/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-
package jalview.io;
import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.TreePanel;
+import jalview.io.vamsas.Datasetsequence;
import jalview.io.vamsas.DatastoreItem;
+import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
+import jalview.util.UrlLink;
+import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.IdentityHashMap;
+import java.util.Iterator;
import java.util.Vector;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
import uk.ac.vamsas.client.*;
import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.objects.utils.Properties;
/*
*
* "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
*
*/
-
+/*
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
+ */
public class VamsasAppDatastore
{
/**
public static final String JALVIEW_ANNOTATION_ROW = "JalviewAnnotation";
/**
- * AlignmentAnnotation property to indicate that values should not be interpolated
+ * AlignmentAnnotation property to indicate that values should not be
+ * interpolated
*/
public static final String DISCRETE_ANNOTATION = "discrete";
+
/**
- * continuous property - optional to specify that annotation should be represented
- * as a continous graph line
+ * continuous property - optional to specify that annotation should be
+ * represented as a continous graph line
*/
private static final String CONTINUOUS_ANNOTATION = "continuous";
- private static final String THRESHOLD = "threshold";
-
+ private static final String THRESHOLD = "threshold";
+ /**
+ * template for provenance entries written to vamsas session document
+ */
Entry provEntry = null;
+ /**
+ * Instance of the session document being synchronized with
+ */
IClientDocument cdoc;
+ /**
+ * map Vorba (vamsas object xml ref) IDs to live jalview object references
+ */
Hashtable vobj2jv;
+ /**
+ * map live jalview object references to Vorba IDs
+ */
IdentityHashMap jv2vobj;
+ /**
+ * map jalview sequence set ID (which is vorba ID for alignment) to last
+ * recorded hash value for the alignment viewport (the undo/redo hash value)
+ */
+ 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;
+ buildSkipList();
+ }
+
+ /**
+ * the skipList used to skip over views from Jalview Appdata's that we've
+ * already syncrhonized
+ */
+ Hashtable skipList;
+
+ private void buildSkipList()
+ {
+ skipList = new Hashtable();
+ AlignFrame[] al = Desktop.getAlignframes();
+ for (int f = 0; al != null && f < al.length; f++)
+ {
+ skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
+ }
}
/**
{
return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
+ // check if we're working with a string - then workaround
+ // the use of IdentityHashTable because different strings
+ // have different object IDs.
+ if (jvobj instanceof String)
+ {
+ Object seqsetidobj = null;
+ seqsetidobj = getVamsasObjectBinding().get(jvobj);
+ if (seqsetidobj != null)
+ {
+ if (seqsetidobj instanceof String)
+ {
+ // what is expected. object returned by av.getSequenceSetId() -
+ // reverse lookup to get the 'registered' instance of this string
+ Vobject obj = getjv2vObj(seqsetidobj);
+ if (obj != null && !(obj instanceof Alignment))
+ {
+ Cache.log
+ .warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ + seqsetidobj + " to object " + obj);
+ }
+ return obj;
+ }
+ else
+ {
+ Cache.log.warn("Unexpected mapping for Jalview String Object ID "
+ + seqsetidobj + " to another jalview dataset object "
+ + seqsetidobj);
+ }
+ }
+ }
+
if (Cache.log.isDebugEnabled())
{
Cache.log.debug("Returning null VorbaID binding for jalview object "
* alignViewport to be stored
* @param aFtitle
* title for alignment
+ * @return true if alignment associated with viewport was stored/synchronized
+ * to document
*/
- public void storeVAMSAS(AlignViewport av, String aFtitle)
+ public boolean storeVAMSAS(AlignViewport av, String aFtitle)
{
try
{
jalview.datamodel.AlignmentI jal = av.getAlignment();
+ jalview.datamodel.AlignmentI jds = jal.getDataset();
boolean nw = false;
VAMSAS root = null; // will be resolved based on Dataset Parent.
// /////////////////////////////////////////
// SAVE THE DATASET
DataSet dataset = null;
- if (jal.getDataset() == null)
+ if (jds == null)
{
Cache.log.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
+ jds = jal.getDataset();
}
- dataset = (DataSet) getjv2vObj(jal.getDataset());
+
+ // try and get alignment and association for sequence set id
+
+ Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId());
+ if (alignment != null)
+ {
+ dataset = (DataSet) alignment.getV_parent();
+ }
+ else
+ {
+ // is the dataset already registered
+ dataset = (DataSet) getjv2vObj(jds);
+ }
+
if (dataset == null)
{
// it might be that one of the dataset sequences does actually have a
- // binding, so search for it indirectly.
- jalview.datamodel.SequenceI[] jdatset = jal.getDataset()
- .getSequencesArray();
+ // binding, so search for it indirectly. If it does, then the local
+ // jalview dataset
+ // must be merged with the existing vamsas dataset.
+ jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray();
for (int i = 0; i < jdatset.length; i++)
{
Vobject vbound = getjv2vObj(jdatset[i]);
}
else
{
- if (dataset != vbound.getV_parent())
+ if (vbound.getV_parent() != null
+ && dataset != vbound.getV_parent())
{
throw new Error(
- "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from datasets into the vamsas document.");
+ "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
// This occurs because the dataset for the alignment we are
// trying to
}
if (dataset == null)
{
+ Cache.log.warn("Creating new vamsas dataset for alignment view "
+ + av.getSequenceSetId());
// we create a new dataset on the default vamsas root.
root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
dataset = new DataSet();
root.addDataSet(dataset);
- bindjvvobj(jal.getDataset(), dataset);
+ bindjvvobj(jds, dataset);
dataset.setProvenance(dummyProvenance());
- dataset.getProvenance().addEntry(provEntry);
+ // dataset.getProvenance().addEntry(provEntry);
nw = true;
}
else
}
// update dataset
Sequence sequence;
- DbRef dbref;
// set new dataset and alignment sequences based on alignment Nucleotide
// flag.
// this *will* break when alignment contains both nucleotide and amino
// 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
// referenced
// sequences
// to dataset.
- sequence = (Sequence) getjv2vObj(sq);
- if (sequence == null)
- {
- sequence = new Sequence();
- bindjvvobj(sq, sequence);
- 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());
- dataset.addSequence(sequence);
- }
- else
+ Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(
+ this, sq, dict, dataset);
+ sequence = (Sequence) dssync.getVobj();
+ if (dssync.getModified())
{
- // verify principal attributes. and update any new
- // features/references.
- System.out.println("update dataset sequence object.");
+ dssmods.addElement(sequence);
}
- if (sq.getSequenceFeatures() != null)
- {
- int sfSize = sq.getSequenceFeatures().length;
-
- for (int sf = 0; sf < sfSize; sf++)
- {
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf];
-
- DataSetAnnotations dsa = (DataSetAnnotations) getjv2vObj(feature);
- if (dsa == null)
- {
- dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
- new DataSetAnnotations(), feature);
- if (dsa.getProvenance() == null)
- {
- dsa.setProvenance(new Provenance());
- }
- addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
- // to update
- dsa.addSeqRef(sequence); // we have just created this annotation
- // - so safe to use this
- bindjvvobj(feature, dsa);
- dataset.addDataSetAnnotations(dsa);
- }
- else
- {
- // todo: verify and update dataset annotations for sequence
- System.out.println("update dataset sequence annotations.");
- }
- }
- }
-
- if (sq.getDBRef() != null)
+ ;
+ }
+ if (dssmods.size() > 0)
+ {
+ if (!nw)
{
- DBRefEntry[] entries = sq.getDBRef();
- jalview.datamodel.DBRefEntry dbentry;
- for (int db = 0; db < entries.length; db++)
- {
- Rangetype dbr = new jalview.io.vamsas.Dbref(this,
- dbentry = entries[db], sq, sequence);
- }
-
+ 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
+ if (alignmentWillBeSkipped(av))
+ {
+ // TODO: trees could be written - but for the moment we just
+ addToSkipList(av);
+ // add to the JalviewXML skipList and ..
+ return false;
+ }
- Alignment alignment = (Alignment) getjv2vObj(av); // this is so we can get
- // the alignviewport
- // back
if (alignment == null)
{
alignment = new Alignment();
- bindjvvobj(av, alignment);
+ bindjvvobj(av.getSequenceSetId(), alignment);
if (alignment.getProvenance() == null)
{
alignment.setProvenance(new Provenance());
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, null);
}
+ alignRDHash.put(av.getSequenceSetId(), av.getUndoRedoHash());
}
else
{
+ // always prepare to clone the alignment
+ 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)
+ // && !alignment.isDependedOn())
{
- System.out.println("update alignment in document.");
+ boolean modified = false;
+ // check existing sequences in local and in document.
+ Vector docseqs = new Vector(
+ alignment.getAlignmentSequenceAsReference());
+ for (int i = 0; i < jal.getHeight(); i++)
+ {
+ modified |= syncToAlignmentSequence(jal.getSequenceAt(i),
+ alignment, docseqs);
+ }
+ if (docseqs.size() > 0)
+ {
+ // removeValignmentSequences(alignment, docseqs);
+ docseqs.removeAllElements();
+ System.out
+ .println("Sequence deletion from alignment is not implemented.");
+
+ }
+ 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
+ }
+ }
+ if (alismod)
+ {
+ System.out.println("update alignment in document.");
+ }
+ else
+ {
+ System.out.println("alignment in document left unchanged.");
+ }
}
else
{
+ // unbind alignment from view.
+ // create new binding and new alignment.
+ // mark trail on new alignment as being derived from old ?
System.out
.println("update edited alignment to new alignment in document.");
}
* jalview.datamodel.SequenceFeature[] features = alseq
* .getSequenceFeatures(); for (int f = 0; f < features.length; f++) {
* if (features[f] != null) { AlignmentSequenceAnnotation valseqf = (
- * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf ==
- * null) {
+ * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf
+ * == null) {
*
* valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
* new AlignmentSequenceAnnotation(), features[i]);
* valseqf.setGraph(false);
- * valseqf.addProperty(newProperty("jalview:feature","boolean","true"));
- * if (valseqf.getProvenance() == null) { valseqf.setProvenance(new
- * Provenance()); } addProvenance(valseqf.getProvenance(), "created"); //
- * JBPNote - // need to // update bindjvvobj(features[i], valseqf);
- * valseq.addAlignmentSequenceAnnotation(valseqf); } }
- * }
+ * valseqf.addProperty(newProperty("jalview:feature"
+ * ,"boolean","true")); if (valseqf.getProvenance() == null) {
+ * valseqf.setProvenance(new Provenance()); }
+ * addProvenance(valseqf.getProvenance(), "created"); // JBPNote - //
+ * need to // update bindjvvobj(features[i], valseqf);
+ * valseq.addAlignmentSequenceAnnotation(valseqf); } } }
*/
}
}
{
continue;
}
+ if (aa[i].groupRef != null)
+ {
+ // TODO: store any group associated annotation references
+ Cache.log
+ .warn("Group associated sequence annotation is not stored in VAMSAS document.");
+ continue;
+ }
if (aa[i].sequenceRef != null)
{
// Deal with sequence associated annotation
an.setDescription(aa[i].description);
alignment.addAlignmentAnnotation(an);
Seg vSeg = new Seg(); // TODO: refactor to have a default
- // rangeAnnotationType initer/updater that
- // takes a set of int ranges.
+ // rangeAnnotationType initer/updater that
+ // takes a set of int ranges.
vSeg.setStart(1);
vSeg.setInclusive(true);
vSeg.setEnd(jal.getWidth());
if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
{
an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote
- // -
+ // -
// originally we
// were going to
// store
// of
// utf8
// translation
- ae.addValue(aa[i].annotations[a].value);
+ if (an.isGraph())
+ {
+ ae.addValue(aa[i].annotations[a].value);
+ }
ae.setPosition(a + 1);
if (aa[i].annotations[a].secondaryStructure != ' ')
{
Glyph ss = new Glyph();
- ss
- .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss
- .setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
+ ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setContent(String
+ .valueOf(aa[i].annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
// modifiable flag is supposed to be used.
}
setAnnotationType(an, aa[i]);
-
+
if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
{
an.setGraph(true);
an.setGroup(Integer.toString(aa[i].graphGroup));
- if (aa[i].threshold!=null && aa[i].threshold.displayed)
- an.addProperty(newProperty(THRESHOLD, "float", ""+aa[i].threshold.value));
- if (aa[i].threshold.label!=null)
- an.addProperty(newProperty(THRESHOLD+"Name", "string", ""+aa[i].threshold.label));
+ if (aa[i].threshold != null && aa[i].threshold.displayed)
+ {
+ an.addProperty(Properties.newProperty(THRESHOLD,
+ Properties.FLOATTYPE, "" + aa[i].threshold.value));
+ if (aa[i].threshold.label != null)
+ {
+ an.addProperty(Properties.newProperty(THRESHOLD
+ + "Name", Properties.STRINGTYPE, ""
+ + aa[i].threshold.label));
+ }
}
-
}
-
+
+ }
+
else
{
if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
- // LOCK METHODS)
+ // LOCK METHODS)
{
// verify annotation - update (perhaps)
Cache.log
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.getAlignment() == jal)
+ if (tp.getViewPort().getSequenceSetId()
+ .equals(av.getSequenceSetId()))
{
DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
jal, alignment);
catch (Exception ex)
{
ex.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * very quick test to see if the viewport would be stored in the vamsas
+ * document. Reasons for not storing include the unaligned flag being false
+ * (for all sequences, including the hidden ones!)
+ *
+ * @param av
+ * @return true if alignment associated with this view will be stored in
+ * document.
+ */
+ public boolean alignmentWillBeSkipped(AlignViewport av)
+ {
+ return (!av.getAlignment().isAligned());
+ }
+
+ private void addToSkipList(AlignViewport av)
+ {
+ if (skipList == null)
+ {
+ skipList = new Hashtable();
+ }
+ skipList.put(av.getSequenceSetId(), av);
+ }
+
+ /**
+ * remove docseqs from the given alignment marking provenance appropriately
+ * and removing any references to the sequences.
+ *
+ * @param alignment
+ * @param docseqs
+ */
+ private void removeValignmentSequences(Alignment alignment, Vector docseqs)
+ {
+ // delete these from document. This really needs to be a generic document
+ // API function derived by CASTOR.
+ Enumeration en = docseqs.elements();
+ while (en.hasMoreElements())
+ {
+ alignment.removeAlignmentSequence((AlignmentSequence) en
+ .nextElement());
+ }
+ Entry pe = addProvenance(alignment.getProvenance(), "Removed "
+ + docseqs.size() + " sequences");
+ en = alignment.enumerateAlignmentAnnotation();
+ Vector toremove = new Vector();
+ while (en.hasMoreElements())
+ {
+ uk.ac.vamsas.objects.core.AlignmentAnnotation alan = (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
+ .nextElement();
+ if (alan.getSeqrefsCount() > 0)
+ {
+ int p = 0;
+ Vector storem = new Vector();
+ Enumeration sr = alan.enumerateSeqrefs();
+ while (sr.hasMoreElements())
+ {
+ Object alsr = sr.nextElement();
+ if (docseqs.contains(alsr))
+ {
+ storem.addElement(alsr);
+ }
+ }
+ // remove references to the deleted sequences
+ sr = storem.elements();
+ while (sr.hasMoreElements())
+ {
+ alan.removeSeqrefs(sr.nextElement());
+ }
+
+ if (alan.getSeqrefsCount() == 0)
+ {
+ // should then delete alan from dataset
+ toremove.addElement(alan);
+ }
+ }
+ }
+ // remove any annotation that used to be associated to a specific bunch of
+ // sequences
+ en = toremove.elements();
+ while (en.hasMoreElements())
+ {
+ alignment
+ .removeAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) en
+ .nextElement());
+ }
+ // TODO: search through alignment annotations to remove any references to
+ // this alignment sequence
+ }
+
+ /**
+ * 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. unbounddocseq is a duplicate of the vamsas alignment sequences
+ * and these are removed after being processed w.r.t a bound jvalsq
+ *
+ */
+ private boolean syncToAlignmentSequence(SequenceI jvalsq,
+ Alignment alignment, Vector unbounddocseq)
+ {
+ boolean modal = false;
+ // todo: islocked method here
+ boolean up2doc = false;
+ AlignmentSequence alseq = (AlignmentSequence) getjv2vObj(jvalsq);
+ if (alseq == null)
+ {
+ alseq = new AlignmentSequence();
+ up2doc = true;
}
+ else
+ {
+ if (unbounddocseq != null)
+ {
+ unbounddocseq.removeElement(alseq);
+ }
+ }
+ // 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 (valseq.getDescription() != null)
+ {
+ alseq.setDescription(valseq.getDescription());
+ }
+ else
+ {
+ // inherit description line from dataset.
+ if (alseq.getDatasetSequence().getDescription() != null)
+ {
+ alseq.setDescription(alseq.getDatasetSequence()
+ .getDescription());
+ }
+ }
+ // 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,
{
// we only write an annotation where it really exists.
Glyph ss = new Glyph();
- ss
- .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
ss.setContent(String
.valueOf(alan.annotations[a].secondaryStructure));
ae.addGlyph(ss);
// the Jalview
// specific
// bits.
- if (alan.getThreshold()!=null && alan.getThreshold().displayed)
+ if (alan.getThreshold() != null && alan.getThreshold().displayed)
{
- an.addProperty(newProperty(THRESHOLD, "float", ""+alan.getThreshold().value));
- if (alan.getThreshold().label!=null)
- an.addProperty(newProperty(THRESHOLD+"Name", "string", ""+alan.getThreshold().label));
+ an.addProperty(Properties.newProperty(THRESHOLD,
+ Properties.FLOATTYPE, "" + alan.getThreshold().value));
+ if (alan.getThreshold().label != null)
+ an.addProperty(Properties.newProperty(THRESHOLD + "Name",
+ Properties.STRINGTYPE, "" + alan.getThreshold().label));
}
((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
bindjvvobj(alan, an);
{
// update reference sequence Annotation
if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
- // METHODS)
+ // METHODS)
{
// verify existing alignment sequence annotation is up to date
System.out.println("update dataset sequence annotation.");
* something extracted from another program, etc)
*/
an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix
- // this rough guess ;)
+ // this rough guess ;)
alsref.addAlignmentSequenceAnnotation(an);
bindjvvobj(alan, an);
// These properties are directly supported by the
{
// update reference sequence Annotation
if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
- // METHODS)
+ // METHODS)
{
// verify existing alignment sequence annotation is up to date
System.out.println("update alignment sequence annotation.");
/**
* set vamsas annotation object type from jalview annotation
+ *
* @param an
* @param alan
*/
- private void setAnnotationType(RangeAnnotation an, AlignmentAnnotation alan)
+ private void setAnnotationType(RangeAnnotation an,
+ AlignmentAnnotation alan)
{
if (an instanceof AlignmentSequenceAnnotation)
{
if (alan.graph != AlignmentAnnotation.NO_GRAPH)
{
- ((AlignmentSequenceAnnotation)an).setGraph(true);
- } else
+ ((AlignmentSequenceAnnotation) an).setGraph(true);
+ }
+ else
{
- ((AlignmentSequenceAnnotation)an).setGraph(false);
+ ((AlignmentSequenceAnnotation) an).setGraph(false);
}
}
if (an instanceof uk.ac.vamsas.objects.core.AlignmentAnnotation)
{
if (alan.graph != AlignmentAnnotation.NO_GRAPH)
{
- ((uk.ac.vamsas.objects.core.AlignmentAnnotation)an).setGraph(true);
- } else
+ ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an).setGraph(true);
+ }
+ else
{
- ((uk.ac.vamsas.objects.core.AlignmentAnnotation)an).setGraph(false);
+ ((uk.ac.vamsas.objects.core.AlignmentAnnotation) an)
+ .setGraph(false);
}
}
switch (alan.graph)
{
- case AlignmentAnnotation.BAR_GRAPH:
- an.addProperty(newProperty(DISCRETE_ANNOTATION, "boolean","true"));
- break;
- case AlignmentAnnotation.LINE_GRAPH:
- an.addProperty(newProperty(CONTINUOUS_ANNOTATION, "boolean","true"));
- break;
- default:
- // don't add any kind of discrete or continous property info.
- }
- }
-
- private Property newProperty(String name, String type, String content)
- {
- Property vProperty = new Property();
- vProperty.setName(name);
- if (type != null)
- {
- vProperty.setType(type);
- }
- else
- {
- vProperty.setType("String");
+ case AlignmentAnnotation.BAR_GRAPH:
+ an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION,
+ Properties.BOOLEANTYPE, "true"));
+ break;
+ case AlignmentAnnotation.LINE_GRAPH:
+ an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION,
+ Properties.BOOLEANTYPE, "true"));
+ break;
+ default:
+ // don't add any kind of discrete or continous property info.
}
- vProperty.setContent(content);
- return vProperty;
- }
-
- /**
- * correctly create a RangeAnnotation from a jalview sequence feature
- *
- * @param dsa
- * (typically DataSetAnnotations or AlignmentSequenceAnnotation)
- * @param feature
- * (the feature to be mapped from)
- * @return
- */
- private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
- SequenceFeature feature)
- {
- dsa.setType(feature.getType());
- Seg vSeg = new Seg();
- vSeg.setStart(feature.getBegin());
- vSeg.setEnd(feature.getEnd());
- vSeg.setInclusive(true);
- dsa.addSeg(vSeg);
- dsa.setDescription(feature.getDescription());
- dsa.setStatus(feature.getStatus());
- if (feature.links != null && feature.links.size() > 0)
- {
- for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
- {
- String link = (String) feature.links.elementAt(i);
- int sep = link.indexOf('|');
- if (sep > -1)
- {
- Link vLink = new Link();
- if (sep > 0)
- {
- vLink.setContent(link.substring(0, sep - 1));
- }
- else
- {
- vLink.setContent("");
- }
- vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
- dsa.addLink(vLink);
- }
- }
- }
- dsa.setGroup(feature.getFeatureGroup());
- return dsa;
}
/**
*/
private boolean isJalviewOnly(AlignmentAnnotation annotation)
{
- return annotation.label.equals("Quality")
+ return annotation.autoCalculated || annotation.label.equals("Quality")
|| annotation.label.equals("Conservation")
|| annotation.label.equals("Consensus");
}
+ boolean dojvsync = true;
+
+ // boolean dojvsync = false; // disables Jalview AppData IO
/**
- * This will return the first AlignFrame viewing AlignViewport av. It will
- * break if there are more than one AlignFrames viewing a particular av. This
- * also shouldn't be in the io package.
- *
- * @param av
- * @return alignFrame for av
+ * list of alignment views created when updating Jalview from document.
*/
- public AlignFrame getAlignFrameFor(AlignViewport av)
+ private Vector newAlignmentViews = new Vector();
+
+ /**
+ * update local jalview view settings from the stored appdata (if any)
+ */
+ public void updateJalviewFromAppdata()
{
- if (Desktop.desktop != null)
+ // recover any existing Jalview data from appdata
+ // TODO: recover any PDB files stored as attachments in the vamsas session
+ // and initialise the Jalview2XML.alreadyLoadedPDB hashtable with mappings
+ // to temp files.
{
- javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ final IClientAppdata cappdata = cdoc.getClientAppdata();
+ if (cappdata != null)
+ {
+ if (cappdata.hasClientAppdata())
+ {
+ // TODO: how to check version of Jalview client app data and whether
+ // it has been modified
+ // client data is shared over all app clients
+ try
+ {
+ jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ fromxml.attemptversion1parse = false;
+ fromxml.setUniqueSetSuffix("");
+ fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
+ // and
+ // mapValuesToString
+ fromxml.setSkipList(skipList);
+ jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
+ {
+
+ public String getFilename()
+ {
+
+ // TODO Get the vamsas session ID here
+ return "Jalview Vamsas Document Client Data";
+ }
+
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ jalview.bin.Cache.log
+ .debug("Returning client input stream for Jalview from Vamsas Document.");
+ return new JarInputStream(cappdata.getClientInputStream());
+ }
+ };
+ if (dojvsync)
+ {
+ fromxml.LoadJalviewAlign(jprovider);
+ }
+ } catch (Exception e)
+ {
+
+ } catch (OutOfMemoryError e)
+ {
- for (int t = 0; t < frames.length; t++)
+ } catch (Error e)
+ {
+
+ }
+ }
+ }
+ if (cappdata.hasUserAppdata())
{
- if (frames[t] instanceof AlignFrame)
+ // TODO: how to check version of Jalview user app data and whether it
+ // has been modified
+ // user data overrides data shared over all app clients ?
+ try
{
- if (((AlignFrame) frames[t]).getViewport() == av)
+ jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ fromxml.attemptversion1parse = false;
+ fromxml.setUniqueSetSuffix("");
+ fromxml.setSkipList(skipList);
+ fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
+ mapValuesToString(jv2vobj));
+ jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
{
- return (AlignFrame) frames[t];
+
+ public String getFilename()
+ {
+
+ // TODO Get the vamsas session ID here
+ return "Jalview Vamsas Document User Data";
+ }
+
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ jalview.bin.Cache.log
+ .debug("Returning user input stream for Jalview from Vamsas Document.");
+ return new JarInputStream(cappdata.getUserInputStream());
+ }
+ };
+ if (dojvsync)
+ {
+ fromxml.LoadJalviewAlign(jarstream);
}
+ } catch (Exception e)
+ {
+
+ } catch (OutOfMemoryError e)
+ {
+
+ } catch (Error e)
+ {
+
}
}
+
}
- return null;
+ flushAlignViewports();
}
- public void updateToJalview()
+ /**
+ * remove any spurious views generated by document synchronization
+ */
+ private void flushAlignViewports()
+ {
+ // remove any additional viewports originally recovered from the vamsas
+ // document.
+ // search for all alignframes containing viewports generated from document
+ // sync,
+ // and if any contain more than one view, then remove the one generated by
+ // document update.
+ AlignViewport views[], av = null;
+ AlignFrame af = null;
+ Iterator newviews = newAlignmentViews.iterator();
+ while (newviews.hasNext())
+ {
+ av = (AlignViewport) newviews.next();
+ af = Desktop.getAlignFrameFor(av);
+ // TODO implement this : af.getNumberOfViews
+ String seqsetidobj = av.getSequenceSetId();
+ views = Desktop.getViewports(seqsetidobj);
+ Cache.log.debug("Found "
+ + (views == null ? " no " : "" + views.length)
+ + " views for '" + av.getSequenceSetId() + "'");
+ if (views.length > 1)
+ {
+ // we need to close the original document view.
+
+ // work out how to do this by seeing if the views are gathered.
+ // pretty clunky but the only way to do this without adding more flags
+ // to the align frames.
+ boolean gathered = false;
+ String newviewid = null;
+ AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+ for (int i = 0; i < views.length; i++)
+ {
+ if (views[i] != av)
+ {
+ AlignFrame viewframe = Desktop.getAlignFrameFor(views[i]);
+ if (viewframe == af)
+ {
+ gathered = true;
+ }
+ newviewid = views[i].getSequenceSetId();
+ }
+ else
+ {
+ // lose the reference to the vamsas document created view
+ views[i] = null;
+ }
+ }
+ // close the view generated by the vamsas document synchronization
+ if (gathered)
+ {
+ af.closeView(av);
+ }
+ else
+ {
+ af.closeMenuItem_actionPerformed(false);
+ }
+ replaceJvObjMapping(seqsetidobj, newviewid);
+ seqsetidobj = newviewid;
+ // not sure if we need to do this:
+
+ if (false) // mappings != null)
+ {
+ // ensure sequence mappings from vamsas document view still
+ // active
+ if (mappings != null && mappings.length > 0)
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).addMappings(mappings);
+ }
+ }
+ }
+ // ensure vamsas object binds to the stored views retrieved from
+ // Jalview appdata
+ // jalview.structure.StructureSelectionManager
+ // .getStructureSelectionManager()
+ // .addStructureViewerListener(viewframe.alignPanel);
+
+ }
+
+ newviews = null;
+ newAlignmentViews.clear();
+ }
+
+ /**
+ * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
+ * binding tables
+ *
+ * @param oldjvobject
+ * @param newjvobject
+ * (may be null)
+ */
+ private void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
+ {
+ Object vobject = jv2vobj.remove(oldjvobject);
+ if (vobject == null)
+ {
+ throw new Error(
+ "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
+ + oldjvobject + ")");
+ }
+ if (newjvobject != null)
+ {
+ jv2vobj.put(newjvobject, vobject);
+ vobj2jv.put(vobject, newjvobject);
+ }
+ }
+
+ /**
+ * Update the jalview client and user appdata from the local jalview settings
+ */
+ public void updateJalviewClientAppdata()
+ {
+ final IClientAppdata cappdata = cdoc.getClientAppdata();
+ if (cappdata != null)
+ {
+ try
+ {
+ jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML();
+ jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
+ mapValuesToString(jv2vobj));
+ jxml.setSkipList(skipList);
+ if (dojvsync)
+ {
+ jxml.SaveState(new JarOutputStream(cappdata
+ .getClientOutputStream()));
+ }
+
+ } catch (Exception e)
+ {
+ // TODO raise GUI warning if user requests it.
+ jalview.bin.Cache.log
+ .error("Couldn't update jalview client application data. Giving up - local settings probably lost.",
+ e);
+ }
+ }
+ else
+ {
+ jalview.bin.Cache.log
+ .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
+ }
+ }
+
+ /**
+ * translate the Vobject keys to strings for use in Jalview2XML
+ *
+ * @param jv2vobj2
+ * @return
+ */
+ private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2)
+ {
+ IdentityHashMap mapped = new IdentityHashMap();
+ Iterator keys = jv2vobj2.keySet().iterator();
+ while (keys.hasNext())
+ {
+ Object key = keys.next();
+ mapped.put(key, jv2vobj2.get(key).toString());
+ }
+ return mapped;
+ }
+
+ /**
+ * translate the Vobject values to strings for use in Jalview2XML
+ *
+ * @param vobj2jv2
+ * @return hashtable with string values
+ */
+ private Hashtable mapKeysToString(Hashtable vobj2jv2)
+ {
+ Hashtable mapped = new Hashtable();
+ Iterator keys = vobj2jv2.keySet().iterator();
+ while (keys.hasNext())
+ {
+ Object key = keys.next();
+ mapped.put(key.toString(), vobj2jv2.get(key));
+ }
+ return mapped;
+ }
+
+ /**
+ * synchronize Jalview from the vamsas document
+ *
+ * @return number of new views from document
+ */
+ public int updateToJalview()
{
VAMSAS _roots[] = cdoc.getVamsasRoots();
for (i = 0; i < iSize; i++)
{
Sequence vdseq = dataset.getSequence(i);
- jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq);
- if (dsseq != null)
- {
- if (!dsseq.getSequenceAsString().equals(vdseq.getSequence()))
- {
- throw new Error(
- "Broken! - mismatch of dataset sequence: and jalview internal dataset sequence.");
- }
- jremain--;
- }
- else
+ jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(
+ this, vdseq);
+
+ jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj();
+ if (dssync.isAddfromdoc())
{
- dsseq = new jalview.datamodel.Sequence(dataset.getSequence(i)
- .getName(), dataset.getSequence(i).getSequence(),
- (int) dataset.getSequence(i).getStart(), (int) dataset
- .getSequence(i).getEnd());
- dsseq.setDescription(dataset.getSequence(i).getDescription());
- bindjvvobj(dsseq, dataset.getSequence(i));
- dsseq.setVamsasId(dataset.getSequence(i).getVorbaId().getId());
dsseqs.add(dsseq);
}
if (vdseq.getDbRefCount() > 0)
new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq);
}
+ dsseq.updatePDBIds();
}
}
{
SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta
.getSeqRef(0)); // TODO: deal with group dataset
- // annotations
+ // annotations
if (dsSeq == null)
{
jalview.bin.Cache.log
{
if (dseta.getAnnotationElementCount() == 0)
{
- jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) getvObj2jv(dseta);
- if (sf == null)
- {
- dsSeq
- .addSequenceFeature(sf = getJalviewSeqFeature(dseta));
- bindjvvobj(sf, dseta);
- }
+ new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
+
}
else
{
}
}
}
+ else
+ {
+ Cache.log
+ .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
+ }
}
}
if (dataset.getAlignmentCount() > 0)
{
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
- AlignViewport av = (AlignViewport) getvObj2jv(alignment);
+ // TODO check this handles multiple views properly
+ AlignViewport av = findViewport(alignment);
+
jalview.datamodel.AlignmentI jal = null;
if (av != null)
{
- jal = av.getAlignment();
+ // TODO check that correct alignment object is retrieved when
+ // hidden seqs exist.
+ jal = (av.hasHiddenRows()) ? av.getAlignment()
+ .getHiddenSequences().getFullAlignment() : av
+ .getAlignment();
}
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
+ // document
if (jal != null)
{
dsseqs = jal.getSequences(); // for merge/update
for (i = 0; i < iSize; i++)
{
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
- jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
- if (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));
- jremain--;
- }
- else
+ jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
+ if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
+ dsseqs) && alseq != null)
{
- 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);
+ // updated to sequence from the document
+ jremain--;
+ refreshal = true;
}
if (valseq.getAlignmentSequenceAnnotationCount() > 0)
{
for (int a = 0; a < vasannot.length; a++)
{
jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
- // 1:many
- // jalview
- // alignment
- // sequence
- // annotations
+ // 1:many
+ // jalview
+ // alignment
+ // sequence
+ // annotations
if (asa == null)
{
int se[] = getBounds(vasannot[a]);
asa = getjAlignmentAnnotation(jal, vasannot[a]);
asa.setSequenceRef(alseq);
asa.createSequenceMapping(alseq, se[0], false); // TODO:
- // verify
- // that
- // positions
- // in
- // alseqAnnotation
- // correspond
- // to
- // ungapped
- // residue
- // positions.
+ // verify
+ // that
+ // positions
+ // in
+ // alseqAnnotation
+ // correspond
+ // to
+ // ungapped
+ // residue
+ // positions.
alseq.addAlignmentAnnotation(asa);
bindjvvobj(asa, vasannot[a]);
+ refreshal = true;
newasAnnots.add(asa);
}
else
{
// update existing annotation - can do this in place
if (vasannot[a].getModifiable() == null) // TODO: USE
- // VAMSAS LIBRARY
- // OBJECT LOCK
- // METHODS)
+ // VAMSAS LIBRARY
+ // OBJECT LOCK
+ // METHODS)
{
Cache.log
.info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
Cache.log
.debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
if (an[j].getModifiable() == null) // TODO: USE VAMSAS
- // LIBRARY OBJECT LOCK
- // METHODS)
+ // LIBRARY OBJECT LOCK
+ // METHODS)
{
// TODO: user defined annotation is totally mutable... - so
// load it up or throw away if locally edited.
else
{
jan = getjAlignmentAnnotation(jal, an[j]);
+ // TODO: ensure we add the alignment annotation before the
+ // automatic annotation rows
jal.addAnnotation(jan);
bindjvvobj(jan, an[j]);
+ refreshal = true;
}
}
}
// ///////////////////////////////
// construct alignment view
alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId()
+ .toString());
av = alignFrame.getViewport();
- String title = alignment.getProvenance().getEntry(
- alignment.getProvenance().getEntryCount() - 1)
+ newAlignmentViews.addElement(av);
+ String title = alignment
+ .getProvenance()
+ .getEntry(
+ alignment.getProvenance().getEntryCount() - 1)
.getAction();
if (alignment.getPropertyCount() > 0)
{
for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
{
- if (alignment.getProperty(p).getName().equals(
- "title"))
+ if (alignment.getProperty(p).getName().equals("title"))
{
title = alignment.getProperty(p).getContent();
}
// alignment using its provenance.
if (Cache.log.isDebugEnabled())
{
- title = title + "("
- + alignment.getVorbaId() + ")";
-
+ title = title + "(" + alignment.getVorbaId() + ")";
+
}
- jalview.gui.Desktop.addInternalFrame(alignFrame, title
- ,
+ jalview.gui.Desktop.addInternalFrame(alignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- bindjvvobj(av, alignment);
+ bindjvvobj(av.getSequenceSetId(), alignment);
}
else
{
// find the alignFrame for jal.
// TODO: fix this so we retrieve the alignFrame handing av
- // *directly*
- alignFrame = getAlignFrameFor(av);
+ // *directly* (JBPNote - don't understand this now)
+ // TODO: make sure all associated views are refreshed
+ alignFrame = Desktop.getAlignFrameFor(av);
+ if (refreshal)
+ {
+ av.alignmentChanged(alignFrame.alignPanel);
+ alignFrame.alignPanel.adjustAnnotationHeight();
+ }
}
// LOAD TREES
// /////////////////////////////////////
this, alignFrame, alignment.getTree(t));
TreePanel tp = null;
if (vstree.isValidTree())
- {
- tp = alignFrame
- .ShowNewickTree(vstree.getNewickTree(), vstree
- .getTitle(), vstree.getInputData(), 600,
- 500, t * 20 + 50, t * 20 + 50);
+ {
+ tp = alignFrame.ShowNewickTree(vstree.getNewickTree(),
+ vstree.getTitle(), vstree.getInputData(), 600,
+ 500, t * 20 + 50, t * 20 + 50);
+
}
- if (tp!=null)
+ if (tp != null)
+ {
bindjvvobj(tp, alignment.getTree(t));
+ try
+ {
+ vstree.UpdateSequenceTreeMap(tp);
+ } catch (RuntimeException e)
+ {
+ Cache.log.warn("update of labels failed.", e);
+ }
+ }
else
{
- Cache.log.warn("Cannot create tree for tree "+t+" in document ("+alignment.getTree(t).getVorbaId());
+ Cache.log.warn("Cannot create tree for tree " + t
+ + " in document ("
+ + alignment.getTree(t).getVorbaId());
}
}
}
}
}
+ return newAlignmentViews.size();
+ }
+
+ public AlignViewport findViewport(Alignment alignment)
+ {
+ AlignViewport av = null;
+ AlignViewport[] avs = Desktop
+ .getViewports((String) getvObj2jv(alignment));
+ if (avs != null)
+ {
+ av = avs[0];
+ }
+ return av;
}
// bitfields - should be a template in j1.5
{ new jalview.datamodel.Annotation[rangeMap.length],
new jalview.datamodel.Annotation[rangeMap.length] };
boolean mergeable = true; // false if 'after positions cant be placed on
- // same annotation row as positions.
+ // same annotation row as positions.
if (annotation.getAnnotationElementCount() > 0)
{
for (int aa = 0; aa < ae.length; aa++)
{
int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to
- // (|seg.start-seg.end|+1)
+ // (|seg.start-seg.end|+1)
if (pos >= 0 && pos < rangeMap.length)
{
int row = ae[aa].getAfter() ? 1 : 0;
}
}
String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" :
- // ae[aa].getDisplayCharacter();
+ // ae[aa].getDisplayCharacter();
String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" :
- // ae[aa].getSecondaryStructure();
+ // ae[aa].getSecondaryStructure();
java.awt.Color colour = null;
if (ae[aa].getGlyphCount() > 0)
{
{
if (glyphs[g]
.getDict()
- .equals(
- uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
+ .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
{
ss = glyphs[g].getContent();
AeContent[HASSECSTR] = true;
}
else if (glyphs[g]
.getDict()
- .equals(
- uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
+ .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
Cache.log.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
}
else
{
- Cache.log.debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
- + glyphs[g].getDict());
+ Cache.log
+ .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ + glyphs[g].getDict());
}
}
}
{
Cache.log.warn("ignoring additional "
+ (ae[aa].getValueCount() - 1)
- + "values in annotation element.");
+ + " values in annotation element.");
}
val = ae[aa].getValue(0);
}
if (colour == null)
{
anot[row][pos] = new jalview.datamodel.Annotation(
- (dc != null) ? dc : "", desc, (ss != null) ? ss
- .charAt(0) : ' ', val);
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val);
}
else
{
anot[row][pos] = new jalview.datamodel.Annotation(
- (dc != null) ? dc : "", desc, (ss != null) ? ss
- .charAt(0) : ' ', val, colour);
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val, colour);
}
}
else
anot[0][i] = anot[1][i];
anot[0][i].description = anot[0][i].description + " (after)";
AeContent[HASDESCSTR] = true; // we have valid description string
- // data
+ // data
anot[1][i] = null;
}
}
Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation);
String a_label = annotation.getLabel();
String a_descr = annotation.getDescription();
- GraphLine gl=null;
- int type=0;
- boolean interp=true; // cleared if annotation is DISCRETE
+ GraphLine gl = null;
+ int type = 0;
+ boolean interp = true; // cleared if annotation is DISCRETE
// set type and other attributes from properties
if (annotation.getPropertyCount() > 0)
{
// look for special jalview properties
- uk.ac.vamsas.objects.core.Property[] props = annotation
- .getProperty();
+ uk.ac.vamsas.objects.core.Property[] props = annotation.getProperty();
for (int p = 0; p < props.length; p++)
{
if (props[p].getName().equalsIgnoreCase(DISCRETE_ANNOTATION))
{
type = AlignmentAnnotation.BAR_GRAPH;
- interp=false;
- } else if
- (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION)) {
+ interp = false;
+ }
+ else if (props[p].getName().equalsIgnoreCase(CONTINUOUS_ANNOTATION))
+ {
type = AlignmentAnnotation.LINE_GRAPH;
- } else if
- (props[p].getName().equalsIgnoreCase(THRESHOLD))
+ }
+ else if (props[p].getName().equalsIgnoreCase(THRESHOLD))
{
- Float val=null;
- try {
+ Float val = null;
+ try
+ {
val = new Float(props[p].getContent());
- }catch (Exception e)
+ } catch (Exception e)
{
Cache.log.warn("Failed to parse threshold property");
}
- if (val!=null)
- if (gl==null)
- {
- gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
- } else
- {
- gl.value = val.floatValue();
- }
+ if (val != null)
+ if (gl == null)
+ {
+ gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
+ }
+ else
+ {
+ gl.value = val.floatValue();
+ }
}
- else if (props[p].getName().equalsIgnoreCase(THRESHOLD+"Name"))
+ else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
{
- if (gl==null)
+ if (gl == null)
gl = new GraphLine(0, "", java.awt.Color.black);
gl.label = props[p].getContent();
}
// way its 'odd' - there is already an existing TODO about removing this
// flag as being redundant
/*
- * if
- * ((annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class) &&
- * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph()) ||
- * (hasSequenceRef=true &&
- * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
+ * if((annotation.getClass().equals(uk.ac.vamsas.objects.core.
+ * AlignmentAnnotation.class) &&
+ * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
+ * || (hasSequenceRef=true &&
+ * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
+ * )annotation).getGraph())) {
*/
if (has[HASVALS])
{
- if (type==0)
+ if (type == 0)
{
- type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default type of value annotation
+ type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
+ // type of
+ // value
+ // annotation
if (has[HASHPHOB])
{
// no hints - so we ensure HPHOB display is like this.
if (!has[HASDC])
{
if (!interp)
- {
- if (arow[i].description!=null && arow[i].description.length()<3)
+ {
+ if (arow[i].description != null
+ && arow[i].description.length() < 3)
{
// copy over the description as the display char.
arow[i].displayCharacter = new String(arow[i].description);
}
- } else
- {
- // mark the position as a point used for the interpolation.
+ }
+ else
+ {
+ // mark the position as a point used for the interpolation.
arow[i].displayCharacter = arow[i].value + "";
- }
+ }
}
}
}
}
else
{
- if (annotation.getAnnotationElementCount()==0)
+ if (annotation.getAnnotationElementCount() == 0)
{
// empty annotation array
- // TODO: alignment 'features' compare rangeType spec to alignment width - if it is not complete, then mark regions on the annotation row.
+ // TODO: alignment 'features' compare rangeType spec to alignment
+ // width - if it is not complete, then mark regions on the annotation
+ // row.
}
jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
arow);
jan.setThreshold(null);
+ jan.annotationId = annotation.getVorbaId().toString(); // keep all the
+ // ids together.
}
if (annotation.getLinkCount() > 0)
{
Cache.log.warn("Ignoring " + annotation.getLinkCount()
+ "links added to AlignmentAnnotation.");
}
- if (annotation.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
- // LOCK METHODS)
+ if (annotation.getModifiable() == null
+ || annotation.getModifiable().length() == 0) // TODO: USE VAMSAS
+ // LIBRARY OBJECT
+ // LOCK METHODS)
{
jan.editable = true;
}
if (annotation.getGroup() != null
&& annotation.getGroup().length() > 0)
{
- jan.graphGroup = Integer.parseInt(annotation.getGroup());
+ jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
+ // group
+ // similarly
+ // named
+ // annotation
+ // together
+ // ?
}
} catch (Exception e)
{
return null;
}
- private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
- {
- int[] se = getBounds(dseta);
- SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta
- .getType(), dseta.getDescription(), dseta.getStatus(), se[0],
- se[1], dseta.getGroup());
- if (dseta.getLinkCount() > 0)
- {
- Link[] links = dseta.getLink();
- for (int i = 0; i < links.length; i++)
- {
- sf.addLink(links[i].getContent() + "|" + links[i].getHref());
- }
- }
- return sf;
- }
-
/**
* get real bounds of a RangeType's specification. start and end are an
* inclusive range within which all segments and positions lie. TODO: refactor
* @param maprange
* where the from range is the local mapped range, and the to range
* is the 'mapped' range in the MapRangeType
- * @param default
- * unit for local
- * @param default
- * unit for mapped
+ * @param default unit for local
+ * @param default unit for mapped
* @return MapList
*/
private jalview.util.MapList parsemapType(MapType maprange, int localu,
*
* if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
* entries.length; i++) { provEntry = new Entry(); try { date = new
- * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) {
- * ex.printStackTrace();
+ * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex)
+ * { ex.printStackTrace();
*
* date = new org.exolab.castor.types.Date(entries[i].getDate()); }
* provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
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()
Cache.log.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
- dataset = (DataSet) getjv2vObj(jal.getDataset());
+ dataset = (DataSet) ((Alignment) getjv2vObj(viewport
+ .getSequenceSetId())).getV_parent(); // jal.getDataset());
+ if (dataset == null)
+ {
+ dataset = (DataSet) getjv2vObj(jal.getDataset());
+ Cache.log
+ .error("Can't find the correct dataset for the alignment in this view. Creating new one.");
+
+ }
// Store any sequence mappings.
if (av.getAlignment().getCodonFrames() != null
&& av.getAlignment().getCodonFrames().length > 0)
.getCodonFrames();
for (int cf = 0; cf < cframes.length; cf++)
{
- if (cframes[cf].getdnaSeqs().length > 0)
+ if (cframes[cf].getdnaSeqs() != null
+ && cframes[cf].getdnaSeqs().length > 0)
{
jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
{
Cache.log
.warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
- + mfrom.getName()
+ + dmps[smp].getDisplayId(true)
+ " to "
+ mps[smp].getTo().getName());
}
e);
}
}
+
+ public void clearSkipList()
+ {
+ if (skipList != null)
+ {
+ skipList.clear();
+ }
+ }
+
+ /**
+ * @return the skipList
+ */
+ public Hashtable getSkipList()
+ {
+ return skipList;
+ }
+
+ /**
+ * @param skipList
+ * the skipList to set
+ */
+ public void setSkipList(Hashtable skipList)
+ {
+ this.skipList = skipList;
+ }
+
+ /**
+ * registry for datastoreItems
+ */
+ DatastoreRegistry dsReg = new DatastoreRegistry();
+
+ public DatastoreRegistry getDatastoreRegisty()
+ {
+ if (dsReg == null)
+ {
+ dsReg = new DatastoreRegistry();
+ }
+ return dsReg;
+ }
}
git://source.jalview.org / jalview.git / blobdiff