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.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;
/*
*
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,
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
{
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++)
}
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();
// 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)
{
// 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)
{
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));
}
}
}
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);
}
/**
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());
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
// 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);
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<end range of segment, adjusting for inclusivity flag and
*/
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)
+ {
+
+ } catch (Error e)
+ {
+
+ }
+ }
+ }
+ if (cappdata.hasUserAppdata())
+ {
+ // 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
+ {
+ 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()
+ {
+
+ 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)
+ {
- for (int t = 0; t < frames.length; t++)
+ } catch (Error e)
+ {
+
+ }
+ }
+
+ }
+ flushAlignViewports();
+ }
+
+ /**
+ * 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)
{
- 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();
// 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)
{
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
{
.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.");
}
}
}
{
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;
// ///////////////////////////////
// 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();
{
// 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);
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];
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;
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)
{
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
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;
+ }
}
git://source.jalview.org / jalview.git / commitdiff