From ed12859f49530c561c9d069c71333ddac9fc8a30 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 12 Nov 2008 17:05:08 +0000 Subject: [PATCH] new viewport IDs and jalview XML storage/sync in vamsas appdata and refactored more code to use of jalview.io.vamsas.DatastoreItem --- src/jalview/io/VamsasAppDatastore.java | 755 ++++++++++++++++++++------------ 1 file changed, 470 insertions(+), 285 deletions(-) diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index c2031cc..34219b4 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -19,6 +19,7 @@ package jalview.io; import jalview.bin.Cache; +import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; @@ -30,17 +31,24 @@ import jalview.gui.AlignFrame; 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.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; /* * @@ -71,14 +79,30 @@ public class VamsasAppDatastore 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, @@ -89,6 +113,23 @@ public class VamsasAppDatastore 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]); + } } /** @@ -100,6 +141,36 @@ public class VamsasAppDatastore { 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 " @@ -181,8 +252,9 @@ public class VamsasAppDatastore * 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 { @@ -197,11 +269,22 @@ public class VamsasAppDatastore Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); } - 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(jal.getDataset()); + } + if (dataset == null) { // it might be that one of the dataset sequences does actually have a - // binding, so search for it indirectly. + // 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 = jal.getDataset() .getSequencesArray(); for (int i = 0; i < jdatset.length; i++) @@ -217,10 +300,10 @@ public class VamsasAppDatastore } 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 } @@ -232,6 +315,8 @@ public class VamsasAppDatastore 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(); @@ -261,107 +346,11 @@ public class VamsasAppDatastore // 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(sq.getName()); - sequence.setStart(sq.getStart()); - sequence.setEnd(sq.getEnd()); - sequence.setDescription(sq.getDescription()); - dataset.addSequence(sequence); - dssmods.addElement(dssmods); - } - else - { - 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]; - - 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.getDatasetSequence() == null && sq.getDBRef() != null) - { - // only sync database references for dataset sequences - 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); - } - - } + Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, sq, dict, dataset); + sequence = (Sequence) dssync.getVobj(); + if (dssync.getModified()) { + dssmods.addElement(sequence); + }; } if (dssmods.size() > 0) { @@ -377,23 +366,12 @@ public class VamsasAppDatastore // 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 alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); // bind - // to - // the - // value - // used - // to - // associate - // different - // views - // to - // same - // alignment + { + // TODO: trees could be written - but for the moment we just + addToSkipList(av); + // add to the JalviewXML skipList and .. + return false; + } if (alignment == null) { @@ -659,12 +637,12 @@ public class VamsasAppDatastore an.setGroup(Integer.toString(aa[i].graphGroup)); if (aa[i].threshold != null && aa[i].threshold.displayed) { - an.addProperty(newProperty(THRESHOLD, "float", "" + an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, "" + aa[i].threshold.value)); if (aa[i].threshold.label != null) { - an.addProperty(newProperty(THRESHOLD + "Name", - "string", "" + aa[i].threshold.label)); + an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE, + "" + aa[i].threshold.label)); } } } @@ -722,8 +700,18 @@ public class VamsasAppDatastore catch (Exception ex) { ex.printStackTrace(); + return false; } + return true; + } + private void addToSkipList(AlignViewport av) + { + if (skipList == null) + { + skipList = new Hashtable(); + } + skipList.put(av.getSequenceSetId(), av); } /** @@ -894,8 +882,7 @@ public class VamsasAppDatastore modal = true; alseq.setName(valseq.getName()); } - if (alseq.getDescription() == null - || (valseq.getDescription() == null || alseq.getDescription() + if (alseq.getDescription()==null || (valseq.getDescription() != null && !alseq.getDescription() .equals(valseq.getDescription()))) { alseq.setDescription(valseq.getDescription()); @@ -912,11 +899,21 @@ public class VamsasAppDatastore 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 @@ -1037,10 +1034,11 @@ public class VamsasAppDatastore // bits. if (alan.getThreshold() != null && alan.getThreshold().displayed) { - an.addProperty(newProperty(THRESHOLD, "float", "" + an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, + "" + alan.getThreshold().value)); if (alan.getThreshold().label != null) - an.addProperty(newProperty(THRESHOLD + "Name", "string", "" + an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE, "" + alan.getThreshold().label)); } ((DataSet) sref.getV_parent()).addDataSetAnnotations(an); @@ -1167,78 +1165,16 @@ public class VamsasAppDatastore switch (alan.graph) { case AlignmentAnnotation.BAR_GRAPH: - an.addProperty(newProperty(DISCRETE_ANNOTATION, "boolean", "true")); + an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, Properties.BOOLEANTYPE, "true")); break; case AlignmentAnnotation.LINE_GRAPH: - an.addProperty(newProperty(CONTINUOUS_ANNOTATION, "boolean", "true")); + an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION, Properties.BOOLEANTYPE, "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"); - } - 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; - } /** * get start 1) { - if (frames[t] instanceof AlignFrame) + // 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) { - if (((AlignFrame) frames[t]).getViewport() == av) + 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) { - return (AlignFrame) frames[t]; + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().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."); } - return null; } + /** + * 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 + */ public void updateToJalview() { VAMSAS _roots[] = cdoc.getVamsasRoots(); @@ -1342,28 +1552,15 @@ public class VamsasAppDatastore // TODO: test sequence merging - we preserve existing non vamsas // sequences but add in any new vamsas ones, and don't yet update any // sequence attributes - for (i = 0; i < iSize; i++) + for (i = 0; i < iSize + ; i++) { Sequence vdseq = dataset.getSequence(i); - jalview.datamodel.SequenceI dsseq = (SequenceI) getvObj2jv(vdseq); - if (dsseq != null) + jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(this, vdseq); + + jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj(); + if (dssync.isAddfromdoc()) { - if (!dsseq.getSequenceAsString().equals(vdseq.getSequence())) - { - throw new Error( - "Broken! - mismatch of dataset sequence: and jalview internal dataset sequence."); - } - jremain--; - } - else - { - 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) @@ -1415,13 +1612,8 @@ public class VamsasAppDatastore { 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 { @@ -1434,6 +1626,8 @@ public class VamsasAppDatastore .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview."); } } + } else { + Cache.log.warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features."); } } } @@ -1445,12 +1639,17 @@ public class VamsasAppDatastore { uk.ac.vamsas.objects.core.Alignment alignment = dataset .getAlignment(al); + // 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; @@ -1612,8 +1811,10 @@ public class VamsasAppDatastore // /////////////////////////////// // construct alignment view alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId() + .toString()); av = alignFrame.getViewport(); + newAlignmentViews.addElement(av); String title = alignment.getProvenance().getEntry( alignment.getProvenance().getEntryCount() - 1) .getAction(); @@ -1642,8 +1843,9 @@ public class VamsasAppDatastore { // 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); @@ -1709,7 +1911,8 @@ public class VamsasAppDatastore public AlignViewport findViewport(Alignment alignment) { AlignViewport av = null; - AlignViewport[] avs = findViewportForSequenceSetId((String) getvObj2jv(alignment)); + AlignViewport[] avs = Desktop + .getViewports((String) getvObj2jv(alignment)); if (avs != null) { av = avs[0]; @@ -1717,34 +1920,6 @@ public class VamsasAppDatastore return av; } - private AlignViewport[] findViewportForSequenceSetId(String sequenceSetId) - { - Vector viewp = new Vector(); - if (Desktop.desktop != null) - { - javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof AlignFrame) - { - if (((AlignFrame) frames[t]).getViewport().getSequenceSetId() - .equals(sequenceSetId)) - { - viewp.addElement(((AlignFrame) frames[t]).getViewport()); - } - } - } - if (viewp.size() > 0) - { - AlignViewport[] vp = new AlignViewport[viewp.size()]; - viewp.copyInto(vp); - return vp; - } - } - return null; - } - // bitfields - should be a template in j1.5 private static int HASSECSTR = 0; @@ -2139,6 +2314,8 @@ public class VamsasAppDatastore 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) { @@ -2177,22 +2354,6 @@ public class VamsasAppDatastore 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 @@ -2522,4 +2683,28 @@ public class VamsasAppDatastore 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; + } } -- 1.7.10.2