X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=45c76ee6981bc1dc4ba15a4108e2b31a34018a91;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=e15f54bdacd2a39520798a842b9b3bb03ddc5fc6;hpb=629aab8cacd34324f5bd6aad568db5857fec8c81;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java old mode 100755 new mode 100644 index e15f54b..105209f --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,58 +1,235 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors + * + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; - -import jalview.schemes.*; - +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 jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; - - - +import jalview.schemes.*; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.jarInputStreamProvider; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.dm.AAConSettings; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.AutoCalcSetting; +import jalview.ws.params.WsParamSetI; /** - * 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 $Revision$ + * @version $Revision: 1.134 $ */ public class Jalview2XML { + /** + * create/return unique hash string for sq + * + * @param sq + * @return new or existing unique string for sq + */ + String seqHash(SequenceI sq) + { + if (seqsToIds == null) + { + initSeqRefs(); + } + if (seqsToIds.containsKey(sq)) + { + return (String) seqsToIds.get(sq); + } + else + { + // create sequential key + String key = "sq" + (seqsToIds.size() + 1); + key = makeHashCode(sq, key); // check we don't have an external reference + // for it already. + seqsToIds.put(sq, key); + return key; + } + } + + void clearSeqRefs() + { + if (_cleartables) + { + if (seqRefIds != null) + { + seqRefIds.clear(); + } + if (seqsToIds != null) + { + seqsToIds.clear(); + } + // seqRefIds = null; + // seqsToIds = null; + } + else + { + // do nothing + warn("clearSeqRefs called when _cleartables was not set. Doing nothing."); + // seqRefIds = new Hashtable(); + // seqsToIds = new IdentityHashMap(); + } + } + + void initSeqRefs() + { + if (seqsToIds == null) + { + seqsToIds = new IdentityHashMap(); + } + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + } + + /** + * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps + * of sequence objects are created. + */ + java.util.IdentityHashMap seqsToIds = null; + + /** + * jalview XML Sequence ID to jalview sequence object reference (both dataset + * and alignment sequences. Populated as XML reps of sequence objects are + * created.) + */ + java.util.Hashtable seqRefIds = null; // key->SequenceI resolution + + Vector frefedSequence = null; - Hashtable seqRefIds; + boolean raiseGUI = true; // whether errors are raised in dialog boxes or not + + public Jalview2XML() + { + } + + public Jalview2XML(boolean raiseGUI) + { + this.raiseGUI = raiseGUI; + } + + public void resolveFrefedSequences() + { + if (frefedSequence.size() > 0) + { + int r = 0, rSize = frefedSequence.size(); + while (r < rSize) + { + Object[] ref = (Object[]) frefedSequence.elementAt(r); + if (ref != null) + { + String sref = (String) ref[0]; + if (seqRefIds.containsKey(sref)) + { + if (ref[1] instanceof jalview.datamodel.Mapping) + { + SequenceI seq = (SequenceI) seqRefIds.get(sref); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + ((jalview.datamodel.Mapping) ref[1]).setTo(seq); + } + else + { + if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame) + { + SequenceI seq = (SequenceI) seqRefIds.get(sref); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + if (ref[2] != null + && ref[2] instanceof jalview.datamodel.Mapping) + { + jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2]; + ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap( + seq, mp.getTo(), mp.getMap()); + } + else + { + System.err + .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving " + + ref[2].getClass() + " type objects."); + } + } + else + { + System.err + .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " + + ref[1].getClass() + " type objects."); + } + } + frefedSequence.remove(r); + rSize--; + } + else + { + System.err + .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string " + + ref[0] + + " with objecttype " + + ref[1].getClass()); + r++; + } + } + else + { + // empty reference + frefedSequence.remove(r); + rSize--; + } + } + } + } /** - * This maintains a list of viewports, the key being the - * seqSetId. Important to set historyItem and redoList - * for multiple views + * This maintains a list of viewports, the key being the seqSetId. Important + * to set historyItem and redoList for multiple views */ Hashtable viewportsAdded; @@ -60,1677 +237,4187 @@ public class Jalview2XML String uniqueSetSuffix = ""; + /** + * List of pdbfiles added to Jar + */ + Vector pdbfiles = null; - // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE - public void SaveState(File statefile) + // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE + public void SaveState(File statefile) + { + try { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + FileOutputStream fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); + SaveState(jout); - if (frames == null) - { - return; - } + } 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(); + } - try + /** + * Writes a jalview project archive to the given Jar output stream. + * + * @param jout + */ + public void SaveState(JarOutputStream jout) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + + if (frames == null) + { + return; + } + + Hashtable dsses = new Hashtable(); + + try + { + + // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS + // ////////////////////////////////////////////////// + // NOTE ALSO new PrintWriter must be used for each new JarEntry + PrintWriter out = null; + + Vector shortNames = new Vector(); + + // REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); + AlignFrame af = (AlignFrame) frames[i]; + // skip ? + if (skipList != null + && skipList.containsKey(af.getViewport() + .getSequenceSetId())) + { + continue; + } - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); + String shortName = af.getTitle(); + + if (shortName.indexOf(File.separatorChar) > -1) + { + shortName = shortName.substring(shortName + .lastIndexOf(File.separatorChar) + 1); + } - Vector shortNames = new Vector(); + int count = 1; - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + while (shortNames.contains(shortName)) + { + if (shortName.endsWith("_" + (count - 1))) { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; - - String shortName = af.getTitle(); + shortName = shortName + .substring(0, shortName.lastIndexOf("_")); + } - if (shortName.indexOf(File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - File.separatorChar) + 1); - } + shortName = shortName.concat("_" + count); + count++; + } - int count = 1; + shortNames.addElement(shortName); - while (shortNames.contains(shortName)) - { - if (shortName.endsWith("_" + (count - 1))) - { - shortName = shortName.substring(0, - shortName.lastIndexOf("_")); - } - - shortName = shortName.concat("_" + count); - count++; - } + if (!shortName.endsWith(".xml")) + { + shortName = shortName + ".xml"; + } - shortNames.addElement(shortName); + int ap, apSize = af.alignPanels.size(); - if (!shortName.endsWith(".xml")) - { - shortName = shortName + ".xml"; - } + 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"; + } - int ap, apSize= af.alignPanels.size(); - for (ap = 0; ap < apSize; ap++) - { - AlignmentPanel apanel = (AlignmentPanel) af.alignPanels. - elementAt(ap); + SaveState(apanel, fileName, jout); - SaveState(apanel, - apSize == 1 ? shortName : ap+shortName, - jout, out); - } - } + String dssid = getDatasetIdRef(af.getViewport().getAlignment() + .getDataset()); + if (!dsses.containsKey(dssid)) + { + dsses.put(dssid, af); } - out.close(); - jout.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); + } } + } + + writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix, + jout); + + try + { + jout.flush(); + } catch (Exception foo) + { + } + ; + jout.close(); + } catch (Exception ex) + { + // TODO: inform user of the problem - they need to know if their data was + // not saved ! + if (errorMessage == null) + { + errorMessage = "Couldn't write Jalview Archive - see error output for details"; + } + ex.printStackTrace(); } + } - // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public boolean SaveAlignment(AlignFrame af, String jarFile, - String fileName) + // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW + public boolean SaveAlignment(AlignFrame af, String jarFile, + String fileName) + { + try { - try + int ap, apSize = af.alignPanels.size(); + FileOutputStream fos = new FileOutputStream(jarFile); + JarOutputStream jout = new JarOutputStream(fos); + Hashtable dsses = new Hashtable(); + for (ap = 0; ap < apSize; ap++) + { + AlignmentPanel apanel = (AlignmentPanel) af.alignPanels + .elementAt(ap); + String jfileName = apSize == 1 ? fileName : fileName + ap; + if (!jfileName.endsWith(".xml")) { - 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 dsses, + String fileName, JarOutputStream jout) + { - Vector userColours = new Vector(); + for (String dssids : dsses.keySet()) + { + AlignFrame _af = dsses.get(dssids); + String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()}); + if (!jfileName.endsWith(".xml")) + { + jfileName = jfileName + ".xml"; + } + SaveState(_af.alignPanel, jfileName, true, jout); + } + } - 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) + { + return SaveState(ap, fileName, false, jout); + } - JalviewModel object = new JalviewModel(); - object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); + /** + * 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 storeDS + * when true, only write the dataset for the alignment, not the data + * associated with the view. + * @param jout + * jar output stream + * @param out + * jar entry name + */ + public JalviewModel SaveState(AlignmentPanel ap, String fileName, + boolean storeDS, JarOutputStream jout) + { + initSeqRefs(); + Vector jmolViewIds = new Vector(); // + Vector userColours = new Vector(); - object.setCreationDate(new java.util.Date(System.currentTimeMillis())); - object.setVersion(jalview.bin.Cache.getProperty("VERSION")); + AlignViewport av = ap.av; - jalview.datamodel.AlignmentI jal = av.alignment; + JalviewModel object = new JalviewModel(); + object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); - if(av.hasHiddenRows) - { - jal = jal.getHiddenSequences().getFullAlignment(); - } + object.setCreationDate(new java.util.Date(System.currentTimeMillis())); + object.setVersion(jalview.bin.Cache.getDefault("VERSION", + "Development Build")); - SequenceSet vamsasSet = new SequenceSet(); - Sequence vamsasSeq; - JalviewModelSequence jms = new JalviewModelSequence(); + jalview.datamodel.AlignmentI jal = av.getAlignment(); - vamsasSet.setGapChar(jal.getGapCharacter() + ""); + if (av.hasHiddenRows()) + { + jal = jal.getHiddenSequences().getFullAlignment(); + } - JSeq jseq; - Vector pdbfiles = null; + SequenceSet vamsasSet = new SequenceSet(); + Sequence vamsasSeq; + JalviewModelSequence jms = new JalviewModelSequence(); - //SAVE SEQUENCES - int id = 0; - jalview.datamodel.SequenceI jds; - for (int i = 0; i < jal.getHeight(); i++) - { - jds = jal.getSequenceAt(i); - id = jds.hashCode(); + vamsasSet.setGapChar(jal.getGapCharacter() + ""); - if(seqRefIds.get(id+"")!=null) - { + if (jal.getDataset() != null) + { + // dataset id is the dataset's hashcode + vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset())); + if (storeDS) + { + // switch jal and the dataset + jal = 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); + } + } - } - else - { - vamsasSeq = new Sequence(); - vamsasSeq.setId(id + ""); - vamsasSeq.setName(jds.getName()); - vamsasSeq.setSequence(jds.getSequenceAsString()); - vamsasSeq.setDescription(jds.getDescription()); + JSeq jseq; + Set calcIdSet = new HashSet(); - if (jds.getDatasetSequence().getDBRef() != null) - { - jalview.datamodel.DBRefEntry[] dbrefs = - jds.getDatasetSequence().getDBRef(); + // SAVE SEQUENCES + String id = ""; + jalview.datamodel.SequenceI jds, jdatasq; + for (int i = 0; i < jal.getHeight(); i++) + { + jds = jal.getSequenceAt(i); + jdatasq = jds.getDatasetSequence() == null ? jds : jds + .getDatasetSequence(); + id = seqHash(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); - } - } + 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); + } - vamsasSet.addSequence(vamsasSeq); - seqRefIds.put(id+"", jal.getSequenceAt(i)); - } + jseq = new JSeq(); + jseq.setStart(jds.getStart()); + jseq.setEnd(jds.getEnd()); + jseq.setColour(av.getSequenceColour(jds).getRGB()); - jseq = new JSeq(); - jseq.setStart(jds.getStart()); - jseq.setEnd(jds.getEnd()); - jseq.setColour( av.getSequenceColour(jds).getRGB()); + jseq.setId(id); // jseq id should be a string not a number + if (!storeDS) + { + // Store any sequences this sequence represents + if (av.hasHiddenRows()) + { + jseq.setHidden(av.getAlignment().getHiddenSequences() + .isHidden(jds)); - jseq.setId(id); + if (av.isHiddenRepSequence(jal.getSequenceAt(i))) + { + jalview.datamodel.SequenceI[] reps = av + .getRepresentedSequences(jal.getSequenceAt(i)) + .getSequencesInOrder(jal); - if (av.hasHiddenRows) + for (int h = 0; h < reps.length; h++) { - jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); - - if(av.hiddenRepSequences!=null - && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i))) + if (reps[h] != jal.getSequenceAt(i)) { - jalview.datamodel.SequenceI[] reps = - ( (jalview.datamodel.SequenceGroup) - av.hiddenRepSequences.get( - jal.getSequenceAt(i))).getSequencesInOrder(jal); - - 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) + 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) + if (jds == jmol.jmb.sequence[peid][smap]) { - 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()); + state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap)); + state.setColourwithAlignPanel(jmol + .isUsedforcolourby(ap)); + state.setColourByJmol(jmol.isColouredByJmol()); + if (!jmolViewIds.contains(state.getViewId())) { - File file = new File(entry.getFile()); - if(file.exists() && jout!=null) - { - byte[] data = new byte[ (int) file.length()]; - jout.putNextEntry(new JarEntry(entry.getId())); - DataInputStream dis = new DataInputStream(new - FileInputStream(file)); - dis.readFully(data); - - DataOutputStream dout = new DataOutputStream(jout); - dout.write(data, 0, data.length); - jout.closeEntry(); - } + // 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(); - - if(aa[i].annotationId!=null) - { - annotationIds.put(aa[i].annotationId, aa[i]); - } - - an.setId(aa[i].annotationId); - - 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; - } - - - 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 + - ""); + 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].annotations[a].colour!=java.awt.Color.black) - ae.setColour(aa[i].annotations[a].colour.getRGB()); + jseq.addPdbids(pdb); + } + } - an.addAnnotationElement(ae); - } + jms.addJSeq(jseq); + } - vamsasSet.addAnnotation(an); - } + if (!storeDS && av.hasHiddenRows()) + { + jal = av.getAlignment(); + } + // 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)); - } - - groups[i].setPidThreshold(sg.cs.getThreshold()); - } - - groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); - groups[i].setDisplayBoxes(sg.getDisplayBoxes()); - groups[i].setDisplayText(sg.getDisplayText()); - groups[i].setColourText(sg.getColourText()); - groups[i].setTextCol1(sg.textColour.getRGB()); - groups[i].setTextCol2(sg.textColour2.getRGB()); - groups[i].setTextColThreshold(sg.thresholdTextColour); - - for (int s = 0; s < sg.getSize(); s++) - { - jalview.datamodel.Sequence seq = - (jalview.datamodel.Sequence) sg.getSequenceAt(s); - groups[i].addSeq(seq.hashCode()); - } - } - - jms.setJGroup(groups); + SequenceI[] dnas = jac[i].getdnaSeqs(); + jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings(); + for (int m = 0; m < pmaps.length; m++) + { + AlcodMap alcmap = new AlcodMap(); + alcmap.setDnasq(seqHash(dnas[m])); + alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, + false)); + alc.addAlcodMap(alcmap); + } } + } + } + // SAVE TREES + // ///////////////////////////////// + if (!storeDS && av.currentTree != null) + { + // FIND ANY ASSOCIATED TREES + // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT + if (Desktop.desktop != null) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - ///////////SAVE VIEWPORT - Viewport view = new Viewport(); - view.setTitle(ap.alignFrame.getTitle()); - view.setSequenceSetId(av.getSequenceSetId()); - view.setViewName(av.viewName); - view.setGatheredViews(av.gatherViewsHere); - - - if (ap.av.explodedPosition != null) + for (int t = 0; t < frames.length; t++) { - view.setXpos(av.explodedPosition.x); - view.setYpos(av.explodedPosition.y); - view.setWidth(av.explodedPosition.width); - view.setHeight(av.explodedPosition.height); + if (frames[t] instanceof TreePanel) + { + TreePanel tp = (TreePanel) frames[t]; + + if (tp.treeCanvas.av.getAlignment() == 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); + } + } } - else + } + } + // SAVE ANNOTATIONS + /** + * store forward refs from an annotationRow to any groups + */ + IdentityHashMap groupRefs = new IdentityHashMap(); + if (storeDS) + { + for (SequenceI sq : jal.getSequences()) + { + // Store annotation on dataset sequences only + jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation(); + if (aa != null && aa.length > 0) { - view.setXpos(ap.alignFrame.getBounds().x); - view.setYpos(ap.alignFrame.getBounds().y); - view.setWidth(ap.alignFrame.getBounds().width); - view.setHeight(ap.alignFrame.getBounds().height); + storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS, + vamsasSet); } + } + } + else + { + if (jal.getAlignmentAnnotation() != null) + { + // Store the annotation shown on the alignment. + jalview.datamodel.AlignmentAnnotation[] aa = jal + .getAlignmentAnnotation(); + storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS, + vamsasSet); + } + } + // SAVE GROUPS + if (jal.getGroups() != null) + { + JGroup[] groups = new JGroup[jal.getGroups().size()]; + int i = -1; + for (jalview.datamodel.SequenceGroup sg : jal.getGroups()) + { + groups[++i] = new JGroup(); - view.setStartRes(av.startRes); - view.setStartSeq(av.startSeq); - - if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) + groups[i].setStart(sg.getStartRes()); + groups[i].setEnd(sg.getEndRes()); + groups[i].setName(sg.getName()); + if (groupRefs.containsKey(sg)) { - view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), - userColours, jms)); + // group has references so set it's ID field + groups[i].setId(groupRefs.get(sg).toString()); } - else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) + if (sg.cs != null) { - jalview.schemes.AnnotationColourGradient acg - = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme(); + if (sg.cs.conservationApplied()) + { + groups[i].setConsThreshold(sg.cs.getConservationInc()); - 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)); + if (sg.cs instanceof jalview.schemes.UserColourScheme) + { + groups[i].setColour(SetUserColourScheme(sg.cs, userColours, + jms)); + } else - ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour())); + { + groups[i] + .setColour(ColourSchemeProperty.getColourName(sg.cs)); + } + } + else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) + { + groups[i].setColour("AnnotationColourGradient"); + groups[i].setAnnotationColours(constructAnnotationColours( + (jalview.schemes.AnnotationColourGradient) sg.cs, + userColours, jms)); + } + else if (sg.cs instanceof jalview.schemes.UserColourScheme) + { + groups[i] + .setColour(SetUserColourScheme(sg.cs, userColours, jms)); + } + else + { + groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs)); + } - ac.setMaxColour(acg.getMaxColour().getRGB()); - ac.setMinColour(acg.getMinColour().getRGB()); - view.setAnnotationColours(ac); - view.setBgColour("AnnotationColourGradient"); + groups[i].setPidThreshold(sg.cs.getThreshold()); } - else + + groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); + groups[i].setDisplayBoxes(sg.getDisplayBoxes()); + groups[i].setDisplayText(sg.getDisplayText()); + groups[i].setColourText(sg.getColourText()); + groups[i].setTextCol1(sg.textColour.getRGB()); + groups[i].setTextCol2(sg.textColour2.getRGB()); + groups[i].setTextColThreshold(sg.thresholdTextColour); + groups[i].setShowUnconserved(sg.getShowNonconserved()); + groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); + groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); + groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); + groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo()); + for (int s = 0; s < sg.getSize(); s++) { - view.setBgColour(ColourSchemeProperty.getColourName( - av.getGlobalColourScheme())); + jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg + .getSequenceAt(s); + groups[i].addSeq(seqHash(seq)); } + } + + jms.setJGroup(groups); + } + if (!storeDS) + { + // /////////SAVE VIEWPORT + Viewport view = new Viewport(); + view.setTitle(ap.alignFrame.getTitle()); + view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), + av.getSequenceSetId())); + view.setId(av.getViewId()); + view.setViewName(av.viewName); + view.setGatheredViews(av.gatherViewsHere); + + if (ap.av.explodedPosition != null) + { + view.setXpos(av.explodedPosition.x); + view.setYpos(av.explodedPosition.y); + view.setWidth(av.explodedPosition.width); + view.setHeight(av.explodedPosition.height); + } + else + { + view.setXpos(ap.alignFrame.getBounds().x); + view.setYpos(ap.alignFrame.getBounds().y); + view.setWidth(ap.alignFrame.getBounds().width); + view.setHeight(ap.alignFrame.getBounds().height); + } + + view.setStartRes(av.startRes); + view.setStartSeq(av.startSeq); + + if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) + { + view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), + userColours, jms)); + } + else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) + { + AnnotationColours ac = constructAnnotationColours( + (jalview.schemes.AnnotationColourGradient) av + .getGlobalColourScheme(), + userColours, jms); + + view.setAnnotationColours(ac); + view.setBgColour("AnnotationColourGradient"); + } + else + { + view.setBgColour(ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); + } - ColourSchemeI cs = av.getGlobalColourScheme(); + ColourSchemeI cs = av.getGlobalColourScheme(); - if(cs!=null) + if (cs != null) + { + if (cs.conservationApplied()) { - if (cs.conservationApplied()) + view.setConsThreshold(cs.getConservationInc()); + if (cs instanceof jalview.schemes.UserColourScheme) { - view.setConsThreshold(cs.getConservationInc()); - if (cs instanceof jalview.schemes.UserColourScheme) - view.setBgColour(SetUserColourScheme(cs, userColours, jms)); + view.setBgColour(SetUserColourScheme(cs, userColours, jms)); } + } - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold(cs.getThreshold()); - } + if (cs instanceof ResidueColourScheme) + { + view.setPidThreshold(cs.getThreshold()); } + } - view.setConservationSelected(av.getConservationSelected()); - view.setPidSelected(av.getAbovePIDThreshold()); - view.setFontName(av.font.getName()); - view.setFontSize(av.font.getSize()); - view.setFontStyle(av.font.getStyle()); - view.setRenderGaps(av.renderGaps); - view.setShowAnnotation(av.getShowAnnotation()); - view.setShowBoxes(av.getShowBoxes()); - view.setShowColourText(av.getColourText()); - view.setShowFullId(av.getShowJVSuffix()); - view.setRightAlignIds(av.rightAlignIds); - view.setShowSequenceFeatures(av.showSequenceFeatures); - view.setShowText(av.getShowText()); - view.setWrapAlignment(av.getWrapAlignment()); - view.setTextCol1(av.textColour.getRGB()); - view.setTextCol2(av.textColour2.getRGB()); - view.setTextColThreshold(av.thresholdTextColour); + 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.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo()); + view.setShowGroupConsensus(av.isShowGroupConsensus()); + view.setShowGroupConservation(av.isShowGroupConservation()); + view.setShowNPfeatureTooltip(av.isShowNpFeats()); + view.setShowDbRefTooltip(av.isShowDbRefs()); + view.setFollowHighlight(av.followHighlight); + view.setFollowSelection(av.followSelection); + view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); + if (av.featuresDisplayed != null) + { + jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); + String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; - if(av.featuresDisplayed!=null) + Vector settingsAdded = new Vector(); + Object gstyle = null; + GraduatedColor gcol = null; + if (renderOrder != null) { - jalview.schemabinding.version2.FeatureSettings fs - = new jalview.schemabinding.version2.FeatureSettings(); - - String [] renderOrder = - ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; - - Vector settingsAdded = new Vector(); - for(int ro=0; ro -1) + { + setting.setOrder(rorder); + } fs.addSetting(setting); settingsAdded.addElement(renderOrder[ro]); } + } - //Make sure we save none displayed feature settings - Enumeration en = - ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys(); - while(en.hasMoreElements()) + // Make sure we save none displayed feature settings + Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours + .keySet().iterator(); + while (en.hasNext()) + { + String key = en.next().toString(); + if (settingsAdded.contains(key)) { - 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() - ); + continue; + } - setting.setDisplay(false); + Setting setting = new Setting(); + setting.setType(key); + setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + .getColour(key).getRGB()); - fs.addSetting(setting); - settingsAdded.addElement(key); + setting.setDisplay(false); + float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getOrder(key); + if (rorder > -1) + { + setting.setOrder(rorder); + } + fs.addSetting(setting); + settingsAdded.addElement(key); + } + en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups + .keySet().iterator(); + Vector groupsAdded = new Vector(); + while (en.hasNext()) + { + String grp = en.next().toString(); + if (groupsAdded.contains(grp)) + { + continue; } + Group g = new Group(); + g.setName(grp); + g.setDisplay(((Boolean) ap.seqPanel.seqCanvas + .getFeatureRenderer().featureGroups.get(grp)) + .booleanValue()); + fs.addGroup(g); + groupsAdded.addElement(grp); + } + jms.setFeatureSettings(fs); - jms.setFeatureSettings(fs); + } + if (av.hasHiddenColumns()) + { + if (av.getColumnSelection() == null + || av.getColumnSelection().getHiddenColumns() == null) + { + warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); } - - if(av.hasHiddenColumns) + else { - for(int c=0; c 0) + { + for (String calcId : calcIdSet) { - //We may not want to right the object to disk, - //eg we can copy the alignViewport to a new view object - //using save and then load - try + if (calcId.trim().length() > 0) { - if (!fileName.endsWith(".xml")) + CalcIdParam cidp = createCalcIdParam(calcId, av); + // Some calcIds have no parameters. + if (cidp != null) { - fileName = fileName + ".xml"; + view.addCalcIdParam(cidp); } - - JarEntry entry = new JarEntry(fileName); - jout.putNextEntry(entry); - - object.marshal(out); - } - catch (Exception ex) - { - ex.printStackTrace(); } } - return object; + } + + jms.addViewport(view); } + object.setJalviewModelSequence(jms); + object.getVamsasModel().addSequenceSet(vamsasSet); - String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, - Vector userColours, JalviewModelSequence jms) + if (jout != null && fileName != null) + { + // We may not want to write the object to disk, + // eg we can copy the alignViewport to a new view object + // using save and then load + try + { + JarEntry entry = new JarEntry(fileName); + jout.putNextEntry(entry); + PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout, + "UTF-8")); + org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller( + pout); + marshaller.marshal(object); + pout.flush(); + jout.closeEntry(); + } catch (Exception ex) + { + // TODO: raise error in GUI if marshalling failed. + ex.printStackTrace(); + } + } + return object; + } + + private AnnotationColours constructAnnotationColours( + AnnotationColourGradient acg, Vector userColours, + JalviewModelSequence jms) + { + AnnotationColours ac = new AnnotationColours(); + ac.setAboveThreshold(acg.getAboveThreshold()); + ac.setThreshold(acg.getAnnotationThreshold()); + ac.setAnnotation(acg.getAnnotation()); + if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) { - String id = null; - jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; + ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(), + userColours, jms)); + } + else + { + ac.setColourScheme(ColourSchemeProperty.getColourName(acg + .getBaseColour())); + } - if (!userColours.contains(ucs)) - { - userColours.add(ucs); + ac.setMaxColour(acg.getMaxColour().getRGB()); + ac.setMinColour(acg.getMinColour().getRGB()); + ac.setPerSequence(acg.isSeqAssociated()); + ac.setPredefinedColours(acg.isPredefinedColours()); + return ac; + } - 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(); + private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, + IdentityHashMap groupRefs, AlignmentViewport av, + Set calcIdSet, boolean storeDS, SequenceSet vamsasSet) + { - 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); - } - } + for (int i = 0; i < aa.length; i++) + { + Annotation an = new Annotation(); - id = "ucs" + userColours.indexOf(ucs); - uc.setId(id); - uc.setUserColourScheme(jbucs); - jms.addUserColours(uc); - } + if (aa[i].annotationId != null) + { + annotationIds.put(aa[i].annotationId, aa[i]); + } - return id; - } + an.setId(aa[i].annotationId); - jalview.schemes.UserColourScheme GetUserColourScheme( - JalviewModelSequence jms, String id) - { - UserColours[] uc = jms.getUserColours(); - UserColours colours = null; + an.setVisible(aa[i].visible); - for (int i = 0; i < uc.length; i++) - { - if (uc[i].getId().equals(id)) - { - colours = uc[i]; + an.setDescription(aa[i].description); - break; - } + if (aa[i].sequenceRef != null) + { + // TODO later annotation sequenceRef should be the XML ID of the + // sequence rather than its display name + an.setSequenceRef(aa[i].sequenceRef.getName()); + } + if (aa[i].groupRef != null) + { + Object groupIdr = groupRefs.get(aa[i].groupRef); + if (groupIdr == null) + { + // make a locally unique String + groupRefs.put(aa[i].groupRef, + groupIdr = ("" + System.currentTimeMillis() + + aa[i].groupRef.getName() + groupRefs.size())); } + an.setGroupRef(groupIdr.toString()); + } - java.awt.Color[] newColours = new java.awt.Color[24]; + // store all visualization attributes for annotation + an.setGraphHeight(aa[i].graphHeight); + an.setCentreColLabels(aa[i].centreColLabels); + an.setScaleColLabels(aa[i].scaleColLabel); + an.setShowAllColLabels(aa[i].showAllColLabels); + an.setBelowAlignment(aa[i].belowAlignment); - for (int i = 0; i < 24; i++) + if (aa[i].graph > 0) + { + an.setGraph(true); + an.setGraphType(aa[i].graph); + an.setGraphGroup(aa[i].graphGroup); + if (aa[i].getThreshold() != null) { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour(i).getRGB(), 16)); + 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); - jalview.schemes.UserColourScheme ucs = - new jalview.schemes.UserColourScheme(newColours); + if (aa[i] == av.getAlignmentQualityAnnot() + || aa[i] == av.getAlignmentConservationAnnotation() + || aa[i] == av.getAlignmentConsensusAnnotation() + || aa[i].autoCalculated) + { + // new way of indicating autocalculated annotation - + an.setAutoCalculated(aa[i].autoCalculated); + } + if (aa[i].hasScore()) + { + an.setScore(aa[i].getScore()); + } - if (colours.getUserColourScheme().getColourCount() > 24) + if (aa[i].getCalcId() != null) + { + calcIdSet.add(aa[i].getCalcId()); + an.setCalcId(aa[i].getCalcId()); + } + + AnnotationElement ae; + if (aa[i].annotations != null) + { + an.setScoreOnly(false); + for (int a = 0; a < aa[i].annotations.length; a++) { - newColours = new java.awt.Color[23]; - for (int i = 0; i < 23; i++) + if ((aa[i] == null) || (aa[i].annotations[a] == null)) { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour(i+24).getRGB(), 16)); + continue; } - ucs.setLowerCaseColours(newColours); - } - - return ucs; - } - - - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - */ - public AlignFrame LoadJalviewAlign(final String file) - { - uniqueSetSuffix = System.currentTimeMillis()%100000 +""; - jalview.gui.AlignFrame af = null; + ae = new AnnotationElement(); + if (aa[i].annotations[a].description != null) + ae.setDescription(aa[i].annotations[a].description); + if (aa[i].annotations[a].displayCharacter != null) + ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); - seqRefIds = new Hashtable(); - viewportsAdded = new Hashtable(); + if (!Float.isNaN(aa[i].annotations[a].value)) + ae.setValue(aa[i].annotations[a].value); - Vector gatherToThisFrame= new Vector(); + ae.setPosition(a); + if (aa[i].annotations[a].secondaryStructure != ' ' + && aa[i].annotations[a].secondaryStructure != '\0') + ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + + ""); - try - { - //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING - URL url = null; + if (aa[i].annotations[a].colour != null + && aa[i].annotations[a].colour != java.awt.Color.black) + { + ae.setColour(aa[i].annotations[a].colour.getRGB()); + } - if (file.startsWith("http://")) - { - url = new URL(file); - } + an.addAnnotationElement(ae); + if (aa[i].autoCalculated) + { + // only write one non-null entry into the annotation row - + // sufficient to get the visualization attributes necessary to + // display data + continue; + } + } + } + else + { + an.setScoreOnly(true); + } + if (!storeDS || (storeDS && !aa[i].autoCalculated)) + { + // skip autocalculated annotation - these are only provided for + // alignments + vamsasSet.addAnnotation(an); + } + } - JarInputStream jin = null; - JarEntry jarentry = null; - int entryCount = 1; + } - do - { - if (url != null) - { - jin = new JarInputStream(url.openStream()); - } - else - { - jin = new JarInputStream(new FileInputStream(file)); - } - - for (int i = 0; i < entryCount; i++) - { - jarentry = jin.getNextJarEntry(); - } - - if (jarentry != null && jarentry.getName().endsWith(".xml")) - { - InputStreamReader in = new InputStreamReader(jin, "UTF-8"); - JalviewModel object = new JalviewModel(); - - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal( in ); + private CalcIdParam createCalcIdParam(String calcId, AlignViewport av) + { + AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId); + if (settings != null) + { + CalcIdParam vCalcIdParam = new CalcIdParam(); + vCalcIdParam.setCalcId(calcId); + vCalcIdParam.addServiceURL(settings.getServiceURI()); + // generic URI allowing a third party to resolve another instance of the + // service used for this calculation + for (String urls : settings.getServiceURLs()) + { + vCalcIdParam.addServiceURL(urls); + } + vCalcIdParam.setVersion("1.0"); + if (settings.getPreset() != null) + { + WsParamSetI setting = settings.getPreset(); + vCalcIdParam.setName(setting.getName()); + vCalcIdParam.setDescription(setting.getDescription()); + } + else + { + vCalcIdParam.setName(""); + vCalcIdParam.setDescription("Last used parameters"); + } + // need to be able to recover 1) settings 2) user-defined presets or + // recreate settings from preset 3) predefined settings provided by + // service - or settings that can be transferred (or discarded) + vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n", + "|\\n|")); + vCalcIdParam.setAutoUpdate(settings.isAutoUpdate()); + // todo - decide if updateImmediately is needed for any projects. + + return vCalcIdParam; + } + return null; + } - 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) + private boolean recoverCalcIdParam(CalcIdParam calcIdParam, + AlignViewport av) + { + if (calcIdParam.getVersion().equals("1.0")) + { + Jws2Instance service = Jws2Discoverer.getDiscoverer() + .getPreferredServiceFor(calcIdParam.getServiceURL()); + if (service != null) + { + WsParamSetI parmSet = null; + try { - 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); - } - }); + parmSet = service.getParamStore().parseServiceParameterFile( + calcIdParam.getName(), calcIdParam.getDescription(), + calcIdParam.getServiceURL(), + calcIdParam.getParameters().replace("|\\n|", "\n")); + } catch (IOException x) + { + warn("Couldn't parse parameter data for " + + calcIdParam.getCalcId(), x); + return false; } - catch (Exception ex) + List argList = null; + if (calcIdParam.getName().length() > 0) { - //Is Version 1 Jar file? - af = new Jalview2XML_V1().LoadJalviewAlign(file); - - if(af!=null) + parmSet = service.getParamStore() + .getPreset(calcIdParam.getName()); + if (parmSet != null) { - System.out.println("Successfully loaded archive file"); - return af; + // TODO : check we have a good match with settings in AACon - + // otherwise we'll need to create a new preset } - ex.printStackTrace(); - - System.err.println("Exception whilst loading jalview XML file : " + - ex + "\n"); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Error loading " + file, - "Error loading Jalview file", - JOptionPane.WARNING_MESSAGE); - }}); } - - if (Desktop.instance != null) - Desktop.instance.stopLoading(); - - for (int i = 0; i < gatherToThisFrame.size(); i++) + else { - Desktop.instance.gatherViews( - (AlignFrame) gatherToThisFrame.elementAt(i)); + argList = parmSet.getArguments(); + parmSet = null; } + AAConSettings settings = new AAConSettings( + calcIdParam.isAutoUpdate(), service, parmSet, argList); + av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings, + calcIdParam.isNeedsUpdate()); + return true; + } + else + { + warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server."); + return false; + } + } + throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{calcIdParam.toString()})); + } - return af; + /** + * External mapping between jalview objects and objects yielding a valid and + * unique object ID string. This is null for normal Jalview project IO, but + * non-null when a jalview project is being read or written as part of a + * vamsas session. + */ + IdentityHashMap jv2vobj = null; + + /** + * Construct a unique ID for jvobj using either existing bindings or if none + * exist, the result of the hashcode call for the object. + * + * @param jvobj + * jalview data object + * @return unique ID for referring to jvobj + */ + private String makeHashCode(Object jvobj, String altCode) + { + if (jv2vobj != null) + { + Object id = jv2vobj.get(jvobj); + if (id != null) + { + return id.toString(); + } + // check string ID mappings + if (jvids2vobj != null && jvobj instanceof String) + { + id = jvids2vobj.get(jvobj); + } + if (id != null) + { + return id.toString(); + } + // give up and warn that something has gone wrong + warn("Cannot find ID for object in external mapping : " + jvobj); + } + return altCode; + } + + /** + * return local jalview object mapped to ID, if it exists + * + * @param idcode + * (may be null) + * @return null or object bound to idcode + */ + private Object retrieveExistingObj(String idcode) + { + if (idcode != null && vobj2jv != null) + { + return vobj2jv.get(idcode); } + return null; + } - String loadPDBFile(String file, String pdbId) + /** + * 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) { - System.out.println(file +" "+pdbId); - try + 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++) { - JarInputStream jin = null; + DBRef dbref = new DBRef(); + dbref.setSource(dbrefs[d].getSource()); + dbref.setVersion(dbrefs[d].getVersion()); + dbref.setAccessionId(dbrefs[d].getAccessionId()); + if (dbrefs[d].hasMap()) + { + Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, + jds, recurse); + dbref.setMapping(mp); + } + vamsasSeq.addDBRef(dbref); + } + } + return vamsasSeq; + } + + private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp, + SequenceI parentseq, SequenceI jds, boolean recurse) + { + Mapping mp = null; + if (jmp.getMap() != null) + { + mp = new Mapping(); - if (file.startsWith("http://")) + 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())) { - jin = new JarInputStream(new URL(file).openStream()); + mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()), + jmp.getTo(), jds)); } else { - jin = new JarInputStream(new FileInputStream(file)); + String jmpid = ""; + SequenceI ps = null; + if (parentseq != jmp.getTo() + && parentseq.getDatasetSequence() != jmp.getTo()) + { + // chaining dbref rather than a handshaking one + jmpid = seqHash(ps = jmp.getTo()); + } + else + { + jmpid = seqHash(ps = parentseq); + } + mpc.setDseqFor(jmpid); + if (!seqRefIds.containsKey(mpc.getDseqFor())) + { + jalview.bin.Cache.log.debug("creatign new DseqFor ID"); + seqRefIds.put(mpc.getDseqFor(), ps); + } + else + { + jalview.bin.Cache.log.debug("reusing DseqFor ID"); + } } + mp.setMappingChoice(mpc); + } + } + return mp; + } + + String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, + Vector userColours, JalviewModelSequence jms) + { + String id = null; + jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; + boolean newucs = false; + if (!userColours.contains(ucs)) + { + userColours.add(ucs); + newucs = true; + } + id = "ucs" + userColours.indexOf(ucs); + if (newucs) + { + // actually create the scheme's entry in the XML model + java.awt.Color[] colours = ucs.getColours(); + jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); + jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); - JarEntry entry = null; - do + 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++) { - entry = jin.getNextJarEntry(); + 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); } - while (!entry.getName().equals(pdbId)); + } - BufferedReader in = new BufferedReader(new InputStreamReader(jin)); - File outFile = File.createTempFile("jalview_pdb", ".txt"); - outFile.deleteOnExit(); - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; + uc.setId(id); + uc.setUserColourScheme(jbucs); + jms.addUserColours(uc); + } - while ( (data = in.readLine()) != null) - { - out.println(data); - } - out.close(); - return outFile.getAbsolutePath(); + return id; + } - } - catch (Exception ex) + jalview.schemes.UserColourScheme GetUserColourScheme( + JalviewModelSequence jms, String id) + { + UserColours[] uc = jms.getUserColours(); + UserColours colours = null; + + for (int i = 0; i < uc.length; i++) + { + if (uc[i].getId().equals(id)) { - ex.printStackTrace(); - } + colours = uc[i]; - return null; + break; + } } + java.awt.Color[] newColours = new java.awt.Color[24]; - AlignFrame LoadFromObject(JalviewModel object, - String file, - boolean loadTrees ) + for (int i = 0; i < 24; i++) { - SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); - Sequence[] vamsasSeq = vamsasSet.getSequence(); - - JalviewModelSequence jms = object.getJalviewModelSequence(); + newColours[i] = new java.awt.Color(Integer.parseInt(colours + .getUserColourScheme().getColour(i).getRGB(), 16)); + } - Viewport view = jms.getViewport(0); + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( + newColours); - ////////////////////////////////// - //LOAD SEQUENCES + 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); + } - Vector hiddenSeqs = null; - jalview.datamodel.Sequence jseq; + return ucs; + } - ArrayList tmpseqs = new ArrayList(); + /** + * contains last error message (if any) encountered by XML loader. + */ + String errorMessage = null; - boolean multipleView = false; + /** + * flag to control whether the Jalview2XML_V1 parser should be deferred to if + * exceptions are raised during project XML parsing + */ + public boolean attemptversion1parse = true; - JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); - for (int i = 0; i < JSEQ.length; i++) - { - String seqId = JSEQ[i].getId() + ""; + /** + * Load a jalview project archive from a jar file + * + * @param file + * - HTTP URL or filename + */ + public AlignFrame LoadJalviewAlign(final String file) + { - if (seqRefIds.get(seqId) != null) - { - tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId)); - multipleView = true; - } - else - { - jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), - vamsasSeq[i].getSequence()); - jseq.setDescription(vamsasSeq[i].getDescription()); - jseq.setStart(JSEQ[i].getStart()); - jseq.setEnd(JSEQ[i].getEnd()); - seqRefIds.put(vamsasSeq[i].getId(), jseq); - tmpseqs.add( jseq ); - } + jalview.gui.AlignFrame af = null; + try + { + // create list to store references for any new Jmol viewers created + newStructureViewers = new Vector(); + // 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); - if (JSEQ[i].getHidden()) + } catch (MalformedURLException e) + { + errorMessage = "Invalid URL format for '" + file + "'"; + reportErrors(); + } finally + { + try + { + SwingUtilities.invokeAndWait(new Runnable() + { + public void run() { - if (hiddenSeqs == null) - hiddenSeqs = new Vector(); - + setLoadingFinishedForNewStructureViewers(); + }; + }); + } catch (Exception x) + { - hiddenSeqs.addElement( - (jalview.datamodel.Sequence) seqRefIds.get(seqId)); - } + } + } + 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() + { + @Override + public JarInputStream getJarInputStream() throws IOException + { + if (_url != null) + { + return new JarInputStream(_url.openStream()); } + else + { + return new JarInputStream(new FileInputStream(file)); + } + } - ///SequenceFeatures are added to the DatasetSequence, - // so we must create the dataset before loading features - ///////////////////////////////// - - - jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[ - tmpseqs.size()]; - - tmpseqs.toArray(orderedSeqs) ; - - - jalview.datamodel.Alignment al = - new jalview.datamodel.Alignment(orderedSeqs); + @Override + public String getFilename() + { + return file; + } + }; + } - al.setDataset(null); - ///////////////////////////////// + /** + * Recover jalview session from a jalview project archive. Caller may + * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence + * themselves. Any null fields will be initialised with default values, + * non-null fields are left alone. + * + * @param jprovider + * @return + */ + public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider) + { + errorMessage = null; + if (uniqueSetSuffix == null) + { + uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; + } + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + if (viewportsAdded == null) + { + viewportsAdded = new Hashtable(); + } + if (frefedSequence == null) + { + frefedSequence = new Vector(); + } + jalview.gui.AlignFrame af = null, _af = null; + Hashtable gatherToThisFrame = new Hashtable(); + final String file = jprovider.getFilename(); + try + { + JarInputStream jin = null; + JarEntry jarentry = null; + int entryCount = 1; - Hashtable pdbloaded = new Hashtable(); - if(!multipleView) + do + { + jin = jprovider.getJarInputStream(); + for (int i = 0; i < entryCount; i++) { - 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()); - - } + jarentry = jin.getNextJarEntry(); + } - 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()); - } + if (jarentry != null && jarentry.getName().endsWith(".xml")) + { + InputStreamReader in = new InputStreamReader(jin, "UTF-8"); + JalviewModel object = new JalviewModel(); - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); - } - } - if (vamsasSeq[i].getDBRefCount() > 0) + Unmarshaller unmar = new Unmarshaller(object); + unmar.setValidation(false); + object = (JalviewModel) unmar.unmarshal(in); + if (true) // !skipViewport(object)) + { + _af = LoadFromObject(object, file, true, jprovider); + if (object.getJalviewModelSequence().getViewportCount() > 0) { - for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++) + af = _af; + if (af.viewport.gatherViewsHere) { - 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); + gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); } - } } + entryCount++; } - - - ///////////////////////////////// - ////////////////////////////////// - //LOAD ANNOTATIONS - boolean hideQuality = true, - hideConservation = true, - hideConsensus = true; - - if (vamsasSet.getAnnotationCount()>0) + else if (jarentry != null) + { + // Some other file here. + entryCount++; + } + } while (jarentry != null); + resolveFrefedSequences(); + } catch (java.io.FileNotFoundException ex) + { + ex.printStackTrace(); + errorMessage = "Couldn't locate Jalview XML file : " + file; + System.err.println("Exception whilst loading jalview XML file : " + + ex + "\n"); + } catch (java.net.UnknownHostException ex) + { + ex.printStackTrace(); + errorMessage = "Couldn't locate Jalview XML file : " + file; + System.err.println("Exception whilst loading jalview XML file : " + + ex + "\n"); + } catch (Exception ex) + { + System.err.println("Parsing as Jalview Version 2 file failed."); + ex.printStackTrace(System.err); + if (attemptversion1parse) + { + // Is Version 1 Jar file? + try { - Annotation[] an = vamsasSet.getAnnotation(); + af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); + } catch (Exception ex2) + { + System.err.println("Exception whilst loading as jalviewXMLV1:"); + ex2.printStackTrace(); + af = null; + } + } + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } + if (af != null) + { + System.out.println("Successfully loaded archive file"); + return af; + } + ex.printStackTrace(); - for (int i = 0; i < an.length; i++) - { - if (an[i].getLabel().equals("Quality")) - { - hideQuality = false; - continue; - } - else if(an[i].getLabel().equals("Conservation")) - { - hideConservation = false; - continue; - } - else if(an[i].getLabel().equals("Consensus")) - { - hideConsensus = false; - continue; - } - - if (an[i].getId() != null - && annotationIds.containsKey(an[i].getId())) - { - al.addAnnotation( - (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId()) - ); - - continue; - } + 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(); + } - AnnotationElement[] ae = an[i].getAnnotationElement(); - jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()]; + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } - for (int aa = 0; aa < ae.length && aa 0) ? jms.getViewport(0) + : null; + + // //////////////////////////////// + // LOAD SEQUENCES + + Vector hiddenSeqs = null; + jalview.datamodel.Sequence jseq; + + ArrayList tmpseqs = new ArrayList(); + + boolean multipleView = false; + + JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); + int vi = 0; // counter in vamsasSeq array + for (int i = 0; i < JSEQ.length; i++) + { + String seqId = JSEQ[i].getId(); + + if (seqRefIds.get(seqId) != null) + { + tmpseqs.add(seqRefIds.get(seqId)); + multipleView = true; + } + else + { + jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), + vamsasSeq[vi].getSequence()); + jseq.setDescription(vamsasSeq[vi].getDescription()); + jseq.setStart(JSEQ[i].getStart()); + jseq.setEnd(JSEQ[i].getEnd()); + jseq.setVamsasId(uniqueSetSuffix + seqId); + seqRefIds.put(vamsasSeq[vi].getId(), jseq); + tmpseqs.add(jseq); + vi++; + } + + if (JSEQ[i].getHidden()) + { + if (hiddenSeqs == null) + { + hiddenSeqs = new Vector(); + } + + hiddenSeqs.addElement(seqRefIds.get(seqId)); + } + + } + + // / + // Create the alignment object from the sequence set + // /////////////////////////////// + jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs + .size()]; + + tmpseqs.toArray(orderedSeqs); + + jalview.datamodel.Alignment al = new jalview.datamodel.Alignment( + orderedSeqs); + + // / Add the alignment properties + for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) + { + SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); + al.setProperty(ssp.getKey(), ssp.getValue()); + } + + // / + // SequenceFeatures are added to the DatasetSequence, + // so we must create or recover the dataset before loading features + // /////////////////////////////// + if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") + { + // older jalview projects do not have a dataset id. + al.setDataset(null); + } + else + { + recoverDatasetFor(vamsasSet, al); + } + // /////////////////////////////// + + Hashtable pdbloaded = new Hashtable(); + if (!multipleView) + { + // load sequence features, database references and any associated PDB + // structures for the alignment + for (int i = 0; i < vamsasSeq.length; i++) + { + if (JSEQ[i].getFeaturesCount() > 0) + { + Features[] features = JSEQ[i].getFeatures(); + for (int f = 0; f < features.length; f++) + { + jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature( + features[f].getType(), features[f].getDescription(), + features[f].getStatus(), features[f].getBegin(), + features[f].getEnd(), features[f].getFeatureGroup()); + + sf.setScore(features[f].getScore()); + for (int od = 0; od < features[f].getOtherDataCount(); od++) + { + OtherData keyValue = features[f].getOtherData(od); + if (keyValue.getKey().startsWith("LINK")) + { + sf.addLink(keyValue.getValue()); + } + else + { + sf.setValue(keyValue.getKey(), keyValue.getValue()); + } + + } + + al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + } + } + if (vamsasSeq[i].getDBRefCount() > 0) + { + addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); + } + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); + entry.setId(ids[p].getId()); + entry.setType(ids[p].getType()); + if (ids[p].getFile() != null) + { + if (!pdbloaded.containsKey(ids[p].getFile())) + { + entry.setFile(loadPDBFile(jprovider, ids[p].getId())); + } + else + { + entry.setFile(pdbloaded.get(ids[p].getId()).toString()); + } + } + + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + } + } + } // end !multipleview + + // /////////////////////////////// + // LOAD SEQUENCE MAPPINGS + + if (vamsasSet.getAlcodonFrameCount() > 0) + { + // TODO Potentially this should only be done once for all views of an + // alignment + AlcodonFrame[] alc = vamsasSet.getAlcodonFrame(); + for (int i = 0; i < alc.length; i++) + { + jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame( + alc[i].getAlcodonCount()); + if (alc[i].getAlcodonCount() > 0) + { + Alcodon[] alcods = alc[i].getAlcodon(); + for (int p = 0; p < cf.codons.length; p++) + { + if (alcods[p].hasPos1() && alcods[p].hasPos2() + && alcods[p].hasPos3()) + { + // translated codons require three valid positions + cf.codons[p] = new int[3]; + cf.codons[p][0] = (int) alcods[p].getPos1(); + cf.codons[p][1] = (int) alcods[p].getPos2(); + cf.codons[p][2] = (int) alcods[p].getPos3(); + } + else + { + cf.codons[p] = null; + } + } + } + if (alc[i].getAlcodMapCount() > 0) + { + AlcodMap[] maps = alc[i].getAlcodMap(); + for (int m = 0; m < maps.length; m++) + { + SequenceI dnaseq = (SequenceI) seqRefIds + .get(maps[m].getDnasq()); + // Load Mapping + jalview.datamodel.Mapping mapping = null; + // attach to dna sequence reference. + if (maps[m].getMapping() != null) + { + mapping = addMapping(maps[m].getMapping()); + } + if (dnaseq != null) + { + cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); + } + else + { + // defer to later + frefedSequence.add(new Object[] + { maps[m].getDnasq(), cf, mapping }); + } + } + } + al.addCodonFrame(cf); + } + + } + + // //////////////////////////////// + // LOAD ANNOTATIONS + ArrayList autoAlan = new ArrayList(); + /** + * store any annotations which forward reference a group's ID + */ + Hashtable> groupAnnotRefs = new Hashtable>(); + + if (vamsasSet.getAnnotationCount() > 0) + { + Annotation[] an = vamsasSet.getAnnotation(); + + for (int i = 0; i < an.length; i++) + { + /** + * test if annotation is automatically calculated for this view only + */ + boolean autoForView = false; + if (an[i].getLabel().equals("Quality") + || an[i].getLabel().equals("Conservation") + || an[i].getLabel().equals("Consensus")) + { + // Kludge for pre 2.5 projects which lacked the autocalculated flag + autoForView = true; + if (!an[i].hasAutoCalculated()) + { + an[i].setAutoCalculated(true); + } + } + if (autoForView + || (an[i].hasAutoCalculated() && an[i].isAutoCalculated())) + { + // remove ID - we don't recover annotation from other views for + // view-specific annotation + an[i].setId(null); + } + + // set visiblity for other annotation in this view + if (an[i].getId() != null + && annotationIds.containsKey(an[i].getId())) + { + jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds + .get(an[i].getId()); + // in principle Visible should always be true for annotation displayed + // in multiple views + if (an[i].hasVisible()) + jda.visible = an[i].getVisible(); + + al.addAnnotation(jda); + + continue; + } + // Construct new annotation from model. + AnnotationElement[] ae = an[i].getAnnotationElement(); + jalview.datamodel.Annotation[] anot = null; + java.awt.Color firstColour = null; + int anpos; + if (!an[i].getScoreOnly()) + { + anot = new jalview.datamodel.Annotation[al.getWidth()]; + for (int aa = 0; aa < ae.length && aa < anot.length; aa++) + { + anpos = ae[aa].getPosition(); + + if (anpos >= anot.length) + continue; + + anot[anpos] = 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[anpos].colour = new java.awt.Color(ae[aa].getColour()); + if (firstColour == null) + { + firstColour = anot[anpos].colour; + } + } + } + jalview.datamodel.AlignmentAnnotation jaa = null; + + if (an[i].getGraph()) + { + float llim = 0, hlim = 0; + // if (autoForView || an[i].isAutoCalculated()) { + // hlim=11f; + // } + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot, llim, hlim, + an[i].getGraphType()); + + jaa.graphGroup = an[i].getGraphGroup(); + jaa._linecolour = firstColour; + if (an[i].getThresholdLine() != null) + { + jaa.setThreshold(new jalview.datamodel.GraphLine(an[i] + .getThresholdLine().getValue(), an[i] + .getThresholdLine().getLabel(), new java.awt.Color( + an[i].getThresholdLine().getColour()))); + + } + if (autoForView || an[i].isAutoCalculated()) + { + // Hardwire the symbol display line to ensure that labels for + // histograms are displayed + jaa.hasText = true; + } + } + else + { + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot); + jaa._linecolour = firstColour; + } + // register new annotation + if (an[i].getId() != null) + { + annotationIds.put(an[i].getId(), jaa); + jaa.annotationId = an[i].getId(); + } + // recover sequence association + if (an[i].getSequenceRef() != null) + { + if (al.findName(an[i].getSequenceRef()) != null) + { + jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()), + 1, true); + al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); + } + } + // and make a note of any group association + if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0) + { + ArrayList aal = groupAnnotRefs + .get(an[i].getGroupRef()); + if (aal == null) + { + aal = new ArrayList(); + groupAnnotRefs.put(an[i].getGroupRef(), aal); + } + aal.add(jaa); + } + + if (an[i].hasScore()) + { + jaa.setScore(an[i].getScore()); + } + if (an[i].hasVisible()) + jaa.visible = an[i].getVisible(); + + if (an[i].hasCentreColLabels()) + jaa.centreColLabels = an[i].getCentreColLabels(); + + if (an[i].hasScaleColLabels()) + { + jaa.scaleColLabel = an[i].getScaleColLabels(); + } + if (an[i].hasAutoCalculated() && an[i].isAutoCalculated()) + { + // newer files have an 'autoCalculated' flag and store calculation + // state in viewport properties + jaa.autoCalculated = true; // means annotation will be marked for + // update at end of load. + } + if (an[i].hasGraphHeight()) + { + jaa.graphHeight = an[i].getGraphHeight(); + } + if (an[i].hasBelowAlignment()) + { + jaa.belowAlignment = an[i].isBelowAlignment(); + } + jaa.setCalcId(an[i].getCalcId()); + + if (jaa.autoCalculated) + { + autoAlan.add(new JvAnnotRow(i, jaa)); + } + else + // if (!autoForView) + { + // add autocalculated group annotation and any user created annotation + // for the view + al.addAnnotation(jaa); + } + } + } + // /////////////////////// + // LOAD GROUPS + // Create alignment markup and styles for this view + if (jms.getJGroupCount() > 0) + { + JGroup[] groups = jms.getJGroup(); + boolean addAnnotSchemeGroup = false; + for (int i = 0; i < groups.length; i++) + { + ColourSchemeI cs = null; + + if (groups[i].getColour() != null) + { + if (groups[i].getColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, groups[i].getColour()); + } + else if (groups[i].getColour().equals("AnnotationColourGradient") + && groups[i].getAnnotationColours() != null) + { + addAnnotSchemeGroup = true; + cs = null; + } + else + { + cs = ColourSchemeProperty.getColour(al, groups[i].getColour()); + } + + if (cs != null) + { + cs.setThreshold(groups[i].getPidThreshold(), true); + } + } + + Vector seqs = new Vector(); + + for (int s = 0; s < groups[i].getSeqCount(); s++) + { + String seqId = groups[i].getSeq(s) + ""; + jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds + .get(seqId); + + if (ts != null) + { + seqs.addElement(ts); + } + } + + if (seqs.size() < 1) + { + continue; + } + + jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup( + seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(), + groups[i].getDisplayText(), groups[i].getColourText(), + groups[i].getStart(), groups[i].getEnd()); + + sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour())); + + sg.textColour = new java.awt.Color(groups[i].getTextCol1()); + sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); + sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] + .isShowUnconserved() : false); + sg.thresholdTextColour = groups[i].getTextColThreshold(); + if (groups[i].hasShowConsensusHistogram()) + { + sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); + } + ; + if (groups[i].hasShowSequenceLogo()) + { + sg.setshowSequenceLogo(groups[i].isShowSequenceLogo()); + } + if (groups[i].hasNormaliseSequenceLogo()) + { + sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo()); + } + if (groups[i].hasIgnoreGapsinConsensus()) + { + sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus()); + } + if (groups[i].getConsThreshold() != 0) + { + jalview.analysis.Conservation c = new jalview.analysis.Conservation( + "All", ResidueProperties.propHash, 3, + sg.getSequences(null), 0, sg.getWidth() - 1); + c.calculate(); + c.verdict(false, 25); + sg.cs.setConservation(c); + } + + if (groups[i].getId() != null && groupAnnotRefs.size() > 0) + { + // re-instate unique group/annotation row reference + ArrayList jaal = groupAnnotRefs + .get(groups[i].getId()); + if (jaal != null) + { + for (jalview.datamodel.AlignmentAnnotation jaa : jaal) + { + jaa.groupRef = sg; + if (jaa.autoCalculated) + { + // match up and try to set group autocalc alignment row for this + // annotation + if (jaa.label.startsWith("Consensus for ")) + { + sg.setConsensus(jaa); + } + // match up and try to set group autocalc alignment row for this + // annotation + if (jaa.label.startsWith("Conservation for ")) + { + sg.setConservationRow(jaa); } - else - { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot); - } + } + } + } + } + al.addGroup(sg); + if (addAnnotSchemeGroup) + { + // reconstruct the annotation colourscheme + sg.cs = constructAnnotationColour( + groups[i].getAnnotationColours(), null, al, jms, false); + } + } + } + if (view == null) + { + // only dataset in this model, so just return. + return null; + } + // /////////////////////////////// + // LOAD VIEWPORT + + // If we just load in the same jar file again, the sequenceSetId + // will be the same, and we end up with multiple references + // to the same sequenceSet. We must modify this id on load + // so that each load of the file gives a unique id + String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; + String viewId = (view.getId() == null ? null : view.getId() + + uniqueSetSuffix); + AlignFrame af = null; + AlignViewport av = null; + // now check to see if we really need to create a new viewport. + if (multipleView && viewportsAdded.size() == 0) + { + // We recovered an alignment for which a viewport already exists. + // TODO: fix up any settings necessary for overlaying stored state onto + // state recovered from another document. (may not be necessary). + // we may need a binding from a viewport in memory to one recovered from + // XML. + // and then recover its containing af to allow the settings to be applied. + // TODO: fix for vamsas demo + System.err + .println("About to recover a viewport for existing alignment: Sequence set ID is " + + uniqueSeqSetId); + Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); + if (seqsetobj != null) + { + if (seqsetobj instanceof String) + { + uniqueSeqSetId = (String) seqsetobj; + System.err + .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + + uniqueSeqSetId); + } + else + { + System.err + .println("Warning : Collision between sequence set ID string and existing jalview object mapping."); + } + + } + } + /** + * indicate that annotation colours are applied across all groups (pre + * Jalview 2.8.1 behaviour) + */ + boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1", + object.getVersion()); + + AlignmentPanel ap = null; + boolean isnewview = true; + if (viewId != null) + { + // Check to see if this alignment already has a view id == viewId + jalview.gui.AlignmentPanel views[] = Desktop + .getAlignmentPanels(uniqueSeqSetId); + if (views != null && views.length > 0) + { + for (int v = 0; v < views.length; v++) + { + if (views[v].av.getViewId().equalsIgnoreCase(viewId)) + { + // recover the existing alignpanel, alignframe, viewport + af = views[v].alignFrame; + av = views[v].av; + ap = views[v]; + // TODO: could even skip resetting view settings if we don't want to + // change the local settings from other jalview processes + isnewview = false; + } + } + } + } + + if (isnewview) + { + af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view, + uniqueSeqSetId, viewId, autoAlan); + av = af.viewport; + ap = af.alignPanel; + } + // LOAD TREES + // ///////////////////////////////////// + if (loadTreesAndStructures && jms.getTreeCount() > 0) + { + try + { + for (int t = 0; t < jms.getTreeCount(); t++) + { + + Tree tree = jms.getTree(t); + + TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); + if (tp == null) + { + tp = af.ShowNewickTree( + new jalview.io.NewickFile(tree.getNewick()), + tree.getTitle(), tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); + if (tree.getId() != null) + { + // perhaps bind the tree id to something ? + } + } + else + { + // update local tree attributes ? + // TODO: should check if tp has been manipulated by user - if so its + // settings shouldn't be modified + tp.setTitle(tree.getTitle()); + tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree + .getWidth(), tree.getHeight())); + tp.av = av; // af.viewport; // TODO: verify 'associate with all + // views' + // works still + tp.treeCanvas.av = av; // af.viewport; + tp.treeCanvas.ap = ap; // af.alignPanel; + + } + if (tp == null) + { + warn("There was a problem recovering stored Newick tree: \n" + + tree.getNewick()); + continue; + } + + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_actionPerformed(null); + + if (tree.getFontName() != null) + { + tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree + .getFontStyle(), tree.getFontSize())); + } + else + { + tp.setTreeFont(new java.awt.Font(view.getFontName(), view + .getFontStyle(), tree.getFontSize())); + } + + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); + + tp.treeCanvas.threshold = tree.getThreshold(); + + if (tree.getCurrentTree()) + { + af.viewport.setCurrentTree(tp.getTree()); + } + } + + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + // //LOAD STRUCTURES + if (loadTreesAndStructures) + { + // run through all PDB ids on the alignment, and collect mappings between + // jmol view ids and all sequences referring to it + Hashtable jmolViewIds = new Hashtable(); + + for (int i = 0; i < JSEQ.length; i++) + { + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + for (int s = 0; s < ids[p].getStructureStateCount(); s++) + { + // check to see if we haven't already created this structure view + String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null + : ids[p].getStructureState(s).getViewId() + + uniqueSetSuffix; + jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); + // Originally : ids[p].getFile() + // : TODO: verify external PDB file recovery still works in normal + // jalview project load + jpdb.setFile(loadPDBFile(jprovider, ids[p].getId())); + jpdb.setId(ids[p].getId()); + + int x = ids[p].getStructureState(s).getXpos(); + int y = ids[p].getStructureState(s).getYpos(); + int width = ids[p].getStructureState(s).getWidth(); + int height = ids[p].getStructureState(s).getHeight(); + + // Probably don't need to do this anymore... + // Desktop.desktop.getComponentAt(x, y); + // TODO: NOW: check that this recovers the PDB file correctly. + String pdbFile = loadPDBFile(jprovider, ids[p].getId()); + jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds + .get(JSEQ[i].getId() + ""); + if (sviewid == null) + { + sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + + "," + height; + } + if (!jmolViewIds.containsKey(sviewid)) + { + jmolViewIds.put(sviewid, new Object[] + { new int[] + { x, y, width, height }, "", + new Hashtable(), new boolean[] + { false, false, true } }); + // Legacy pre-2.7 conversion JAL-823 : + // do not assume any view has to be linked for colour by + // sequence + } - if(an[i].getId()!=null) + // assemble String[] { pdb files }, String[] { id for each + // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { + // seqs_file 2}, boolean[] { + // linkAlignPanel,superposeWithAlignpanel}} from hash + Object[] jmoldat = jmolViewIds.get(sviewid); + ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s) + .hasAlignwithAlignPanel() ? ids[p].getStructureState( + s).getAlignwithAlignPanel() : false; + // never colour by linked panel if not specified + ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s) + .hasColourwithAlignPanel() ? ids[p] + .getStructureState(s).getColourwithAlignPanel() + : false; + // default for pre-2.7 projects is that Jmol colouring is enabled + ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s) + .hasColourByJmol() ? ids[p].getStructureState(s) + .getColourByJmol() : true; + + if (((String) jmoldat[1]).length() < ids[p] + .getStructureState(s).getContent().length()) + { { - annotationIds.put(an[i].getId(), jaa); - jaa.annotationId = an[i].getId(); + jmoldat[1] = ids[p].getStructureState(s).getContent(); } - - if(an[i].getSequenceRef()!=null) + } + if (ids[p].getFile() != null) + { + File mapkey = new File(ids[p].getFile()); + Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2]) + .get(mapkey); + if (seqstrmaps == null) { - jaa.createSequenceMapping( - al.findName(an[i].getSequenceRef()), 1, true - ); - al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); + ((Hashtable) jmoldat[2]).put(mapkey, + seqstrmaps = new Object[] + { pdbFile, ids[p].getId(), new Vector(), + new Vector() }); } - - al.addAnnotation(jaa); + if (!((Vector) seqstrmaps[2]).contains(seq)) + { + ((Vector) seqstrmaps[2]).addElement(seq); + // ((Vector)seqstrmaps[3]).addElement(n) : + // in principle, chains + // should be stored here : do we need to + // TODO: store and recover seq/pdb_id : + // chain mappings + } + } + else + { + errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747"); + warn(errorMessage); + } } + } } + } + { - ///////////////////////// - //LOAD GROUPS - if (jms.getJGroupCount() > 0) + // Instantiate the associated Jmol views + for (Entry entry : jmolViewIds.entrySet()) { - JGroup[] groups = jms.getJGroup(); + String sviewid = entry.getKey(); + Object[] svattrib = entry.getValue(); + int[] geom = (int[]) svattrib[0]; + String state = (String) svattrib[1]; + Hashtable oldFiles = (Hashtable) svattrib[2]; + final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2]; + int x = geom[0], y = geom[1], width = geom[2], height = geom[3]; + // collate the pdbfile -> sequence mappings from this view + Vector pdbfilenames = new Vector(); + Vector seqmaps = new Vector(); + Vector pdbids = new Vector(); + + // Search to see if we've already created this Jmol view + AppJmol comp = null; + JInternalFrame[] frames = null; + do + { + try + { + frames = Desktop.desktop.getAllFrames(); + } catch (ArrayIndexOutOfBoundsException e) + { + // occasional No such child exceptions are thrown here... + frames = null; + try + { + Thread.sleep(10); + } catch (Exception f) + { + } + ; + } + } while (frames == null); + // search for any Jmol windows already open from other + // alignment views that exactly match the stored structure state + for (int f = 0; comp == null && f < frames.length; f++) + { + if (frames[f] instanceof AppJmol) + { + if (sviewid != null + && ((AppJmol) frames[f]).getViewId().equals(sviewid)) + { + // post jalview 2.4 schema includes structure view id + comp = (AppJmol) frames[f]; + } + else if (frames[f].getX() == x && frames[f].getY() == y + && frames[f].getHeight() == height + && frames[f].getWidth() == width) + { + comp = (AppJmol) frames[f]; + } + } + } - for (int i = 0; i < groups.length; i++) + 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(); + } + do + { + // look for next filename in load statement + 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)); + newFileLoc.append(Platform + .escapeString((String) filedat[0])); + pdbfilenames.addElement((String) filedat[0]); + pdbids.addElement((String) filedat[1]); + seqmaps.addElement(((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. + } while ((ncp = state.indexOf("/*file*/", cp)) > -1); + } + if (cp > 0) { - ColourSchemeI cs = null; + // 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 (File 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(((Vector) filedat[2]) + .toArray(new SequenceI[0])); + newFileLoc.append(" \""); + newFileLoc.append((String) filedat[0]); + newFileLoc.append("\""); - if (groups[i].getColour() != null) + } + 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 = pdbfilenames + .toArray(new String[pdbfilenames.size()]), id = pdbids + .toArray(new String[pdbids.size()]); + final SequenceI[][] sq = 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() { - if (groups[i].getColour().startsWith("ucs")) + @Override + public void run() + { + JalviewStructureDisplayI sview = null; + try { - cs = GetUserColourScheme(jms, groups[i].getColour()); - } - else + // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera! + sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel, + useinJmolsuperpos, usetoColourbyseq, + jmolColouring, fileloc, rect, vid); + addNewStructureViewer(sview); + } catch (OutOfMemoryError ex) { - cs = ColourSchemeProperty.getColour(al, - groups[i].getColour()); + 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); - if(cs!=null) - cs.setThreshold(groups[i].getPidThreshold(), true); - } - - Vector seqs = new Vector(); + } catch (InterruptedException e) + { + // e.printStackTrace(); + } + } - 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); + } + else + // if (comp != null) + { + // NOTE: if the jalview project is part of a shared session then + // view synchronization should/could be done here. - if (ts != null) - seqs.addElement(ts); - } + // add mapping for sequences in this view to an already open Jmol + // instance + for (File 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 = ((Vector) filedat[2]) + .toArray(new SequenceI[0]); + comp.jmb.ssm.setMapping(seq, null, pdbFile, + jalview.io.AppletFormatAdapter.FILE); + comp.jmb.addSequenceForStructFile(pdbFile, seq); + } + // and add the AlignmentPanel's reference to the Jmol view + comp.addAlignmentPanel(ap); + if (useinJmolsuperpos) + { + comp.useAlignmentPanelForSuperposition(ap); + } + else + { + comp.excludeAlignmentPanelForSuperposition(ap); + } + if (usetoColourbyseq) + { + comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring); + } + else + { + comp.excludeAlignmentPanelForColourbyseq(ap); + } + } + } + } + } + // and finally return. + return af; + } - if(seqs.size()<1) - continue; + /** + * + * @param supported + * - minimum version we are comparing against + * @param version + * - version of data being processsed. + * @return true if version is development/null or evaluates to the same or + * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*) + */ + private boolean isVersionStringLaterThan(String supported, String version) + { + if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD") + || version.equalsIgnoreCase("Test") + || version.equalsIgnoreCase("AUTOMATED BUILD")) + { + System.err.println("Assuming project file with " + + (version == null ? "null" : version) + + " is compatible with Jalview version " + supported); + return true; + } + else + { + StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer( + version, "."); + while (currentV.hasMoreTokens() && fileV.hasMoreTokens()) + { + // convert b to decimal to catch bugfix releases within a series + String curT = currentV.nextToken().toLowerCase().replace('b', '.'); + String fileT = fileV.nextToken().toLowerCase().replace('b', '.'); + try + { + if (Float.valueOf(curT) > Float.valueOf(fileT)) + { + // current version is newer than the version that wrote the file + return false; + } + } catch (NumberFormatException nfe) + { + System.err + .println("** WARNING: Version comparison failed for tokens (" + + curT + + ") and (" + + fileT + + ")\n** Current: '" + + supported + "' and Version: '" + version + "'"); + } + } + if (currentV.hasMoreElements()) + { + // fileV has no minor version but identical series to current + return false; + } + } + return true; + } - 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()); + Vector newStructureViewers = null; - sg.setOutlineColour(new java.awt.Color( - groups[i].getOutlineColour())); + protected void addNewStructureViewer(JalviewStructureDisplayI sview) + { + if (newStructureViewers != null) + { + sview.getBinding().setFinishedLoadingFromArchive(false); + newStructureViewers.add(sview); + } + } - sg.textColour = new java.awt.Color(groups[i].getTextCol1()); - sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); - sg.thresholdTextColour = groups[i].getTextColThreshold(); + protected void setLoadingFinishedForNewStructureViewers() + { + if (newStructureViewers != null) + { + for (JalviewStructureDisplayI sview : newStructureViewers) + { + sview.getBinding().setFinishedLoadingFromArchive(true); + } + newStructureViewers.clear(); + newStructureViewers = null; + } + } - 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); - } + AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs, + Alignment al, JalviewModelSequence jms, Viewport view, + String uniqueSeqSetId, String viewId, + ArrayList autoAlan) + { + AlignFrame af = null; + af = new AlignFrame(al, view.getWidth(), view.getHeight(), + uniqueSeqSetId, viewId); - al.addGroup(sg); - } - } + af.setFileName(file, "Jalview"); + for (int i = 0; i < JSEQ.length; i++) + { + af.viewport.setSequenceColour(af.viewport.getAlignment() + .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); + } - ///////////////////////////////// - // LOAD VIEWPORT + af.viewport.gatherViewsHere = view.getGatheredViews(); - AlignFrame af = new AlignFrame(al, - view.getWidth(), - view.getHeight() ); + if (view.getSequenceSetId() != null) + { + jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded + .get(uniqueSeqSetId); - af.setFileName(file, "Jalview"); + af.viewport.setSequenceSetId(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 i = 0; i < JSEQ.length; i++) + for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { - af.viewport.setSequenceColour( - af.viewport.alignment.getSequenceAt(i), - new java.awt.Color( - JSEQ[i].getColour())); + 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()]; - //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; + for (int s = 0; s < hiddenSeqs.size(); s++) + { + hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); + } - af.viewport.gatherViewsHere = view.getGatheredViews(); + af.viewport.hideSequence(hseqs); - if (view.getSequenceSetId() != null) - { - jalview.gui.AlignViewport av = - (jalview.gui.AlignViewport) - viewportsAdded.get(uniqueSeqSetId); + } + // 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")) + { + AnnotationColours viewAnnColour = view.getAnnotationColours(); + cs = constructAnnotationColour(viewAnnColour, af, al, jms, true); + + // annpos + + } + else + { + cs = ColourSchemeProperty.getColour(al, view.getBgColour()); + } + + if (cs != null) + { + cs.setThreshold(view.getPidThreshold(), true); + cs.setConsensus(af.viewport.getSequenceConsensusHash()); + } + } + + 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.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(), + null); + } + 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.setShowSequenceLogo(view.getShowSequenceLogo()); + } + else + { + af.viewport.setShowSequenceLogo(false); + } + if (view.hasNormaliseSequenceLogo()) + { + af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo()); + } + 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); + } - af.viewport.sequenceSetID = uniqueSeqSetId; - if(av!=null) + // 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())); + } + } - af.viewport.historyList = av.historyList; - af.viewport.redoList = av.redoList; + if (view.getHiddenColumnsCount() > 0) + { + for (int c = 0; c < view.getHiddenColumnsCount(); c++) + { + af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view + .getHiddenColumns(c).getEnd() // +1 + ); + } + } + if (view.getCalcIdParam() != null) + { + for (CalcIdParam calcIdParam : view.getCalcIdParam()) + { + if (calcIdParam != null) + { + if (recoverCalcIdParam(calcIdParam, af.viewport)) + { } else { - viewportsAdded.put(uniqueSeqSetId, af.viewport); + warn("Couldn't recover parameters for " + + calcIdParam.getCalcId()); } - - PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); } - if(hiddenSeqs!=null) + } + } + 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, true); // recompute any autoannotation + reorderAutoannotation(af, al, autoAlan); + af.alignPanel.alignmentChanged(); + return af; + } + + private ColourSchemeI constructAnnotationColour( + AnnotationColours viewAnnColour, AlignFrame af, Alignment al, + JalviewModelSequence jms, boolean checkGroupAnnColour) + { + boolean propagateAnnColour = false; + ColourSchemeI cs = null; + AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al; + if (checkGroupAnnColour && al.getGroups() != null + && al.getGroups().size() > 0) + { + // pre 2.8.1 behaviour + // check to see if we should transfer annotation colours + propagateAnnColour = true; + for (jalview.datamodel.SequenceGroup sg : al.getGroups()) + { + if (sg.cs instanceof AnnotationColourGradient) + { + propagateAnnColour = false; + } + } + } + // int find annotation + if (annAlignment.getAlignmentAnnotation() != null) + { + for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++) + { + if (annAlignment.getAlignmentAnnotation()[i].label + .equals(viewAnnColour.getAnnotation())) { - for(int s=0; s