + } + if (datasetId == null) + { + datasetId = "ds" + dataset2Ids.size() + 1; + dataset2Ids.put(dataset, datasetId); + } + } + return datasetId; + } + + private void addDBRefs(SequenceI datasetSequence, Sequence sequence) + { + for (int d = 0; d < sequence.getDBRefCount(); d++) + { + DBRef dr = sequence.getDBRef(d); + jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( + sequence.getDBRef(d).getSource(), sequence.getDBRef(d) + .getVersion(), sequence.getDBRef(d).getAccessionId()); + if (dr.getMapping() != null) + { + entry.setMap(addMapping(dr.getMapping())); + } + datasetSequence.addDBRef(entry); + } + } + + private jalview.datamodel.Mapping addMapping(Mapping m) + { + SequenceI dsto = null; + // Mapping m = dr.getMapping(); + int fr[] = new int[m.getMapListFromCount() * 2]; + Enumeration f = m.enumerateMapListFrom(); + for (int _i = 0; f.hasMoreElements(); _i += 2) + { + MapListFrom mf = (MapListFrom) f.nextElement(); + fr[_i] = mf.getStart(); + fr[_i + 1] = mf.getEnd(); + } + int fto[] = new int[m.getMapListToCount() * 2]; + f = m.enumerateMapListTo(); + for (int _i = 0; f.hasMoreElements(); _i += 2) + { + MapListTo mf = (MapListTo) f.nextElement(); + fto[_i] = mf.getStart(); + fto[_i + 1] = mf.getEnd(); + } + jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, + fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit()); + if (m.getMappingChoice() != null) + { + MappingChoice mc = m.getMappingChoice(); + if (mc.getDseqFor() != null) + { + String dsfor = "" + mc.getDseqFor(); + if (seqRefIds.containsKey(dsfor)) + { + /** + * recover from hash + */ + jmap.setTo((SequenceI) seqRefIds.get(dsfor)); + } + else + { + frefedSequence.add(new Object[] + { dsfor, jmap }); + } + } + else + { + /** + * local sequence definition + */ + Sequence ms = mc.getSequence(); + jalview.datamodel.Sequence djs = null; + String sqid = ms.getDsseqid(); + if (sqid != null && sqid.length() > 0) + { + /* + * recover dataset sequence + */ + djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid); + } + else + { + System.err + .println("Warning - making up dataset sequence id for DbRef sequence map reference"); + sqid = ((Object) ms).toString(); // make up a new hascode for + // undefined dataset sequence hash + // (unlikely to happen) + } + + if (djs == null) + { + /** + * make a new dataset sequence and add it to refIds hash + */ + djs = new jalview.datamodel.Sequence(ms.getName(), + ms.getSequence()); + djs.setStart(jmap.getMap().getToLowest()); + djs.setEnd(jmap.getMap().getToHighest()); + djs.setVamsasId(uniqueSetSuffix + sqid); + jmap.setTo(djs); + seqRefIds.put(sqid, djs); + + } + jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); + addDBRefs(djs, ms); + + } + } + return (jmap); + + } + + public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, + boolean keepSeqRefs) + { + initSeqRefs(); + jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null, + null); + + if (!keepSeqRefs) + { + clearSeqRefs(); + jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); + } + else + { + uniqueSetSuffix = ""; + jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't + // overwrite the + // view we just + // copied + } + if (this.frefedSequence == null) + { + frefedSequence = new Vector(); + } + + viewportsAdded = new Hashtable(); + + AlignFrame af = LoadFromObject(jm, null, false, null); + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); + + /* + * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; + * i