X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=1c90889d9ac232a6e93ffdfc1e6e68fa71094748;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=9e312db255208265b04feefca6fa067ec1d47b9b;hpb=a65ca83c82eff63dc3599e9906d547646c43bbb4;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 9e312db..1c90889 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.analysis.Conservation; import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; @@ -313,6 +314,7 @@ public class Jalview2XML } return sq; } + /** * @return true if the forward reference was fully resolved */ @@ -387,35 +389,44 @@ public class Jalview2XML public void resolveFrefedSequences() { - Iterator nextFref=frefedSequence.iterator(); - int toresolve=frefedSequence.size(); - int unresolved=0,failedtoresolve=0; - while (nextFref.hasNext()) { + Iterator nextFref = frefedSequence.iterator(); + int toresolve = frefedSequence.size(); + int unresolved = 0, failedtoresolve = 0; + while (nextFref.hasNext()) + { SeqFref ref = nextFref.next(); if (ref.isResolvable()) { - try { + try + { if (ref.resolve()) { nextFref.remove(); - } else { + } + else + { failedtoresolve++; } - } catch (Exception x) { - System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref()); + } catch (Exception x) + { + System.err + .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence " + + ref.getSref()); x.printStackTrace(); failedtoresolve++; - } - } else { + } + } + else + { unresolved++; } } - if (unresolved>0) + if (unresolved > 0) { System.err.println("Jalview Project Import: There were " + unresolved + " forward references left unresolved on the stack."); } - if (failedtoresolve>0) + if (failedtoresolve > 0) { System.err.println("SERIOUS! " + failedtoresolve + " resolvable forward references failed to resolve."); @@ -793,37 +804,42 @@ public class Jalview2XML JSeq jseq; Set calcIdSet = new HashSet(); - + // record the set of vamsas sequence XML POJO we create. + HashMap vamsasSetIds = new HashMap(); // SAVE SEQUENCES for (final SequenceI jds : rjal.getSequences()) { final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds : jds.getDatasetSequence(); String 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, jds); + if (vamsasSetIds.get(id) == null) + { + if (seqRefIds.get(id) != null && !storeDS) + { + // 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); + vamsasSetIds.put(id, vamsasSeq); + seqRefIds.put(id, jds); + } } - jseq = new JSeq(); jseq.setStart(jds.getStart()); jseq.setEnd(jds.getEnd()); @@ -842,8 +858,7 @@ public class Jalview2XML if (av.isHiddenRepSequence(jds)) { jalview.datamodel.SequenceI[] reps = av - .getRepresentedSequences(jds) - .getSequencesInOrder(rjal); + .getRepresentedSequences(jds).getSequencesInOrder(rjal); for (int h = 0; h < reps.length; h++) { @@ -977,17 +992,16 @@ public class Jalview2XML } } - if (entry.getProperty() != null && !entry.getProperty().isEmpty()) + Enumeration props = entry.getProperties(); + if (props.hasMoreElements()) { PdbentryItem item = new PdbentryItem(); - Hashtable properties = entry.getProperty(); - Enumeration en2 = properties.keys(); - while (en2.hasMoreElements()) + while (props.hasMoreElements()) { Property prop = new Property(); - String key = en2.nextElement().toString(); + String key = props.nextElement(); prop.setName(key); - prop.setValue(properties.get(key).toString()); + prop.setValue(entry.getProperty(key).toString()); item.addProperty(prop); } pdb.addPdbentryItem(item); @@ -1335,8 +1349,7 @@ public class Jalview2XML for (String featureType : renderOrder) { FeatureColourI fcol = ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getFeatureStyle(featureType); + .getFeatureRenderer().getFeatureStyle(featureType); Setting setting = new Setting(); setting.setType(featureType); if (!fcol.isSimpleColour()) @@ -1349,8 +1362,8 @@ public class Jalview2XML setting.setAutoScale(fcol.isAutoScaled()); setting.setThreshold(fcol.getThreshold()); // -1 = No threshold, 0 = Below, 1 = Above - setting.setThreshstate(fcol.isAboveThreshold() ? 1 - : (fcol.isBelowThreshold() ? 0 : -1)); + setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol + .isBelowThreshold() ? 0 : -1)); } else { @@ -1372,8 +1385,7 @@ public class Jalview2XML // is groups actually supposed to be a map here ? Iterator en = ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getFeatureGroups().iterator(); + .getFeatureRenderer().getFeatureGroups().iterator(); Vector groupsAdded = new Vector(); while (en.hasNext()) { @@ -2531,6 +2543,8 @@ public class Jalview2XML SplitFrame sf = createSplitFrame(dnaFrame, af); addedToSplitFrames.add(dnaFrame); addedToSplitFrames.add(af); + dnaFrame.setMenusForViewport(); + af.setMenusForViewport(); if (af.viewport.isGatherViewsHere()) { gatherTo.add(sf); @@ -2552,6 +2566,7 @@ public class Jalview2XML Viewport view = candidate.getKey(); Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); + af.setMenusForViewport(); System.err.println("Failed to restore view " + view.getTitle() + " to split frame"); } @@ -2655,14 +2670,16 @@ public class Jalview2XML * @param pdbId * @return */ - String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) + String loadPDBFile(jarInputStreamProvider jprovider, String pdbId, + String origFile) { if (alreadyLoadedPDB.containsKey(pdbId)) { return alreadyLoadedPDB.get(pdbId).toString(); } - String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb"); + String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb", + origFile); if (tempFile != null) { alreadyLoadedPDB.put(pdbId, tempFile); @@ -2679,14 +2696,26 @@ public class Jalview2XML * @param prefix * a prefix for the temporary file name, must be at least three * characters long + * @param origFile + * null or original file - so new file can be given the same suffix + * as the old one * @return */ protected String copyJarEntry(jarInputStreamProvider jprovider, - String jarEntryName, String prefix) + String jarEntryName, String prefix, String origFile) { BufferedReader in = null; PrintWriter out = null; - + String suffix = ".tmp"; + if (origFile == null) + { + origFile = jarEntryName; + } + int sfpos = origFile.lastIndexOf("."); + if (sfpos > -1 && sfpos < (origFile.length() - 3)) + { + suffix = "." + origFile.substring(sfpos + 1); + } try { JarInputStream jin = jprovider.getJarInputStream(); @@ -2704,7 +2733,7 @@ public class Jalview2XML if (entry != null) { in = new BufferedReader(new InputStreamReader(jin, UTF_8)); - File outFile = File.createTempFile(prefix, ".tmp"); + File outFile = File.createTempFile(prefix, suffix); outFile.deleteOnExit(); out = new PrintWriter(new FileOutputStream(outFile)); String data; @@ -2793,7 +2822,6 @@ public class Jalview2XML List hiddenSeqs = null; - List tmpseqs = new ArrayList(); boolean multipleView = false; @@ -2810,19 +2838,35 @@ public class Jalview2XML if (!incompleteSeqs.containsKey(seqId)) { // may not need this check, but keep it for at least 2.9,1 release - if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd()) - { + if (tmpSeq.getStart() != jseqs[i].getStart() + || tmpSeq.getEnd() != jseqs[i].getEnd()) + { System.err .println("Warning JAL-2154 regression: updating start/end for sequence " - + tmpSeq.toString()); + + tmpSeq.toString() + " to " + jseqs[i]); } - } else { + } + else + { incompleteSeqs.remove(seqId); } + if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId)) + { + // most likely we are reading a dataset XML document so + // update from vamsasSeq section of XML for this sequence + tmpSeq.setName(vamsasSeq[vi].getName()); + tmpSeq.setDescription(vamsasSeq[vi].getDescription()); + tmpSeq.setSequence(vamsasSeq[vi].getSequence()); + vi++; + } + else + { + // reading multiple views, so vamsasSeq set is a subset of JSeq + multipleView = true; + } tmpSeq.setStart(jseqs[i].getStart()); tmpSeq.setEnd(jseqs[i].getEnd()); tmpseqs.add(tmpSeq); - multipleView = true; } else { @@ -2911,6 +2955,12 @@ public class Jalview2XML { // load sequence features, database references and any associated PDB // structures for the alignment + // + // prior to 2.10, this part would only be executed the first time a + // sequence was encountered, but not afterwards. + // now, for 2.10 projects, this is also done if the xml doc includes + // dataset sequences not actually present in any particular view. + // for (int i = 0; i < vamsasSeq.length; i++) { if (jseqs[i].getFeaturesCount() > 0) @@ -2937,13 +2987,17 @@ public class Jalview2XML } } - - al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + // adds feature to datasequence's feature set (since Jalview 2.10) + al.getSequenceAt(i).addSequenceFeature(sf); } } if (vamsasSeq[i].getDBRefCount() > 0) { - addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); + // adds dbrefs to datasequence's set (since Jalview 2.10) + addDBRefs( + al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i) + : al.getSequenceAt(i).getDatasetSequence(), + vamsasSeq[i]); } if (jseqs[i].getPdbidsCount() > 0) { @@ -2954,29 +3008,49 @@ public class Jalview2XML entry.setId(ids[p].getId()); if (ids[p].getType() != null) { - if (ids[p].getType().equalsIgnoreCase("PDB")) + if (PDBEntry.Type.getType(ids[p].getType()) != null) { - entry.setType(PDBEntry.Type.PDB); + entry.setType(PDBEntry.Type.getType(ids[p].getType())); } else { entry.setType(PDBEntry.Type.FILE); } } - if (ids[p].getFile() != null) + // jprovider is null when executing 'New View' + if (ids[p].getFile() != null && jprovider != null) { if (!pdbloaded.containsKey(ids[p].getFile())) { - entry.setFile(loadPDBFile(jprovider, ids[p].getId())); + entry.setFile(loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile())); } else { entry.setFile(pdbloaded.get(ids[p].getId()).toString()); } } + if (ids[p].getPdbentryItem() != null) + { + for (PdbentryItem item : ids[p].getPdbentryItem()) + { + for (Property pr : item.getProperty()) + { + entry.setProperty(pr.getName(), pr.getValue()); + } + } + } StructureSelectionManager.getStructureSelectionManager( Desktop.instance).registerPDBEntry(entry); - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + // adds PDBEntry to datasequence's set (since Jalview 2.10) + if (al.getSequenceAt(i).getDatasetSequence() != null) + { + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + else + { + al.getSequenceAt(i).addPDBId(entry); + } } } } @@ -3005,16 +3079,16 @@ public class Jalview2XML if (maps[m].getMapping() != null) { mapping = addMapping(maps[m].getMapping()); - } - if (dnaseq != null && mapping.getTo() != null) - { - cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); - } - else - { - // defer to later - frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf, - mapping)); + if (dnaseq != null && mapping.getTo() != null) + { + cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); + } + else + { + // defer to later + frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf, + mapping)); + } } } al.addCodonFrame(cf); @@ -3327,8 +3401,7 @@ public class Jalview2XML } if (jGroup.getConsThreshold() != 0) { - jalview.analysis.Conservation c = new jalview.analysis.Conservation( - "All", ResidueProperties.propHash, 3, + Conservation c = new Conservation("All", 3, sg.getSequences(null), 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); @@ -3518,7 +3591,7 @@ public class Jalview2XML String rnaTitle = ss.getTitle(); String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, - "varna"); + "varna", null); RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); appVarna.addModelSession(rna, rnaTitle, tempStateFile); } @@ -3693,7 +3766,8 @@ public class Jalview2XML // 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.setFile(loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile())); jpdb.setId(ids[p].getId()); int x = structureState.getXpos(); @@ -3704,7 +3778,8 @@ public class Jalview2XML // 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()); + String pdbFile = loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile()); jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i] .getId() + ""); if (sviewid == null) @@ -3864,7 +3939,7 @@ public class Jalview2XML */ String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera"); + "chimera", null); Set> fileData = data.getFileData() .entrySet(); @@ -3945,6 +4020,11 @@ public class Jalview2XML // filename // translation differently. StructureData filedat = oldFiles.get(new File(oldfilenam)); + if (filedat == null) + { + String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\"); + filedat = oldFiles.get(new File(reformatedOldFilename)); + } newFileLoc.append(Platform.escapeString(filedat.getFilePath())); pdbfilenames.add(filedat.getFilePath()); pdbids.add(filedat.getPdbId()); @@ -4904,7 +4984,7 @@ public class Jalview2XML for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) { Sequence vamsasSeq = vamsasSet.getSequence(i); - ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed); + ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i); } // create a new dataset if (ds == null) @@ -4931,18 +5011,29 @@ public class Jalview2XML * dataset alignment * @param dseqs * vector to add new dataset sequence to + * @param ignoreUnrefed + * - when true, don't create new sequences from vamsasSeq if it's id + * doesn't already have an asssociated Jalview sequence. + * @param vseqpos + * - used to reorder the sequence in the alignment according to the + * vamsasSeq array ordering, to preserve ordering of dataset */ private void ensureJalviewDatasetSequence(Sequence vamsasSeq, - AlignmentI ds, Vector dseqs, boolean ignoreUnrefed) + AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos) { // JBP TODO: Check this is called for AlCodonFrames to support recovery of // xRef Codon Maps SequenceI sq = seqRefIds.get(vamsasSeq.getId()); + boolean reorder = false; SequenceI dsq = null; if (sq != null && sq.getDatasetSequence() != null) { dsq = sq.getDatasetSequence(); } + else + { + reorder = true; + } if (sq == null && ignoreUnrefed) { return; @@ -5038,6 +5129,35 @@ public class Jalview2XML // + (post ? "appended" : "")); } } + else + { + // sequence refs are identical. We may need to update the existing dataset + // alignment with this one, though. + if (ds != null && dseqs == null) + { + int opos = ds.findIndex(dsq); + SequenceI tseq = null; + if (opos != -1 && vseqpos != opos) + { + // remove from old position + ds.deleteSequence(dsq); + } + if (vseqpos < ds.getHeight()) + { + if (vseqpos != opos) + { + // save sequence at destination position + tseq = ds.getSequenceAt(vseqpos); + ds.replaceSequenceAt(vseqpos, dsq); + ds.addSequence(tseq); + } + } + else + { + ds.addSequence(dsq); + } + } + } } /*