X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=8497df7361a1323b223abc686fd7886b834b68b6;hb=08598b6cbefd6e268c20f7e5ca9785dd5e243a08;hp=e57e7486e8bc7dafc5b2a77e5f235b1aa9b8a2ab;hpb=10e5f98521859f56139ca49860b2678e78e61da7;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index e57e748..8497df7 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,23 +1,24 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; +import java.awt.Rectangle; import java.io.*; import java.net.*; import java.util.*; @@ -28,31 +29,116 @@ import javax.swing.*; import org.exolab.castor.xml.*; import uk.ac.vamsas.objects.utils.MapList; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; import jalview.schemes.*; import jalview.structure.StructureSelectionManager; +import jalview.util.jarInputStreamProvider; /** - * Write out the current jalview desktop state - * as a Jalview XML stream. + * 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 :) * - * Note: the vamsas objects referred to here are primitive - * versions of the VAMSAS project schema elements - they are - * not the same and most likely never will be :) - * * @author $author$ * @version $Revision$ */ public class Jalview2XML { + /** + * create/return unique hash string for sq + * + * @param sq + * @return new or existing unique string for sq + */ + String seqHash(SequenceI sq) + { + if (seqsToIds == null) + { + initSeqRefs(); + } + if (seqsToIds.containsKey(sq)) + { + return (String) seqsToIds.get(sq); + } + else + { + // create sequential key + String key = "sq" + (seqsToIds.size() + 1); + key = makeHashCode(sq, key); // check we don't have an external reference + // for it already. + seqsToIds.put(sq, key); + return key; + } + } + + void clearSeqRefs() + { + if (_cleartables) + { + if (seqRefIds != null) + { + seqRefIds.clear(); + } + if (seqsToIds != null) + { + seqsToIds.clear(); + } + // seqRefIds = null; + // seqsToIds = null; + } + else + { + // do nothing + warn("clearSeqRefs called when _cleartables was not set. Doing nothing."); + // seqRefIds = new Hashtable(); + // seqsToIds = new IdentityHashMap(); + } + } + + void initSeqRefs() + { + if (seqsToIds == null) + { + seqsToIds = new IdentityHashMap(); + } + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + } - Hashtable seqRefIds = null; + /** + * 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; + 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) @@ -77,20 +163,50 @@ public class Jalview2XML } else { - System.err - .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " - + ref[1].getClass() + " type objects."); + 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--; } @@ -99,9 +215,8 @@ public class Jalview2XML } /** - * 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; @@ -117,6 +232,37 @@ public class Jalview2XML // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE public void SaveState(File statefile) { + try + { + FileOutputStream fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); + SaveState(jout); + + } 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(); + } + + /** + * 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) @@ -126,22 +272,27 @@ public class Jalview2XML try { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); + // 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 + // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AlignFrame) { AlignFrame af = (AlignFrame) frames[i]; + // skip ? + if (skipList != null + && skipList.containsKey(af.getViewport() + .getSequenceSetId())) + { + continue; + } String shortName = af.getTitle(); @@ -177,17 +328,32 @@ public class Jalview2XML { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels .elementAt(ap); + String fileName = apSize == 1 ? shortName : ap + shortName; + if (!fileName.endsWith(".xml")) + { + fileName = fileName + ".xml"; + } - SaveState(apanel, apSize == 1 ? shortName : ap + shortName, - jout, out); + SaveState(apanel, fileName, jout); } } } - - out.close(); + 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(); } } @@ -201,42 +367,52 @@ public class Jalview2XML int ap, apSize = af.alignPanels.size(); FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); for (ap = 0; ap < apSize; ap++) { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels .elementAt(ap); - - SaveState(apanel, apSize == 1 ? fileName : fileName + ap, jout, out); + String jfileName = apSize == 1 ? fileName : fileName + ap; + if (!jfileName.endsWith(".xml")) + { + jfileName = jfileName + ".xml"; + } + SaveState(apanel, jfileName, jout); } - out.close(); + try + { + jout.flush(); + } catch (Exception foo) + { + } + ; jout.close(); return true; } catch (Exception ex) { + errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details"; ex.printStackTrace(); return false; } } /** - * DOCUMENT ME! - * - * @param af DOCUMENT ME! - * @param timeStamp DOCUMENT ME! - * @param fileName DOCUMENT ME! - * @param jout DOCUMENT ME! - * @param out DOCUMENT ME! + * 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, PrintWriter out) + JarOutputStream jout) { - if (seqRefIds == null) - { - seqRefIds = new Hashtable(); - } + initSeqRefs(); Vector userColours = new Vector(); @@ -264,7 +440,7 @@ public class Jalview2XML if (jal.getDataset() != null) { // dataset id is the dataset's hashcode - vamsasSet.setDatasetId(jal.getDataset().hashCode() + ""); + vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset())); } if (jal.getProperties() != null) { @@ -281,23 +457,35 @@ public class Jalview2XML JSeq jseq; - //SAVE SEQUENCES - int id = 0; + // SAVE SEQUENCES + String id = ""; jalview.datamodel.SequenceI jds; for (int i = 0; i < jal.getHeight(); i++) { jds = jal.getSequenceAt(i); - id = jds.hashCode(); - - if (seqRefIds.get(id + "") != null) - { - + id = seqHash(jds); + + 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 + "", jal.getSequenceAt(i)); + seqRefIds.put(id, jds); } jseq = new JSeq(); @@ -305,7 +493,7 @@ public class Jalview2XML jseq.setEnd(jds.getEnd()); jseq.setColour(av.getSequenceColour(jds).getRGB()); - jseq.setId(id); + jseq.setId(id); // jseq id should be a string not a number if (av.hasHiddenRows) { @@ -384,23 +572,26 @@ public class Jalview2XML pdb.setType(entry.getType()); AppJmol jmol; - //This must have been loaded, is it still visible? + // This must have been loaded, is it still visible? JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + String matchedFile=null; for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppJmol) { jmol = (AppJmol) frames[f]; - if (!jmol.pdbentry.getId().equals(entry.getId())) + if (!jmol.pdbentry.getId().equals(entry.getId()) + && !(entry.getId().length()>4 + && entry.getId().toLowerCase().startsWith(jmol.pdbentry.getId().toLowerCase()))) continue; - + matchedFile = jmol.pdbentry.getFile(); // record the file so we can get at it if the ID match is ambiguous (e.g. 1QIP==1qipA) StructureState state = new StructureState(); state.setVisible(true); state.setXpos(jmol.getX()); state.setYpos(jmol.getY()); state.setWidth(jmol.getWidth()); state.setHeight(jmol.getHeight()); - + state.setViewId(jmol.getViewId()); String statestring = jmol.viewer.getStateInfo(); if (state != null) { @@ -416,9 +607,14 @@ public class Jalview2XML } } - if (entry.getFile() != null) + if (matchedFile!=null || entry.getFile() != null ) { - pdb.setFile(entry.getFile()); + if (entry.getFile()!=null) + { + // use entry's file + matchedFile = entry.getFile(); + } + pdb.setFile(matchedFile); // entry.getFile()); if (pdbfiles == null) { pdbfiles = new Vector(); @@ -429,7 +625,7 @@ public class Jalview2XML pdbfiles.addElement(entry.getId()); try { - File file = new File(entry.getFile()); + File file = new File(matchedFile); if (file.exists() && jout != null) { byte[] data = new byte[(int) file.length()]; @@ -440,6 +636,7 @@ public class Jalview2XML DataOutputStream dout = new DataOutputStream(jout); dout.write(data, 0, data.length); + dout.flush(); jout.closeEntry(); } } catch (Exception ex) @@ -485,12 +682,16 @@ public class Jalview2XML { AlcodonFrame alc = new AlcodonFrame(); vamsasSet.addAlcodonFrame(alc); - for (int p = 0; p < jac[i].aaWidth; i++) + for (int p = 0; p < jac[i].aaWidth; p++) { Alcodon cmap = new Alcodon(); - cmap.setPos1(jac[i].codons[p][0]); - cmap.setPos2(jac[i].codons[p][1]); - cmap.setPos3(jac[i].codons[p][2]); + if (jac[i].codons[p]!=null) + { + // Null codons indicate a gapped column in the translated peptide alignment. + cmap.setPos1(jac[i].codons[p][0]); + cmap.setPos2(jac[i].codons[p][1]); + cmap.setPos3(jac[i].codons[p][2]); + } alc.addAlcodon(cmap); } if (jac[i].getProtMappings() != null @@ -501,7 +702,7 @@ public class Jalview2XML for (int m = 0; m < pmaps.length; m++) { AlcodMap alcmap = new AlcodMap(); - alcmap.setDnasq("" + dnas[m].hashCode()); + alcmap.setDnasq(seqHash(dnas[m])); alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, false)); alc.addAlcodMap(alcmap); @@ -510,8 +711,8 @@ public class Jalview2XML } } - //SAVE TREES - /////////////////////////////////// + // SAVE TREES + // ///////////////////////////////// if (av.currentTree != null) { // FIND ANY ASSOCIATED TREES @@ -547,7 +748,7 @@ public class Jalview2XML tree.setWidth(tp.getWidth()); tree.setXpos(tp.getX()); tree.setYpos(tp.getY()); - + tree.setId(makeHashCode(tp, null)); jms.addTree(tree); } } @@ -555,7 +756,7 @@ public class Jalview2XML } } - //SAVE ANNOTATIONS + // SAVE ANNOTATIONS if (jal.getAlignmentAnnotation() != null) { jalview.datamodel.AlignmentAnnotation[] aa = jal @@ -587,6 +788,8 @@ public class Jalview2XML 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()); } @@ -658,7 +861,7 @@ public class Jalview2XML } } - //SAVE GROUPS + // SAVE GROUPS if (jal.getGroups() != null) { JGroup[] groups = new JGroup[jal.getGroups().size()]; @@ -671,7 +874,9 @@ public class Jalview2XML .getGroups().elementAt(i); groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); - groups[i].setName(sg.getName()); + groups[i].setName(sg.getName()); // TODO later sequence group should + // specify IDs of sequences, not just + // names if (sg.cs != null) { if (sg.cs.conservationApplied()) @@ -716,22 +921,24 @@ public class Jalview2XML groups[i].setTextCol1(sg.textColour.getRGB()); groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); - + groups[i].setShowUnconserved(sg.getShowunconserved()); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg .getSequenceAt(s); - groups[i].addSeq(seq.hashCode()); + groups[i].addSeq(seqHash(seq)); } } jms.setJGroup(groups); } - ///////////SAVE VIEWPORT + // /////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(ap.alignFrame.getTitle()); - view.setSequenceSetId(av.getSequenceSetId()); + view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av + .getSequenceSetId())); + view.setId(av.getViewId()); view.setViewName(av.viewName); view.setGatheredViews(av.gatherViewsHere); @@ -821,6 +1028,7 @@ public class Jalview2XML 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()); @@ -852,7 +1060,7 @@ public class Jalview2XML settingsAdded.addElement(renderOrder[ro]); } - //Make sure we save none displayed feature settings + // Make sure we save none displayed feature settings Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours .keys(); while (en.hasMoreElements()) @@ -918,47 +1126,110 @@ public class Jalview2XML object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); - if (out != null) + if (jout != null && fileName != null) { - //We may not want to right the object to disk, - //eg we can copy the alignViewport to a new view object - //using save and then load + // 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 { - if (!fileName.endsWith(".xml")) - { - fileName = fileName + ".xml"; - } - JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); - - object.marshal(out); + 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 Sequence createVamsasSequence(int id, SequenceI jds) + /** + * 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; + } + + /** + * 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, int id, + private Sequence createVamsasSequence(boolean recurse, String id, SequenceI jds, SequenceI parentseq) { Sequence vamsasSeq = new Sequence(); - vamsasSeq.setId(id + ""); + vamsasSeq.setId(id); vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); jalview.datamodel.DBRefEntry[] dbrefs = null; if (jds.getDatasetSequence() != null) { - vamsasSeq.setDsseqid(jds.getDatasetSequence().hashCode() + ""); + vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); if (jds.getDatasetSequence().getDBRef() != null) { dbrefs = jds.getDatasetSequence().getDBRef(); @@ -966,9 +1237,11 @@ public class Jalview2XML } else { + vamsasSeq.setDsseqid(id); // so we can tell which sequences really are + // dataset sequences only dbrefs = jds.getDBRef(); } - if (jds.getDBRef() != null) + if (dbrefs != null) { for (int d = 0; d < dbrefs.length; d++) { @@ -1022,24 +1295,24 @@ public class Jalview2XML && (parentseq != jmp.getTo() || parentseq .getDatasetSequence() != jmp.getTo())) { - mpc.setSequence(createVamsasSequence(false, jmp.getTo() - .hashCode(), jmp.getTo(), jds)); + mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()), + jmp.getTo(), jds)); } else { - long jmpid = 0; + String jmpid = ""; SequenceI ps = null; if (parentseq != jmp.getTo() && parentseq.getDatasetSequence() != jmp.getTo()) { // chaining dbref rather than a handshaking one - jmpid = (ps = jmp.getTo()).hashCode(); + jmpid = seqHash(ps = jmp.getTo()); } else { - jmpid = (ps = parentseq).hashCode(); + jmpid = seqHash(ps = parentseq); } - mpc.setDseqFor("" + jmpid); + mpc.setDseqFor(jmpid); if (!seqRefIds.containsKey(mpc.getDseqFor())) { jalview.bin.Cache.log.debug("creatign new DseqFor ID"); @@ -1140,48 +1413,122 @@ public class Jalview2XML } /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! + * contains last error message (if any) encountered by XML loader. + */ + String errorMessage = null; + + /** + * flag to control whether the Jalview2XML_V1 parser should be deferred to if + * exceptions are raised during project XML parsing + */ + public boolean attemptversion1parse = true; + + /** + * Load a jalview project archive from a jar file + * + * @param file - + * HTTP URL or filename */ public AlignFrame LoadJalviewAlign(final String file) { - uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; jalview.gui.AlignFrame af = null; - seqRefIds = new Hashtable(); - viewportsAdded = new Hashtable(); - frefedSequence = new Vector(); - Hashtable gatherToThisFrame = new Hashtable(); + try + { + // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING + // Workaround is to make sure caller implements the JarInputStreamProvider + // interface + // so we can re-open the jar input stream for each entry. + + jarInputStreamProvider jprovider = createjarInputStreamProvider(file); + af = LoadJalviewAlign(jprovider); + } catch (MalformedURLException e) + { + errorMessage = "Invalid URL format for '" + file + "'"; + reportErrors(); + } + return af; + } - String errorMessage = null; + private jarInputStreamProvider createjarInputStreamProvider( + final String file) throws MalformedURLException + { + URL url = null; + errorMessage = null; + uniqueSetSuffix = null; + seqRefIds = null; + viewportsAdded = null; + frefedSequence = null; - try + if (file.startsWith("http://")) + { + url = new URL(file); + } + final URL _url = url; + return new jarInputStreamProvider() { - //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING - URL url = null; - if (file.startsWith("http://")) + public JarInputStream getJarInputStream() throws IOException { - url = new URL(file); + if (_url != null) + { + return new JarInputStream(_url.openStream()); + } + else + { + return new JarInputStream(new FileInputStream(file)); + } + } + + public String getFilename() + { + return file; } + }; + } + + /** + * Recover jalview session from a jalview project archive. Caller may + * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence + * themselves. Any null fields will be initialised with default values, + * non-null fields are left alone. + * + * @param jprovider + * @return + */ + public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider) + { + errorMessage = null; + if (uniqueSetSuffix == null) + { + uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; + } + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + if (viewportsAdded == null) + { + viewportsAdded = new Hashtable(); + } + if (frefedSequence == null) + { + frefedSequence = new Vector(); + } + jalview.gui.AlignFrame af = null; + Hashtable gatherToThisFrame = new Hashtable(); + final String file = jprovider.getFilename(); + try + { JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; do { - if (url != null) - { - jin = new JarInputStream(url.openStream()); - } - else - { - jin = new JarInputStream(new FileInputStream(file)); - } - + jin = jprovider.getJarInputStream(); for (int i = 0; i < entryCount; i++) { jarentry = jin.getNextJarEntry(); @@ -1195,17 +1542,19 @@ public class Jalview2XML Unmarshaller unmar = new Unmarshaller(object); unmar.setValidation(false); object = (JalviewModel) unmar.unmarshal(in); - - af = LoadFromObject(object, file, true); - if (af.viewport.gatherViewsHere) + if (true) // !skipViewport(object)) { - gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + af = LoadFromObject(object, file, true, jprovider); + if (af.viewport.gatherViewsHere) + { + gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + } } entryCount++; } else if (jarentry != null) { - //Some other file here. + // Some other file here. entryCount++; } } while (jarentry != null); @@ -1224,9 +1573,25 @@ public class Jalview2XML + ex + "\n"); } catch (Exception ex) { - //Is Version 1 Jar file? - af = new Jalview2XML_V1().LoadJalviewAlign(file); - + System.err.println("Parsing as Jalview Version 2 file failed."); + ex.printStackTrace(System.err); + if (attemptversion1parse) + { + // Is Version 1 Jar file? + try + { + af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); + } catch (Exception ex2) + { + System.err.println("Exception whilst loading as jalviewXMLV1:"); + ex2.printStackTrace(); + af = null; + } + } + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } if (af != null) { System.out.println("Successfully loaded archive file"); @@ -1236,6 +1601,10 @@ public class Jalview2XML System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); + } catch (OutOfMemoryError e) + { + new jalview.gui.OOMWarning("loading jalview XML file", e, + Desktop.instance); } if (Desktop.instance != null) @@ -1248,27 +1617,59 @@ public class Jalview2XML { Desktop.instance.gatherViews((AlignFrame) en.nextElement()); } + if (errorMessage != null) + { + reportErrors(); + } + return af; + } + + /** + * check errorMessage for a valid error message and raise an error box in the + * GUI or write the current errorMessage to stderr and then clear the error + * state. + */ + protected void reportErrors() + { + reportErrors(false); + } + protected void reportErrors(final boolean saving) + { if (errorMessage != null) { final String finalErrorMessage = errorMessage; - javax.swing.SwingUtilities.invokeLater(new Runnable() + if (raiseGUI) { - public void run() + javax.swing.SwingUtilities.invokeLater(new Runnable() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - finalErrorMessage, "Error loading Jalview file", - JOptionPane.WARNING_MESSAGE); - } - }); + public void run() + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + finalErrorMessage, "Error " + + (saving ? "saving" : "loading") + + " Jalview file", JOptionPane.WARNING_MESSAGE); + } + }); + } + else + { + System.err.println("Problem loading Jalview file: " + errorMessage); + } } - - return af; + errorMessage = null; } Hashtable alreadyLoadedPDB; - String loadPDBFile(String file, String pdbId) + /** + * when set, local views will be updated from view stored in JalviewXML + * Currently (28th Sep 2008) things will go horribly wrong in vamsas document + * sync if this is set to true. + */ + private boolean updateLocalViews = false; + + String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) { if (alreadyLoadedPDB == null) alreadyLoadedPDB = new Hashtable(); @@ -1278,38 +1679,46 @@ public class Jalview2XML try { - JarInputStream jin = null; - - if (file.startsWith("http://")) - { - jin = new JarInputStream(new URL(file).openStream()); - } - else - { - jin = new JarInputStream(new FileInputStream(file)); - } + JarInputStream jin = jprovider.getJarInputStream(); + /* + * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new + * URL(jprovider).openStream()); } else { jin = new JarInputStream(new + * FileInputStream(jprovider)); } + */ JarEntry entry = null; do { entry = jin.getNextJarEntry(); - } while (!entry.getName().equals(pdbId)); + } while (entry != null && !entry.getName().equals(pdbId)); + if (entry != null) + { + 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; - BufferedReader in = new BufferedReader(new InputStreamReader(jin)); - File outFile = File.createTempFile("jalview_pdb", ".txt"); - outFile.deleteOnExit(); - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; + while ((data = in.readLine()) != null) + { + out.println(data); + } + try + { + out.flush(); + } catch (Exception foo) + { + } + ; + out.close(); - while ((data = in.readLine()) != null) + alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); + return outFile.getAbsolutePath(); + } + else { - out.println(data); + warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId); } - out.close(); - - alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); - return outFile.getAbsolutePath(); - } catch (Exception ex) { ex.printStackTrace(); @@ -1318,8 +1727,21 @@ public class Jalview2XML return null; } + /** + * Load alignment frame from jalview XML DOM object + * + * @param object + * DOM + * @param file + * filename source string + * @param loadTreesAndStructures + * when false only create Viewport + * @param jprovider + * data source provider + * @return alignment frame created from view stored in DOM + */ AlignFrame LoadFromObject(JalviewModel object, String file, - boolean loadTreesAndStructures) + boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); Sequence[] vamsasSeq = vamsasSet.getSequence(); @@ -1327,9 +1749,8 @@ public class Jalview2XML JalviewModelSequence jms = object.getJalviewModelSequence(); Viewport view = jms.getViewport(0); - - ////////////////////////////////// - //LOAD SEQUENCES + // //////////////////////////////// + // LOAD SEQUENCES Vector hiddenSeqs = null; jalview.datamodel.Sequence jseq; @@ -1339,9 +1760,10 @@ public class Jalview2XML 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() + ""; + String seqId = JSEQ[i].getId(); if (seqRefIds.get(seqId) != null) { @@ -1350,14 +1772,15 @@ public class Jalview2XML } else { - jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), - vamsasSeq[i].getSequence()); - jseq.setDescription(vamsasSeq[i].getDescription()); + 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[i].getId(), jseq); + seqRefIds.put(vamsasSeq[vi].getId(), jseq); tmpseqs.add(jseq); + vi++; } if (JSEQ[i].getHidden()) @@ -1373,9 +1796,9 @@ public class Jalview2XML } - /// + // / // Create the alignment object from the sequence set - ///////////////////////////////// + // /////////////////////////////// jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs .size()]; @@ -1384,32 +1807,33 @@ public class Jalview2XML jalview.datamodel.Alignment al = new jalview.datamodel.Alignment( orderedSeqs); - /// Add the alignment properties + // / 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); - // addDatasetRef(al.getDataset()); } 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) @@ -1440,7 +1864,10 @@ public class Jalview2XML 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(); @@ -1453,7 +1880,7 @@ public class Jalview2XML { if (!pdbloaded.containsKey(ids[p].getFile())) { - entry.setFile(loadPDBFile(file, ids[p].getId())); + entry.setFile(loadPDBFile(jprovider, ids[p].getId())); } else { @@ -1464,17 +1891,16 @@ public class Jalview2XML al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); } } - if (vamsasSeq[i].getDBRefCount() > 0) - { - addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); - } } - } + } // 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++) { @@ -1485,10 +1911,16 @@ public class Jalview2XML Alcodon[] alcods = alc[i].getAlcodon(); for (int p = 0; p < cf.codons.length; p++) { - 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(); + 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) @@ -1499,15 +1931,21 @@ public class Jalview2XML 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) { - if (maps[m].getMapping() != null) - { - jalview.datamodel.Mapping mapping = addMapping(maps[m] - .getMapping()); - cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); - } + cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); + } + else + { + // defer to later + frefedSequence.add(new Object[] + { maps[m].getDnasq(), cf, mapping }); } } } @@ -1516,8 +1954,8 @@ public class Jalview2XML } - ////////////////////////////////// - //LOAD ANNOTATIONS + // //////////////////////////////// + // LOAD ANNOTATIONS boolean hideQuality = true, hideConservation = true, hideConsensus = true; if (vamsasSet.getAnnotationCount() > 0) @@ -1526,6 +1964,7 @@ public class Jalview2XML for (int i = 0; i < an.length; i++) { + // set visibility for automatic annotation for this view if (an[i].getLabel().equals("Quality")) { hideQuality = false; @@ -1541,12 +1980,14 @@ public class Jalview2XML hideConsensus = false; continue; } - + // set visiblity for other annotation in this view if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) { jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds .get(an[i].getId()); + // in principle Visible should always be true for annotation displayed + // in multiple views if (an[i].hasVisible()) jda.visible = an[i].getVisible(); @@ -1554,7 +1995,7 @@ public class Jalview2XML continue; } - + // Construct new annotation from model. AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; @@ -1575,7 +2016,13 @@ public class Jalview2XML .getSecondaryStructure().charAt(0), ae[aa].getValue() ); - + // JBPNote: Consider verifying dataflow for IO of secondary + // structure annotation read from Stockholm files + // this was added to try to ensure that + // if (anot[ae[aa].getPosition()].secondaryStructure>' ') + // { + // anot[ae[aa].getPosition()].displayCharacter = ""; + // } anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa] .getColour()); } @@ -1604,13 +2051,13 @@ public class Jalview2XML jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } - + // register new annotation if (an[i].getId() != null) { annotationIds.put(an[i].getId(), jaa); jaa.annotationId = an[i].getId(); } - + // recover sequence association if (an[i].getSequenceRef() != null) { if (al.findName(an[i].getSequenceRef()) != null) @@ -1632,8 +2079,9 @@ public class Jalview2XML } } - ///////////////////////// - //LOAD GROUPS + // /////////////////////// + // LOAD GROUPS + // Create alignment markup and styles for this view if (jms.getJGroupCount() > 0) { JGroup[] groups = jms.getJGroup(); @@ -1689,6 +2137,7 @@ public class Jalview2XML sg.textColour = new java.awt.Color(groups[i].getTextCol1()); sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); + sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false); sg.thresholdTextColour = groups[i].getTextColThreshold(); if (groups[i].getConsThreshold() != 0) @@ -1705,10 +2154,293 @@ public class Jalview2XML } } - ///////////////////////////////// + // /////////////////////////////// // LOAD VIEWPORT - AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); + // 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."); + } + + } + } + 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, hideConsensus, + hideQuality, hideConservation, jms, view, uniqueSeqSetId, + viewId); + av = af.viewport; + ap = af.alignPanel; + } + // LOAD TREES + // ///////////////////////////////////// + if (loadTreesAndStructures && jms.getTreeCount() > 0) + { + try + { + for (int t = 0; t < jms.getTreeCount(); t++) + { + + Tree tree = jms.getTree(t); + + TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); + if (tp == null) + { + tp = af.ShowNewickTree(new jalview.io.NewickFile(tree + .getNewick()), tree.getTitle(), tree.getWidth(), tree + .getHeight(), tree.getXpos(), tree.getYpos()); + if (tree.getId() != null) + { + // perhaps bind the tree id to something ? + } + } + else + { + // update local tree attributes ? + // TODO: should check if tp has been manipulated by user - if so its settings shouldn't be modified + tp.setTitle(tree.getTitle()); + tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree + .getWidth(), tree.getHeight())); + tp.av = av; // af.viewport; // TODO: verify 'associate with all + // views' + // works still + tp.treeCanvas.av = av; // af.viewport; + tp.treeCanvas.ap = ap; // af.alignPanel; + + } + if (tp==null) + { + warn("There was a problem recovering stored Newick tree: \n"+tree.getNewick()); + continue; + } + + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_actionPerformed(null); + + if (tree.getFontName() != null) + { + tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree + .getFontStyle(), tree.getFontSize())); + } + else + { + tp.setTreeFont(new java.awt.Font(view.getFontName(), view + .getFontStyle(), tree.getFontSize())); + } + + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); + + tp.treeCanvas.threshold = tree.getThreshold(); + + if (tree.getCurrentTree()) + { + af.viewport.setCurrentTree(tp.getTree()); + } + } + + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + // //LOAD STRUCTURES + if (loadTreesAndStructures) + { + for (int i = 0; i < JSEQ.length; i++) + { + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + for (int s = 0; s < ids[p].getStructureStateCount(); s++) + { + // 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(); + 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]; + } + } + } + // 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 = new jalview.datamodel.SequenceI[] + { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId() + + "") }; + + if (comp == null) + { + // create a new Jmol window + String state = ids[p].getStructureState(s).getContent(); + StringBuffer newFileLoc=null; + if (state.indexOf("load")>-1) { + newFileLoc = new StringBuffer(state.substring( + 0, state.indexOf("\"", state.indexOf("load")) + 1)); + + newFileLoc.append(jpdb.getFile()); + newFileLoc.append(state.substring(state.indexOf("\"", state + .indexOf("load \"") + 6))); + } else { + System.err.println("Ignoring incomplete Jmol state for PDB "+ids[p].getId()); + + newFileLoc = new StringBuffer(state); + newFileLoc.append("; load \""); + newFileLoc.append(jpdb.getFile()); + newFileLoc.append("\";"); + } + + if (newFileLoc!=null) { + new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel, + newFileLoc.toString(), new java.awt.Rectangle(x, y, + width, height), sviewid); + } + + } + else + // if (comp != null) + { + // NOTE: if the jalview project is part of a shared session then + // view synchronization should/could be done here. + + // add mapping for this sequence to the already open Jmol + // instance (if it doesn't already exist) + // These + StructureSelectionManager.getStructureSelectionManager() + .setMapping(seq, null, pdbFile, + jalview.io.AppletFormatAdapter.FILE); + + ((AppJmol) comp).addSequence(seq); + } + } + } + } + } + } + + return af; + } + + AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs, + Alignment al, boolean hideConsensus, boolean hideQuality, + boolean hideConservation, JalviewModelSequence jms, + Viewport view, String uniqueSeqSetId, String viewId) + { + AlignFrame af = null; + af = new AlignFrame(al, view.getWidth(), view.getHeight(), + uniqueSeqSetId, viewId); af.setFileName(file, "Jalview"); @@ -1718,12 +2450,6 @@ public class Jalview2XML new java.awt.Color(JSEQ[i].getColour())); } - //If we just load in the same jar file again, the sequenceSetId - //will be the same, and we end up with multiple references - //to the same sequenceSet. We must modify this id on load - //so that each load of the file gives a unique id - String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; - af.viewport.gatherViewsHere = view.getGatheredViews(); if (view.getSequenceSetId() != null) @@ -1734,7 +2460,7 @@ public class Jalview2XML af.viewport.sequenceSetID = uniqueSeqSetId; if (av != null) { - + // propagate shared settings to this new view af.viewport.historyList = av.historyList; af.viewport.redoList = av.redoList; } @@ -1742,9 +2468,11 @@ public class Jalview2XML { 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++) @@ -1770,7 +2498,7 @@ public class Jalview2XML af.viewport.hideSequence(hseqs); } - + // set visibility of annotation in view if ((hideConsensus || hideQuality || hideConservation) && al.getAlignmentAnnotation() != null) { @@ -1791,7 +2519,7 @@ public class Jalview2XML } af.alignPanel.adjustAnnotationHeight(); } - + // recover view properties and display parameters if (view.getViewName() != null) { af.viewport.viewName = view.getViewName(); @@ -1824,12 +2552,12 @@ public class Jalview2XML 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")) @@ -1838,7 +2566,7 @@ public class Jalview2XML } else if (view.getBgColour().startsWith("Annotation")) { - //int find annotation + // int find annotation for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++) { if (af.viewport.alignment.getAlignmentAnnotation()[i].label @@ -1895,17 +2623,16 @@ public class Jalview2XML continue; } - /* if (view.getAnnotationColours().getColourScheme().equals("None")) - { - sg.cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], - new java.awt.Color(view.getAnnotationColours(). - getMinColour()), - new java.awt.Color(view.getAnnotationColours(). - getMaxColour()), - view.getAnnotationColours().getAboveThreshold()); - } - else*/ + /* + * if + * (view.getAnnotationColours().getColourScheme().equals("None")) { + * sg.cs = new AnnotationColourGradient( + * af.viewport.alignment.getAlignmentAnnotation()[i], new + * java.awt.Color(view.getAnnotationColours(). getMinColour()), + * new java.awt.Color(view.getAnnotationColours(). + * getMaxColour()), + * view.getAnnotationColours().getAboveThreshold()); } else + */ { sg.cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], @@ -1949,7 +2676,7 @@ public class Jalview2XML { af.viewport.showSequenceFeatures = true; } - + // recover featre settings if (jms.getFeatureSettings() != null) { af.viewport.featuresDisplayed = new Hashtable(); @@ -1958,9 +2685,19 @@ public class Jalview2XML for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); - - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( - setting.getType(), new java.awt.Color(setting.getColour())); + if (setting.hasMincolour()) + { + // TODO: determine how to set data independent bounds for a graduated colour scheme's range. + GraduatedColor gc = 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()); + } + } 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( @@ -1990,141 +2727,72 @@ public class Jalview2XML for (int c = 0; c < view.getHiddenColumnsCount(); c++) { af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view - .getHiddenColumns(c).getEnd() //+1 + .getHiddenColumns(c).getEnd() // +1 ); } } af.setMenusFromViewport(af.viewport); - + // TODO: we don't need to do this if the viewport is aready visible. Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view .getHeight()); + return af; + } - //LOAD TREES - /////////////////////////////////////// - if (loadTreesAndStructures && jms.getTreeCount() > 0) - { - try - { - for (int t = 0; t < jms.getTreeCount(); t++) - { - - Tree tree = jms.getTree(t); - - TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree - .getNewick()), tree.getTitle(), tree.getWidth(), tree - .getHeight(), tree.getXpos(), tree.getYpos()); - - tp.fitToWindow.setState(tree.getFitToWindow()); - tp.fitToWindow_actionPerformed(null); - - if (tree.getFontName() != null) - { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree - .getFontStyle(), tree.getFontSize())); - } - else - { - tp.setTreeFont(new java.awt.Font(view.getFontName(), view - .getFontStyle(), tree.getFontSize())); - } - - tp.showPlaceholders(tree.getMarkUnlinked()); - tp.showBootstrap(tree.getShowBootstrap()); - tp.showDistances(tree.getShowDistances()); - - tp.treeCanvas.threshold = tree.getThreshold(); + Hashtable skipList = null; - if (tree.getCurrentTree()) - { - af.viewport.setCurrentTree(tp.getTree()); - } - } + /** + * TODO remove this method + * + * @param view + * @return AlignFrame bound to sequenceSetId from view, if one exists. private + * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) { + * throw new Error("Implementation Error. No skipList defined for this + * Jalview2XML instance."); } return (AlignFrame) + * skipList.get(view.getSequenceSetId()); } + */ - } catch (Exception ex) + /** + * Check if the Jalview view contained in object should be skipped or not. + * + * @param object + * @return true if view's sequenceSetId is a key in skipList + */ + private boolean skipViewport(JalviewModel object) + { + if (skipList == null) + { + return false; + } + String id; + if (skipList.containsKey(id = object.getJalviewModelSequence() + .getViewport()[0].getSequenceSetId())) + { + if (Cache.log != null && Cache.log.isDebugEnabled()) { - ex.printStackTrace(); + Cache.log.debug("Skipping seuqence set id " + id); } + return true; } + return false; + } - ////LOAD STRUCTURES - if (loadTreesAndStructures) + public void AddToSkipList(AlignFrame af) + { + if (skipList == null) { - for (int i = 0; i < JSEQ.length; i++) - { - if (JSEQ[i].getPdbidsCount() > 0) - { - Pdbids[] ids = JSEQ[i].getPdbids(); - for (int p = 0; p < ids.length; p++) - { - for (int s = 0; s < ids[p].getStructureStateCount(); s++) - { - jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); - - jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId())); - jpdb.setId(ids[p].getId()); - - int x = ids[p].getStructureState(s).getXpos(); - int y = ids[p].getStructureState(s).getYpos(); - int width = ids[p].getStructureState(s).getWidth(); - int height = ids[p].getStructureState(s).getHeight(); - - java.awt.Component comp = null; - - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - for (int f = 0; f < frames.length; f++) - { - if (frames[f] instanceof AppJmol) - { - if (frames[f].getX() == x && frames[f].getY() == y - && frames[f].getHeight() == height - && frames[f].getWidth() == width) - { - comp = frames[f]; - break; - } - } - } - - Desktop.desktop.getComponentAt(x, y); - - String pdbFile = loadPDBFile(file, ids[p].getId()); - - jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[] - { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId() - + "") }; - - if (comp == null) - { - String state = ids[p].getStructureState(s).getContent(); - - StringBuffer newFileLoc = new StringBuffer(state.substring( - 0, state.indexOf("\"", state.indexOf("load")) + 1)); - - newFileLoc.append(jpdb.getFile()); - newFileLoc.append(state.substring(state.indexOf("\"", state - .indexOf("load \"") + 6))); - - new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel, - newFileLoc.toString(), new java.awt.Rectangle(x, y, - width, height)); - - } - else if (comp != null) - { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, null, pdbFile, - jalview.io.AppletFormatAdapter.FILE); - - ((AppJmol) comp).addSequence(seq); - } - } - } - } - } + skipList = new Hashtable(); } + skipList.put(af.getViewport().getSequenceSetId(), af); + } - return af; + public void clearSkipList() + { + if (skipList != null) + { + skipList.clear(); + skipList = null; + } } private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al) @@ -2139,84 +2807,122 @@ public class Jalview2XML for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) { Sequence vamsasSeq = vamsasSet.getSequence(i); - jalview.datamodel.Sequence sq = null; - String sqid = vamsasSeq.getDsseqid(); + ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs); + } + // create a new dataset + if (ds == null) + { + SequenceI[] dsseqs = new SequenceI[dseqs.size()]; + dseqs.copyInto(dsseqs); + ds = new jalview.datamodel.Alignment(dsseqs); + debug("Created new dataset "+vamsasSet.getDatasetId()+" for alignment "+System.identityHashCode(al)); + addDatasetRef(vamsasSet.getDatasetId(), ds); + } + // set the dataset for the newly imported alignment. + if (al.getDataset() == null) + { + al.setDataset(ds); + } + } + + /** + * + * @param vamsasSeq + * sequence definition to create/merge dataset sequence for + * @param ds + * dataset alignment + * @param dseqs + * vector to add new dataset sequence to + */ + private void ensureJalviewDatasetSequence(Sequence vamsasSeq, + AlignmentI ds, Vector dseqs) + { + // JBP TODO: Check this is called for AlCodonFrames to support recovery of + // xRef Codon Maps + jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds + .get(vamsasSeq.getId()); + jalview.datamodel.SequenceI dsq = null; + if (sq != null && sq.getDatasetSequence() != null) + { + dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence(); + } + + String sqid = vamsasSeq.getDsseqid(); + if (dsq == null) + { + // need to create or add a new dataset sequence reference to this sequence if (sqid != null) { - sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq - .getDsseqid()); + dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid); } - if (sq == null) + // check again + if (dsq == null) { - sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId()); - jalview.datamodel.SequenceI dsq = sq.createDatasetSequence(); + // make a new dataset sequence + dsq = sq.createDatasetSequence(); if (sqid == null) { // make up a new dataset reference for this sequence - sqid = "" + dsq.hashCode(); + sqid = seqHash(dsq); } - ((SequenceI) dsq).setVamsasId(uniqueSetSuffix + sqid); + dsq.setVamsasId(uniqueSetSuffix + sqid); seqRefIds.put(sqid, dsq); if (ds == null) { - dseqs.addElement(dsq); + if (dseqs != null) + { + dseqs.addElement(dsq); + } } else { ds.addSequence(dsq); } - } - // TODO: refactor: This is a low-level sequence operation - effectively merging one dataset sequence into another. - // check that dataset sequence really is the union of all references to it - boolean pre = sq.getStart() < sq.getDatasetSequence().getStart(); - boolean post = sq.getEnd() > sq.getDatasetSequence().getEnd(); - if (pre || post) + else { - SequenceI dsq = sq.getDatasetSequence(); - StringBuffer sb = new StringBuffer(); - String newres = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, sq.getSequenceAsString()); + if (sq != dsq) + { // make this dataset sequence sq's dataset sequence + sq.setDatasetSequence(dsq); + } + } + } + // TODO: refactor this as a merge dataset sequence function + // now check that sq (the dataset sequence) sequence really is the union of + // all references to it + // boolean pre = sq.getStart() < dsq.getStart(); + // boolean post = sq.getEnd() > dsq.getEnd(); + // if (pre || post) + if (sq != dsq) + { + StringBuffer sb = new StringBuffer(); + String newres = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, sq.getSequenceAsString()); + if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) + && newres.length() > dsq.getLength()) + { + // Update with the longer sequence. synchronized (dsq) { - sb.append(dsq.getSequence()); - if (pre) - { - sb.insert(0, newres - .substring(0, dsq.getStart() - sq.getStart())); - dsq.setStart(sq.getStart()); - } - if (post) - { - sb.append(newres.substring(newres.length() - sq.getEnd() - - dsq.getEnd())); - dsq.setEnd(sq.getEnd()); - } + /* + * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() - + * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) { + * sb.append(newres.substring(newres.length() - sq.getEnd() - + * dsq.getEnd())); dsq.setEnd(sq.getEnd()); } + */ dsq.setSequence(sb.toString()); } - System.err - .println("DEBUG Notice: Merged dataset sequence (" - + (pre ? "prepended" : "") + " " - + (post ? "appended" : "")); + // TODO: merges will never happen if we 'know' we have the real dataset + // sequence - this should be detected when id==dssid + System.err.println("DEBUG Notice: Merged dataset sequence"); // (" + // + (pre ? "prepended" : "") + " " + // + (post ? "appended" : "")); } } - // create a new dataset - if (ds == null) - { - SequenceI[] dsseqs = new SequenceI[dseqs.size()]; - dseqs.copyInto(dsseqs); - ds = new jalview.datamodel.Alignment(dsseqs); - addDatasetRef(vamsasSet.getDatasetId(), ds); - } - // set the dataset for the newly imported alignment. - if (al.getDataset() == null) - { - al.setDataset(ds); - } } java.util.Hashtable datasetIds = null; - + java.util.IdentityHashMap dataset2Ids = null; private Alignment getDatasetFor(String datasetId) { if (datasetIds == null) @@ -2239,7 +2945,35 @@ public class Jalview2XML } datasetIds.put(datasetId, dataset); } - + /** + * make a new dataset ID for this jalview dataset alignment + * @param dataset + * @return + */ + private String getDatasetIdRef(jalview.datamodel.Alignment dataset) + { + if (dataset.getDataset()!=null) + { + warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment..."); + } + String datasetId=makeHashCode(dataset, null); + if (datasetId==null) + { + // make a new datasetId and record it + if (dataset2Ids == null) + { + dataset2Ids = new IdentityHashMap(); + } else { + datasetId = (String) dataset2Ids.get(dataset); + } + if (datasetId==null) + { + datasetId = "ds"+dataset2Ids.size()+1; + dataset2Ids.put(dataset,datasetId); + } + } + return datasetId; + } private void addDBRefs(SequenceI datasetSequence, Sequence sequence) { for (int d = 0; d < sequence.getDBRefCount(); d++) @@ -2283,34 +3017,61 @@ public class Jalview2XML MappingChoice mc = m.getMappingChoice(); if (mc.getDseqFor() != null) { - if (seqRefIds.containsKey(mc.getDseqFor())) + String dsfor = ""+mc.getDseqFor(); + if (seqRefIds.containsKey(dsfor)) { /** * recover from hash */ - jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor())); + jmap.setTo((SequenceI) seqRefIds.get(dsfor)); } else { frefedSequence.add(new Object[] - { mc.getDseqFor(), jmap }); + { dsfor, jmap }); } } else { /** - * make a new sequence and add it to refIds hash + * local sequence definition */ Sequence ms = mc.getSequence(); - jalview.datamodel.Sequence djs = new jalview.datamodel.Sequence(ms - .getName(), ms.getSequence()); - djs.setStart(jmap.getMap().getToLowest()); - djs.setEnd(jmap.getMap().getToHighest()); - djs.setVamsasId(uniqueSetSuffix + ms.getId()); - jmap.setTo(djs); - seqRefIds.put(ms.getId(), djs); + jalview.datamodel.Sequence djs = null; + String sqid = ms.getDsseqid(); + if (sqid != null && sqid.length() > 0) + { + /* + * recover dataset sequence + */ + djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid); + } + else + { + System.err + .println("Warning - making up dataset sequence id for DbRef sequence map reference"); + sqid = ((Object) ms).toString(); // make up a new hascode for + // undefined dataset sequence hash + // (unlikely to happen) + } + + if (djs == null) + { + /** + * make a new dataset sequence and add it to refIds hash + */ + djs = new jalview.datamodel.Sequence(ms.getName(), ms + .getSequence()); + djs.setStart(jmap.getMap().getToLowest()); + djs.setEnd(jmap.getMap().getToHighest()); + djs.setVamsasId(uniqueSetSuffix + sqid); + jmap.setTo(djs); + seqRefIds.put(sqid, djs); + + } jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); addDBRefs(djs, ms); + } } return (jmap); @@ -2320,37 +3081,223 @@ public class Jalview2XML public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs) { + initSeqRefs(); jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null, - null, null); + null); if (!keepSeqRefs) { - seqRefIds.clear(); + clearSeqRefs(); jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); } else { uniqueSetSuffix = ""; + jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied + } + if (this.frefedSequence==null) + { + frefedSequence = new Vector(); } viewportsAdded = new Hashtable(); - AlignFrame af = LoadFromObject(jm, null, false); + AlignFrame af = LoadFromObject(jm, null, false, null); af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); - /* if(ap.av.alignment.getAlignmentAnnotation()!=null) + /* + * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i