IdentityHashMap jv2vobj;
+ Hashtable alignRDHash;
+
public VamsasAppDatastore(IClientDocument cdoc, Hashtable vobj2jv,
- IdentityHashMap jv2vobj, Entry provEntry)
+ IdentityHashMap jv2vobj, Entry provEntry, Hashtable alignRDHash)
{
this.cdoc = cdoc;
this.vobj2jv = vobj2jv;
this.jv2vobj = jv2vobj;
this.provEntry = provEntry;
+ this.alignRDHash = alignRDHash;
}
/**
root.addDataSet(dataset);
bindjvvobj(jal.getDataset(), dataset);
dataset.setProvenance(dummyProvenance());
- dataset.getProvenance().addEntry(provEntry);
+ // dataset.getProvenance().addEntry(provEntry);
nw = true;
}
else
// acid sequences.
String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
: uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
+ Vector dssmods = new Vector();
for (int i = 0; i < jal.getHeight(); i++)
{
SequenceI sq = jal.getSequenceAt(i).getDatasetSequence(); // only insert
sq.setVamsasId(sequence.getVorbaId().getId());
sequence.setSequence(sq.getSequenceAsString());
sequence.setDictionary(dict);
- sequence.setName(jal.getDataset().getSequenceAt(i).getName());
- sequence.setStart(jal.getDataset().getSequenceAt(i).getStart());
- sequence.setEnd(jal.getDataset().getSequenceAt(i).getEnd());
- sequence.setDescription(jal.getDataset().getSequenceAt(i)
- .getDescription());
+ sequence.setName(sq.getName());
+ sequence.setStart(sq.getStart());
+ sequence.setEnd(sq.getEnd());
+ sequence.setDescription(sq.getDescription());
dataset.addSequence(sequence);
+ dssmods.addElement(dssmods);
}
else
{
- // verify principal attributes. and update any new
- // features/references.
- System.out.println("update dataset sequence object.");
+ boolean dsmod = false;
+ // verify and update principal attributes.
+ if (sq.getDescription()!=null && (sequence.getDescription()==null || !sequence.getDescription().equals(sq.getDescription())))
+ {
+ sequence.setDescription(sq.getDescription());
+ dsmod = true;
+ }
+ if (sequence.getSequence()==null || !sequence.getSequence().equals(sq.getSequenceAsString()))
+ {
+ if (sequence.getStart()!=sq.getStart() || sequence.getEnd()!=sq.getEnd())
+ {
+ // update modified sequence.
+ sequence.setSequence(sq.getSequenceAsString());
+ sequence.setStart(sq.getStart());
+ sequence.setEnd(sq.getEnd());
+ dsmod = true;
+ }
+ }
+ if (!dict.equals(sequence.getDictionary()))
+ {
+ sequence.setDictionary(dict);
+ dsmod = true;
+ }
+ if (!sequence.getName().equals(sq.getName()))
+ {
+ sequence.setName(sq.getName());
+ dsmod = true;
+ }
+ if (dsmod)
+ {
+ dssmods.addElement(sequence);
+ }
}
+ // add or update any new features/references on dataset sequence
if (sq.getSequenceFeatures() != null)
{
int sfSize = sq.getSequenceFeatures().length;
for (int sf = 0; sf < sfSize; sf++)
{
+ // TODO: update/modifiable synchronizer
jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
.getSequenceFeatures()[sf];
}
}
+ if (dssmods.size()>0)
+ {
+ if (!nw)
+ {
+ Entry pentry = this.addProvenance(dataset.getProvenance(), "updated sequences");
+ // pentry.addInput(vInput); could write in which sequences were modified.
+ dssmods.removeAllElements();
+ }
+ }
// dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
// ////////////////////////////////////////////
if (!av.getAlignment().isAligned())
return; // TODO: trees could be written - but for the moment we just skip
-
// ////////////////////////////////////////////
// Save the Alignments
alignment.addProperty(title);
}
alignment.setGapChar(String.valueOf(av.getGapCharacter()));
- AlignmentSequence alseq = null;
for (int i = 0; i < jal.getHeight(); i++)
{
- alseq = new AlignmentSequence();
- // TODO: VAMSAS: translate lowercase symbols to annotation ?
- alseq.setSequence(jal.getSequenceAt(i).getSequenceAsString());
- alseq.setName(jal.getSequenceAt(i).getName());
- alseq.setStart(jal.getSequenceAt(i).getStart());
- alseq.setEnd(jal.getSequenceAt(i).getEnd());
- if (getjv2vObj(jal.getSequenceAt(i).getDatasetSequence()) == null)
- {
- Cache.log
- .warn("Serious. Unbound dataset sequence in alignment: "
- + jal.getSequenceAt(i).getDatasetSequence());
- }
- alseq.setRefid(getjv2vObj(jal.getSequenceAt(i)
- .getDatasetSequence()));
- alignment.addAlignmentSequence(alseq);
- bindjvvobj(jal.getSequenceAt(i), alseq);
+ syncToAlignmentSequence(jal.getSequenceAt(i), alignment);
}
+ alignRDHash.put(av.getSequenceSetId(),av.getUndoRedoHash());
}
else
{
+ boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash.get(av.getSequenceSetId()));
// todo: verify and update mutable alignment props.
- if (alignment.getModifiable() == null) // TODO: USE VAMSAS LIBRARY
- // OBJECT LOCK METHODS
+ // TODO: Use isLocked methods
+ if (alignment.getModifiable() == null || alignment.getModifiable().length()==0)
{
+ boolean modified = false;
+ for (int i = 0; i < jal.getHeight(); i++)
+ {
+ modified |= syncToAlignmentSequence(jal.getSequenceAt(i), alignment);
+ }
+ if (modified)
+ {
+ if (alismod)
+ {
+ // info in the undo
+ addProvenance(alignment.getProvenance(), "Edited"); // TODO: insert something sensible here again
+ }
+ else {
+ // info in the undo
+ addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO: insert something sensible here again
+ }
+ }
System.out.println("update alignment in document.");
}
else
}
}
+ /**
+ * sync a jalview alignment seuqence into a vamsas alignment
+ * assumes all lock transformation/bindings have been sorted out before hand.
+ * creates/syncs the vamsas alignment sequence for jvalsq and adds it to the alignment if necessary.
+ */
+ private boolean syncToAlignmentSequence(SequenceI jvalsq,
+ Alignment alignment)
+ {
+ boolean modal = false;
+ // todo: islocked method here
+ boolean up2doc=false;
+ AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq);
+ if (alseq==null)
+ {
+ alseq = new AlignmentSequence();
+ up2doc = true;
+ }
+ // boolean locked = (alignment.getModifiable()==null || alignment.getModifiable().length()>0);
+ // TODO: VAMSAS: translate lowercase symbols to annotation ?
+ if (up2doc || !alseq.getSequence().equals(jvalsq.getSequenceAsString()))
+ {
+ alseq.setSequence(jvalsq.getSequenceAsString());
+ alseq.setStart(jvalsq.getStart());
+ alseq.setEnd(jvalsq.getEnd());
+ modal = true;
+ }
+ if (up2doc || !alseq.getName().equals(jvalsq.getName()))
+ {
+ modal = true;
+ alseq.setName(jvalsq.getName());
+ }
+ if (jvalsq.getDescription()!=null && (alseq.getDescription()==null || !jvalsq.getDescription().equals(alseq.getDescription())))
+ {
+ modal = true;
+ alseq.setDescription(jvalsq.getDescription());
+ }
+ if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
+ {
+ Cache.log
+ .warn("Serious Implementation error - Unbound dataset sequence in alignment: "
+ + jvalsq.getDatasetSequence());
+ }
+ alseq.setRefid(getjv2vObj(jvalsq
+ .getDatasetSequence()));
+ if (up2doc)
+ {
+
+ alignment.addAlignmentSequence(alseq);
+ bindjvvobj(jvalsq, alseq);
+ }
+ return up2doc || modal;
+ }
+ /**
+ * locally sync a jalview alignment seuqence from a vamsas alignment
+ * assumes all lock transformation/bindings have been sorted out before hand.
+ * creates/syncs the jvalsq from the alignment sequence
+ */
+ private boolean syncFromAlignmentSequence(AlignmentSequence valseq, char valGapchar, char gapChar, Vector dsseqs)
+
+ {
+ boolean modal = false;
+ // todo: islocked method here
+ boolean upFromdoc=false;
+ jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
+ if (alseq==null)
+ {
+ upFromdoc = true;
+ }
+ if (alseq != null)
+ {
+
+ // boolean locked = (alignment.getModifiable()==null || alignment.getModifiable().length()>0);
+ // TODO: VAMSAS: translate lowercase symbols to annotation ?
+ if (upFromdoc || !valseq.getSequence().equals(alseq.getSequenceAsString()))
+ {
+ // this might go *horribly* wrong
+ alseq.setSequence(new String(valseq.getSequence()).replace(
+ valGapchar, gapChar));
+ alseq.setStart((int) valseq.getStart());
+ alseq.setEnd((int) valseq.getEnd());
+ modal = true;
+ }
+ if (!valseq.getName().equals(alseq.getName()))
+ {
+ modal = true;
+ alseq.setName(valseq.getName());
+ }
+ if (alseq.getDescription()==null
+ || (valseq.getDescription()==null
+ || alseq.getDescription().equals(valseq.getDescription())))
+ {
+ alseq.setDescription(valseq.getDescription());
+ modal = true;
+ }
+ if (modal && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Updating apparently edited sequence "
+ + alseq.getName());
+ }
+ }
+ else
+ {
+ alseq = new jalview.datamodel.Sequence(valseq.getName(),
+ valseq.getSequence().replace(valGapchar, gapChar),
+ (int) valseq.getStart(), (int) valseq.getEnd());
+
+ Vobject datsetseq = (Vobject) valseq.getRefid();
+ if (datsetseq != null)
+ {
+ alseq
+ .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
+ // if
+ // AlignemntSequence
+ // reference
+ // isn't
+ // a
+ // simple
+ // SequenceI
+ }
+ else
+ {
+ Cache.log
+ .error("Invalid dataset sequence id (null) for alignment sequence "
+ + valseq.getVorbaId());
+ }
+ bindjvvobj(alseq, valseq);
+ alseq.setVamsasId(valseq.getVorbaId().getId());
+ dsseqs.add(alseq);
+ }
+ Vobject datsetseq = (Vobject) valseq.getRefid();
+ if (datsetseq != null)
+ {
+ if (datsetseq != alseq.getDatasetSequence())
+ {
+ modal = true;
+ }
+ alseq
+ .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
+ }
+ return upFromdoc || modal;
+ }
private void initRangeAnnotationType(RangeAnnotation an,
AlignmentAnnotation alan, int[] gapMap)
}
iSize = alignment.getAlignmentSequenceCount();
boolean newal = (jal == null) ? true : false;
+ boolean refreshal = false;
Vector newasAnnots = new Vector();
char gapChar = ' '; // default for new alignments read in from the
// document
for (i = 0; i < iSize; i++)
{
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
- jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
- if (alseq != null)
+ jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
+ if (syncFromAlignmentSequence(valseq, valGapchar, gapChar, dsseqs) && alseq!=null)
{
- // TODO: upperCase/LowerCase situation here ? do we allow it ?
- // if (!alseq.getSequence().equals(valseq.getSequence())) {
- // throw new Error("Broken! - mismatch of dataset sequence and
- // jalview internal dataset sequence.");
- if (Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Updating apparently edited sequence "
- + alseq.getName());
- }
- // this might go *horribly* wrong
- alseq.setSequence(new String(valseq.getSequence()).replace(
- valGapchar, gapChar));
+
+ // updated to sequence from the document
jremain--;
- }
- else
- {
- alseq = new jalview.datamodel.Sequence(valseq.getName(),
- valseq.getSequence().replace(valGapchar, gapChar),
- (int) valseq.getStart(), (int) valseq.getEnd());
-
- Vobject datsetseq = (Vobject) valseq.getRefid();
- if (datsetseq != null)
- {
- alseq
- .setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
- // if
- // AlignemntSequence
- // reference
- // isn't
- // a
- // simple
- // SequenceI
- }
- else
- {
- Cache.log
- .error("Invalid dataset sequence id (null) for alignment sequence "
- + valseq.getVorbaId());
- }
- bindjvvobj(alseq, valseq);
- alseq.setVamsasId(valseq.getVorbaId().getId());
- dsseqs.add(alseq);
+ refreshal = true;
}
if (valseq.getAlignmentSequenceAnnotationCount() > 0)
{
// TODO: fix this so we retrieve the alignFrame handing av
// *directly*
alignFrame = getAlignFrameFor(av);
+ if (refreshal)
+ {
+ av.alignmentChanged(alignFrame.alignPanel);
+ }
}
// LOAD TREES
// /////////////////////////////////////
return prov;
}
- void addProvenance(Provenance p, String action)
+ Entry addProvenance(Provenance p, String action)
{
- p.addEntry(dummyPEntry(action));
+ Entry dentry = dummyPEntry(action);
+ p.addEntry(dentry);
+ return dentry;
}
public Entry getProvEntry()
git://source.jalview.org / jalview.git / commitdiff