From 5239deac5e593160f37532a0e7e657442ded5311 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 19 Aug 2016 11:18:11 +0100 Subject: [PATCH] =?utf8?q?JAL-2154=20belt-and-braces=20patch:=20*=20when=20d?= =?utf8?q?ataset=20XML=20doc=20is=20read=20in,=20all=20vamsasSet=20sequences?= =?utf8?q?=20should=20be=20processed=20in=20sync=20with=20the=20=E2=80=98vie?= =?utf8?q?w=E2=80=99=20JSeq=20entries=20containing=20start/end=20metadata=20?= =?utf8?q?*=20features,=20dbrefs=20and=20pdbentrys=20are=20now=20added=20dir?= =?utf8?q?ect=20to=20dataset=20sequences,=20but=20old=20behaviour=20should=20?= =?utf8?q?be=20preserved=20for=20reading=20alignment=20views=20containing=20?= =?utf8?q?dbrefs=20that=20get=20propagated=20to=20dataset.?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/gui/Jalview2XML.java | 116 +++++++++++++++++++++++++------------- 1 file changed, 76 insertions(+), 40 deletions(-) diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 9e312db..3125cba 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -793,37 +793,42 @@ 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()); @@ -2814,15 +2819,28 @@ public class Jalview2XML { System.err .println("Warning JAL-2154 regression: updating start/end for sequence " - + tmpSeq.toString()); + + tmpSeq.toString() + " to " + jseqs[i]); } } else { incompleteSeqs.remove(seqId); } + if (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 +2929,12 @@ 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 +2961,17 @@ 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) { @@ -2976,7 +3004,15 @@ public class Jalview2XML } 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 +3041,16 @@ 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); -- 1.7.10.2