X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=d5801296ed3a0df7b410c2dfda1cf89297bcd22b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3c6e4414f39c1fac76478c2b2be69941c4b00c44;hpb=9d130129339a0282acccaa70f3b2fcd62822f0ac;p=jalview.git
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 3c6e441..d580129 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,43 +1,78 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
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.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceI;
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.DatastoreRegistry;
+import jalview.io.vamsas.Rangetype;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+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.List;
+import java.util.Set;
import java.util.Vector;
-
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.objects.core.*;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.utils.Properties;
/*
*
@@ -46,47 +81,83 @@ import uk.ac.vamsas.objects.core.*;
* "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
*
*/
-
+/*
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
+ */
public class VamsasAppDatastore
{
- Entry provEntry = null;
+ /**
+ * Type used for general jalview generated annotation added to vamsas document
+ */
+ public static final String JALVIEW_ANNOTATION_ROW = "JalviewAnnotation";
- // AlignViewport av;
+ /**
+ * AlignmentAnnotation property to indicate that values should not be
+ * interpolated
+ */
+ public static final String DISCRETE_ANNOTATION = "discrete";
- org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
- new java.util.Date());
+ /**
+ * 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";
+
+ /**
+ * 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();
}
- /*
- * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the
- * mapping information from the file Mapping map = new
- * Mapping(getClass().getClassLoader()); java.net.URL url =
- * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.
- * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();
- * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =
- * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data
- * with the total price back and print the XML in the console Marshaller
- * marshaller = new Marshaller( new FileWriter(file) );
- *
- * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {
- * e.printStackTrace(); } }
- *
- *
+ /**
+ * 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 the Vobject bound to Jalview datamodel object
*/
@@ -94,17 +165,49 @@ public class VamsasAppDatastore
{
if (jv2vobj.containsKey(jvobj))
{
- return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));
+ 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 "+jvobj);
+ Cache.log.debug("Returning null VorbaID binding for jalview object "
+ + jvobj);
}
return null;
}
/**
- *
+ *
* @param vobj
* @return Jalview datamodel object bound to the vamsas document object
*/
@@ -115,7 +218,7 @@ public class VamsasAppDatastore
{
id = cdoc.registerObject(vobj);
Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ .debug("Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -131,32 +234,41 @@ public class VamsasAppDatastore
if (id == null)
{
id = cdoc.registerObject(vobj);
- if (id == null || vobj.getVorbaId() == null || cdoc.getObject(id)!=vobj)
+ if (id == null || vobj.getVorbaId() == null
+ || cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for " +
- (vobj.isRegisterable() ? "registerable" :
- "unregisterable") + " object " + vobj);
+ Cache.log.error("Failed to get id for "
+ + (vobj.isRegisterable() ? "registerable"
+ : "unregisterable") + " object " + vobj);
}
}
- if (vobj2jv.containsKey(vobj.getVorbaId()) &&
- ! ( (VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
+ if (vobj2jv.containsKey(vobj.getVorbaId())
+ && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug("Warning? Overwriting existing vamsas id binding for " +
- vobj.getVorbaId(),
- new Exception("Overwriting vamsas id binding."));
+ Cache.log
+ .debug("Warning? Overwriting existing vamsas id binding for "
+ + vobj.getVorbaId(),
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_vamsas_id_binding")));
}
- else if (jv2vobj.containsKey(jvobj) &&
- ! ( (VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
+ else if (jv2vobj.containsKey(jvobj)
+ && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
Cache.log.debug(
- "Warning? Overwriting existing jalview object binding for " + jvobj,
- new Exception("Overwriting jalview object binding."));
+ "Warning? Overwriting existing jalview object binding for "
+ + jvobj, new Exception(
+ "Overwriting jalview object binding."));
}
- /* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id " +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+" already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to bindjvvobj"));
- }*/
+ /*
+ * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+ * +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
+ * already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
+ * bindjvvobj")); }
+ */
// we just update the hash's regardless!
- Cache.log.debug("Binding "+vobj.getVorbaId()+" to "+jvobj);
+ Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
@@ -164,33 +276,91 @@ public class VamsasAppDatastore
/**
* put the alignment viewed by AlignViewport into cdoc.
- *
- * @param av alignViewport to be stored
- * @param aFtitle title for alignment
+ *
+ * @param av
+ * 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
- if (jal.getDataset() == null)
+ DataSet dataset = null;
+ if (jds == null)
{
Cache.log.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
+ jds = 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);
}
- DataSet 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. 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]);
+ if (vbound != null)
+ {
+ if (vbound instanceof uk.ac.vamsas.objects.core.Sequence)
+ {
+ if (dataset == null)
+ {
+ dataset = (DataSet) vbound.getV_parent();
+ }
+ else
+ {
+ if (vbound.getV_parent() != null
+ && dataset != vbound.getV_parent())
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_map_alignment_sequences"));
+ // 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
@@ -199,117 +369,53 @@ public class VamsasAppDatastore
}
// 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;
+ 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());
- dataset.addSequence(sequence);
- }
- else
- {
- // verify principal attributes. and update any new
- // features/references.
- System.out.println("update dataset sequence object.");
- }
- if (sq.getSequenceFeatures() != null)
+ Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(
+ this, sq, dict, dataset);
+ sequence = (Sequence) dssync.getVobj();
+ if (dssync.getModified())
{
- 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.setSeqRef(sequence);
- bindjvvobj(feature, dsa);
- dataset.addDataSetAnnotations(dsa);
- }
- else
- {
- // todo: verify and update dataset annotations for sequence
- System.out.println("update dataset sequence annotations.");
- }
- }
+ dssmods.addElement(sequence);
}
-
- 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++)
- {
- dbentry = entries[db];
- dbref = (DbRef) getjv2vObj(dbentry);
- if (dbref == null)
- {
- dbref = new DbRef();
- bindjvvobj(dbentry, dbref);
- dbref.setAccessionId(dbentry.getAccessionId());
- dbref.setSource(dbentry.getSource());
- dbref.setVersion(dbentry.getVersion());
- /*
- * TODO: Maps are not yet supported by Jalview. Map vMap = new
- * Map(); vMap.set dbref.addMap(vMap);
- */
- sequence.addDbRef(dbref);
- }
- else
- {
- // TODO: verify and update dbrefs in vamsas document
- // there will be trouble when a dataset sequence is modified to
- // contain more residues than were originally referenced - we must
- // then make a number of dataset sequence entries
- System.out
- .println("update dataset sequence database references.");
- }
- }
-
+ 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 (alignmentWillBeSkipped(av))
+ {
+ // TODO: trees could be written - but for the moment we just
+ addToSkipList(av);
+ // add to the JalviewXML skipList and ..
+ return false;
+ }
- // ////////////////////////////////////////////
- // Save the Alignments
-
- 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());
@@ -320,80 +426,116 @@ public class VamsasAppDatastore
dataset.addAlignment(alignment);
{
Property title = new Property();
- title.setName("jalview:AlTitle");
+ title.setName("title");
title.setType("string");
title.setContent(aFtitle);
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.");
+ .println("update edited alignment to new alignment in document.");
}
}
// ////////////////////////////////////////////
// SAVE Alignment Sequence Features
- for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize;
- i++)
+ for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
{
AlignmentSequence valseq;
SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
- .getAlignmentSequence(i));
+ .getAlignmentSequence(i));
if (alseq != null && alseq.getSequenceFeatures() != null)
{
- 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)
- {
-
- valseqf = (AlignmentSequenceAnnotation)
- getDSAnnotationFromJalview(
- new AlignmentSequenceAnnotation(), features[i]);
- if (valseqf.getProvenance() == null)
- {
- valseqf.setProvenance(new Provenance());
- }
- addProvenance(valseqf.getProvenance(), "created"); // JBPNote -
- // need to
- // update
- bindjvvobj(features[i], valseqf);
- valseq.addAlignmentSequenceAnnotation(valseqf);
- }
- }
-
- }
+ /*
+ * We do not put local Alignment Sequence Features into the vamsas
+ * document yet.
+ *
+ *
+ * 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) {
+ *
+ * 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); } } }
+ */
}
}
@@ -402,7 +544,7 @@ public class VamsasAppDatastore
if (jal.getAlignmentAnnotation() != null)
{
jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
+ .getAlignmentAnnotation();
java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
// alignment columns to
// sequence positions.
@@ -412,133 +554,53 @@ public class VamsasAppDatastore
{
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)
{
- uk.ac.vamsas.objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
- objects.core.AlignmentSequence) getjv2vObj(aa[i].sequenceRef);
- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.
- vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(aa[
- i]);
- int[] gapMap = null;
- if (AlSeqMaps.containsKey(aa[i].sequenceRef))
+ // Deal with sequence associated annotation
+ Vobject sref = getjv2vObj(aa[i].sequenceRef);
+ if (sref instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
{
- gapMap = (int[]) AlSeqMaps.get(aa[i].sequenceRef);
+ saveAlignmentSequenceAnnotation(AlSeqMaps,
+ (AlignmentSequence) sref, aa[i]);
}
else
{
- gapMap = new int[aa[i].sequenceRef.getLength()];
- // map from alignment position to sequence position.
- int[] sgapMap = aa[i].sequenceRef.gapMap();
- for (int a = 0; a < sgapMap.length; a++)
- {
- gapMap[sgapMap[a]] = a;
- }
- }
- if (an == null)
- {
- an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
- Seg vSeg = new Seg();
- vSeg.setStart(1);
- vSeg.setInclusive(true);
- vSeg.setEnd(gapMap.length);
- an.addSeg(vSeg);
- an.setType("jalview:SecondaryStructurePrediction"); // TODO: better fix this rough guess ;)
- alsref.addAlignmentSequenceAnnotation(an);
- bindjvvobj(aa[i], an);
- // LATER: much of this is verbatim from the alignmentAnnotation
- // method below. suggests refactoring to make rangeAnnotation the
- // base class
- an.setDescription(aa[i].description);
- if (aa[i].graph > 0)
+ // first find the alignment sequence to associate this with.
+ for (SequenceI jvalsq : av.getAlignment().getSequences())
{
- an.setGraph(true); // aa[i].graph);
- }
- else
- {
- an.setGraph(false);
- }
- an.setLabel(aa[i].label);
- an.setProvenance(dummyProvenance()); // get provenance as user
- // created, or jnet, or
- // something else.
- an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
- // originally we
- // were going to
- // store
- // graphGroup in
- // the Jalview
- // specific
- // bits.
- AnnotationElement ae;
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if (aa[i].annotations[a] == null)
- {
- continue;
- }
-
- ae = new AnnotationElement();
- ae.setDescription(aa[i].annotations[a].description);
- ae.addGlyph(new Glyph());
- ae.getGlyph(0)
- .setContent(aa[i].annotations[a].displayCharacter); // assume
- // jax-b
- // takes
- // care
- // of
- // utf8
- // translation
- if (aa[i].graph !=
- jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+ // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
+ // sref, aa[i]);
+ if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
{
- ae.addValue(aa[i].annotations[a].value);
- }
- ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
- // symbols
- if (aa[i].annotations[a].secondaryStructure != ' ')
- {
- // 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.setContent(String
- .valueOf(aa[i].annotations[a].
- secondaryStructure));
- ae.addGlyph(ss);
+ Vobject alsref = getjv2vObj(jvalsq);
+ saveAlignmentSequenceAnnotation(AlSeqMaps,
+ (AlignmentSequence) alsref, aa[i]);
+ break;
}
- an.addAnnotationElement(ae);
- }
- }
- else
- {
- // update reference sequence Annotation
- if (an.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
- {
- // verify existing alignment sequence annotation is up to date
- System.out.println("update alignment sequence annotation.");
- }
- else
- {
- // verify existing alignment sequence annotation is up to date
- System.out
- .println(
- "make new alignment sequence annotation if modification has happened.");
+ ;
}
}
}
else
{
// add Alignment Annotation
- uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.
- objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+ uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
if (an == null)
{
an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
- an.setType("jalview:AnnotationRow");
+ an.setType(JALVIEW_ANNOTATION_ROW);
an.setDescription(aa[i].description);
alignment.addAlignmentAnnotation(an);
- Seg vSeg = new Seg();
+ Seg vSeg = new Seg(); // TODO: refactor to have a default
+ // rangeAnnotationType initer/updater that
+ // takes a set of int ranges.
vSeg.setStart(1);
vSeg.setInclusive(true);
vSeg.setEnd(jal.getWidth());
@@ -549,9 +611,10 @@ public class VamsasAppDatastore
}
an.setLabel(aa[i].label);
an.setProvenance(dummyProvenance());
- if (aa[i].graph != aa[i].NO_GRAPH)
+ if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
{
- an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote -
+ an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote
+ // -
// originally we
// were going to
// store
@@ -569,7 +632,7 @@ public class VamsasAppDatastore
for (int a = 0; a < aa[i].annotations.length; a++)
{
- if ( (aa[i] == null) || (aa[i].annotations[a] == null))
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
{
continue;
}
@@ -577,64 +640,71 @@ public class VamsasAppDatastore
ae = new AnnotationElement();
ae.setDescription(aa[i].annotations[a].description);
ae.addGlyph(new Glyph());
- ae.getGlyph(0)
- .setContent(aa[i].annotations[a].displayCharacter); // assume
+ ae.getGlyph(0).setContent(
+ aa[i].annotations[a].displayCharacter); // assume
// jax-b
// takes
// care
// 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.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
ss.setContent(String
- .valueOf(aa[i].annotations[a].
- secondaryStructure));
+ .valueOf(aa[i].annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
}
if (aa[i].editable)
{
- //an.addProperty(newProperty("jalview:editable", null, "true"));
- // an.setModifiable(""); // TODO: This is not the way the modifiable flag is supposed to be used.
+ // an.addProperty(newProperty("jalview:editable", null,
+ // "true"));
+ // an.setModifiable(""); // TODO: This is not the way the
+ // 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));
- an.addProperty(newProperty("jalview:graphType", null,
- ( (aa[i].graph ==
- jalview.datamodel.AlignmentAnnotation.
- BAR_GRAPH) ? "BAR_GRAPH" :
- "LINE_GRAPH")));
-
- /** and on and on..
- vProperty=new Property();
- vProperty.setName("jalview:graphThreshhold");
- vProperty.setContent(aa[i].threshold);
- */
-
+ 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)
+ if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT
+ // LOCK METHODS)
{
// verify annotation - update (perhaps)
- Cache.log.info(
- "update alignment sequence annotation. not yet implemented.");
+ Cache.log
+ .info("update alignment sequence annotation. not yet implemented.");
}
else
{
// verify annotation - update (perhaps)
- Cache.log.info("updated alignment sequence annotation added.");
+ Cache.log
+ .info("updated alignment sequence annotation added.");
}
}
}
@@ -648,7 +718,8 @@ public class VamsasAppDatastore
// FIND ANY ASSOCIATED TREES
if (Desktop.desktop != null)
{
- javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ javax.swing.JInternalFrame[] frames = Desktop.instance
+ .getAllFrames();
for (int t = 0; t < frames.length; t++)
{
@@ -656,36 +727,11 @@ public class VamsasAppDatastore
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.getAlignment() == jal)
+ if (tp.getViewPort().getSequenceSetId()
+ .equals(av.getSequenceSetId()))
{
- Tree tree = (Tree) getjv2vObj(tp);
- if (tree == null)
- {
- tree = new Tree();
- bindjvvobj(tp, tree);
- tree.setTitle(tp.getTitle());
- Newick newick = new Newick();
- // TODO: translate sequenceI to leaf mappings to vamsas
- // references - see tree specification in schema.
- newick.setContent(tp.getTree().toString());
- newick.setTitle(tp.getTitle());
- tree.addNewick(newick);
- tree.setProvenance(makeTreeProvenance(jal, tp));
- alignment.addTree(tree);
- }
- else
- {
- if (tree.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
- {
- // verify any changes.
- System.out.println("Update tree in document.");
- }
- else
- {
- System.out
- .println("Add modified tree as new tree in document.");
- }
- }
+ DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
+ jal, alignment);
}
}
}
@@ -697,189 +743,510 @@ public class VamsasAppDatastore
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(AlignmentViewport av)
+ {
+ return (!av.getAlignment().isAligned());
}
- private Property newProperty(String name, String type, String content)
+ private void addToSkipList(AlignmentViewport av)
{
- Property vProperty = new Property();
- vProperty.setName(name);
- if (type != null)
- {
- vProperty.setType(type);
- }
- else
+ if (skipList == null)
{
- vProperty.setType("String");
+ skipList = new Hashtable();
}
- vProperty.setContent(content);
- return vProperty;
+ skipList.put(av.getSequenceSetId(), av);
}
/**
- * correctly create a RangeAnnotation from a jalview sequence feature
- *
- * @param dsa
- * (typically DataSetAnnotations or AlignmentSequenceAnnotation)
- * @param feature
- * (the feature to be mapped from)
- * @return
+ * remove docseqs from the given alignment marking provenance appropriately
+ * and removing any references to the sequences.
+ *
+ * @param alignment
+ * @param docseqs
*/
- private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
- SequenceFeature feature)
+ private void removeValignmentSequences(Alignment alignment, Vector docseqs)
{
- 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)
+ // delete these from document. This really needs to be a generic document
+ // API function derived by CASTOR.
+ Enumeration en = docseqs.elements();
+ while (en.hasMoreElements())
{
- for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
+ 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)
{
- String link = (String) feature.links.elementAt(i);
- int sep = link.indexOf('|');
- if (sep > -1)
+ int p = 0;
+ Vector storem = new Vector();
+ Enumeration sr = alan.enumerateSeqrefs();
+ while (sr.hasMoreElements())
{
- Link vLink = new Link();
- if (sep > 0)
- {
- vLink.setContent(link.substring(0, sep - 1));
- }
- else
+ Object alsr = sr.nextElement();
+ if (docseqs.contains(alsr))
{
- vLink.setContent("");
+ storem.addElement(alsr);
}
- vLink.setHref(link.substring(sep + 1)); // TODO: validate href.
- dsa.addLink(vLink);
+ }
+ // 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);
}
}
}
- dsa.setGroup(feature.getFeatureGroup());
- return dsa;
+ // 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
}
/**
- * correctly creates provenance for trees calculated on an alignment by
- * jalview.
- *
- * @param jal
- * @param tp
- * @return
+ * 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 Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
+ private boolean syncToAlignmentSequence(SequenceI jvalsq,
+ Alignment alignment, Vector unbounddocseq)
{
- Provenance prov = new Provenance();
- prov.addEntry(new Entry());
- prov.getEntry(0).setAction("imported " + tp.getTitle());
- prov.getEntry(0).setUser(provEntry.getUser());
- prov.getEntry(0).setApp(provEntry.getApp());
- prov.getEntry(0).setDate(provEntry.getDate());
- if (tp.getTree().hasOriginalSequenceData())
- {
- Input vInput = new Input();
- // LATER: check to see if tree input data is contained in this alignment -
- // or just correctly resolve the tree's seqData to the correct alignment in
- // the document.
- // vInput.setObjRef(getjv2vObj(jal));
- vInput.setObjRef(getjv2vObj(tp.getViewPort()));
- prov.getEntry(0).setAction("created " + tp.getTitle());
- prov.getEntry(0).addInput(vInput);
- vInput.setName("jalview:seqdist");
- prov.getEntry(0).addParam(new Param());
- prov.getEntry(0).getParam(0).setName("treeType");
- prov.getEntry(0).getParam(0).setType("utf8");
- prov.getEntry(0).getParam(0).setContent("NJ");
-
- int ranges[] = tp.getTree().seqData.getVisibleContigs();
- // VisibleContigs are with respect to alignment coordinates. Still need offsets
- int start = tp.getTree().seqData.getAlignmentOrigin();
- for (int r = 0; r < ranges.length; r += 2)
- {
- Seg visSeg = new Seg();
- visSeg.setStart(1 + start + ranges[r]);
- visSeg.setEnd(start + ranges[r + 1]);
- visSeg.setInclusive(true);
- vInput.addSeg(visSeg);
+ 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);
}
}
- return prov;
+ // 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;
}
/**
- *
- * @param tp
- * @return Object[] { AlignmentView, AlignmentI - reference alignment for
- * input }
+ * 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 Object[] recoverInputData(Provenance tp)
+ private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
+ char valGapchar, char gapChar, List dsseqs)
+
{
- for (int pe = 0; pe < tp.getEntryCount(); pe++)
+ boolean modal = false;
+ // todo: islocked method here
+ boolean upFromdoc = false;
+ jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
+ if (alseq == null)
{
- if (tp.getEntry(pe).getInputCount() > 0)
+ 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())
{
- if (tp.getEntry(pe).getInputCount() > 1)
+ 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)
{
- Cache.log.warn("Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
+ alseq.setDescription(valseq.getDescription());
}
- // LATER: deal sensibly with multiple inputs.
- Input vInput = tp.getEntry(pe).getInput(0);
- if (vInput.getObjRef() instanceof uk.ac.vamsas.objects.core.Alignment)
+ else
{
- // recover an AlignmentView for the input data
- AlignViewport javport = (AlignViewport) getvObj2jv( (uk.ac.vamsas.
- client.Vobject) vInput
- .getObjRef());
- jalview.datamodel.AlignmentI jal = javport.getAlignment();
- jalview.datamodel.CigarArray view = javport.getAlignment().
- getCompactAlignment();
- int from = 1, to = jal.getWidth();
- int offset = 0; // deleteRange modifies its frame of reference
- for (int r = 0, s = vInput.getSegCount(); r < s; r++)
+ // inherit description line from dataset.
+ if (alseq.getDatasetSequence().getDescription() != null)
{
- Seg visSeg = vInput.getSeg(r);
- int se[] = getSegRange(visSeg, true); // jalview doesn't do bidirection alignments yet.
- if (to < se[1])
- {
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
- }
- else
- {
- if (se[0] > from)
- {
- view.deleteRange(offset + from - 1, offset + se[0] - 2);
- offset -= se[0] - from;
- }
- from = se[1] + 1;
- }
+ alseq.setDescription(alseq.getDatasetSequence()
+ .getDescription());
}
- if (from < to)
- {
- view.deleteRange(offset + from - 1, offset + to - 1); // final deletion - TODO: check off by
- // one for to
- }
- return new Object[]
- {
- new AlignmentView(view), jal};
}
+ // if
+ // AlignemntSequence
+ // reference
+ // isn't
+ // a
+ // simple
+ // SequenceI
}
+ else
+ {
+ Cache.log
+ .error("Invalid dataset sequence id (null) for alignment sequence "
+ + valseq.getVorbaId());
+ }
+ bindjvvobj(alseq, valseq);
+ alseq.setVamsasId(valseq.getVorbaId().getId());
+ dsseqs.add(alseq);
+ }
+ Vobject datsetseq = (Vobject) valseq.getRefid();
+ if (datsetseq != null)
+ {
+ if (datsetseq != alseq.getDatasetSequence())
+ {
+ modal = true;
+ }
+ alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
+ }
+ return upFromdoc || modal;
+ }
+
+ private void initRangeAnnotationType(RangeAnnotation an,
+ AlignmentAnnotation alan, int[] gapMap)
+ {
+ Seg vSeg = new Seg();
+ vSeg.setStart(1);
+ vSeg.setInclusive(true);
+ vSeg.setEnd(gapMap.length);
+ an.addSeg(vSeg);
+
+ // LATER: much of this is verbatim from the alignmentAnnotation
+ // method below. suggests refactoring to make rangeAnnotation the
+ // base class
+ an.setDescription(alan.description);
+ an.setLabel(alan.label);
+ an.setGroup(Integer.toString(alan.graphGroup));
+ // // JBPNote -
+ // originally we
+ // were going to
+ // store
+ // graphGroup in
+ // the Jalview
+ // specific
+ // bits.
+ AnnotationElement ae;
+ for (int a = 0; a < alan.annotations.length; a++)
+ {
+ if (alan.annotations[a] == null)
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ ae.setDescription(alan.annotations[a].description);
+ ae.addGlyph(new Glyph());
+ ae.getGlyph(0).setContent(alan.annotations[a].displayCharacter); // assume
+ // jax-b
+ // takes
+ // care
+ // of
+ // utf8
+ // translation
+ if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+ {
+ ae.addValue(alan.annotations[a].value);
+ }
+ ae.setPosition(gapMap[a] + 1); // position w.r.t. AlignmentSequence
+ // symbols
+ if (alan.annotations[a].secondaryStructure != ' ')
+ {
+ // 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.setContent(String
+ .valueOf(alan.annotations[a].secondaryStructure));
+ ae.addGlyph(ss);
+ }
+ an.addAnnotationElement(ae);
+ }
+
+ }
+
+ private void saveDatasetSequenceAnnotation(HashMap AlSeqMaps,
+ uk.ac.vamsas.objects.core.Sequence sref, AlignmentAnnotation alan)
+ {
+ // {
+ // uk.ac.vamsas.
+ // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
+ // objects.core.AlignmentSequence) sref;
+ uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan);
+ int[] gapMap = getGapMap(AlSeqMaps, alan);
+ if (an == null)
+ {
+ an = new uk.ac.vamsas.objects.core.DataSetAnnotations();
+ initRangeAnnotationType(an, alan, gapMap);
+
+ an.setProvenance(dummyProvenance()); // get provenance as user
+ // created, or jnet, or
+ // something else.
+ setAnnotationType(an, alan);
+ an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote -
+ // originally we
+ // were going to
+ // store
+ // graphGroup in
+ // the Jalview
+ // specific
+ // bits.
+ if (alan.getThreshold() != null && alan.getThreshold().displayed)
+ {
+ 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);
+ }
+ else
+ {
+ // update reference sequence Annotation
+ if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
+ // METHODS)
+ {
+ // verify existing alignment sequence annotation is up to date
+ System.out.println("update dataset sequence annotation.");
+ }
+ else
+ {
+ // verify existing alignment sequence annotation is up to date
+ System.out
+ .println("make new alignment dataset sequence annotation if modification has happened.");
+ }
+ }
+
+ }
+
+ private int[] getGapMap(HashMap AlSeqMaps, AlignmentAnnotation alan)
+ {
+ int[] gapMap;
+ if (AlSeqMaps.containsKey(alan.sequenceRef))
+ {
+ gapMap = (int[]) AlSeqMaps.get(alan.sequenceRef);
+ }
+ else
+ {
+ gapMap = new int[alan.sequenceRef.getLength()];
+ // map from alignment position to sequence position.
+ int[] sgapMap = alan.sequenceRef.gapMap();
+ for (int a = 0; a < sgapMap.length; a++)
+ {
+ gapMap[sgapMap[a]] = a;
+ }
+ }
+ return gapMap;
+ }
+
+ private void saveAlignmentSequenceAnnotation(HashMap AlSeqMaps,
+ AlignmentSequence alsref, AlignmentAnnotation alan)
+ {
+ // {
+ // uk.ac.vamsas.
+ // objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
+ // objects.core.AlignmentSequence) sref;
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan);
+ int[] gapMap = getGapMap(AlSeqMaps, alan);
+ if (an == null)
+ {
+ an = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation();
+ initRangeAnnotationType(an, alan, gapMap);
+ /**
+ * I mean here that we don't actually have a semantic 'type' for the
+ * annotation (this might be - score, intrinsic property, measurement,
+ * something extracted from another program, etc)
+ */
+ an.setType(JALVIEW_ANNOTATION_ROW); // TODO: better fix
+ // this rough guess ;)
+ alsref.addAlignmentSequenceAnnotation(an);
+ bindjvvobj(alan, an);
+ // These properties are directly supported by the
+ // AlignmentSequenceAnnotation type.
+ setAnnotationType(an, alan);
+ an.setProvenance(dummyProvenance()); // get provenance as user
+ // created, or jnet, or
+ // something else.
+ }
+ else
+ {
+ // update reference sequence Annotation
+ if (an.getModifiable() == null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK
+ // METHODS)
+ {
+ // verify existing alignment sequence annotation is up to date
+ System.out.println("update alignment sequence annotation.");
+ }
+ else
+ {
+ // verify existing alignment sequence annotation is up to date
+ System.out
+ .println("make new alignment sequence annotation if modification has happened.");
+ }
+ }
+ }
+
+ /**
+ * set vamsas annotation object type from jalview annotation
+ *
+ * @param an
+ * @param 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(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(false);
+ }
+ }
+ switch (alan.graph)
+ {
+ 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.
}
- Cache.log.debug("Returning null for input data recovery from provenance.");
- return null;
}
/**
* get start 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;
+ Set 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)
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMappings(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)
+ {
+ // NOTE: this happens if user deletes object in one session then updates
+ // from another client
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_old_jalview_object_not_bound",
+ new String[] { oldjvobject.toString() }));
+ }
+ 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.");
+ }
}
/**
- *
- * @param annotation
- * @return true if annotation is not to be stored in document
+ * translate the Vobject keys to strings for use in Jalview2XML
+ *
+ * @param jv2vobj2
+ * @return
*/
- private boolean isJalviewOnly(AlignmentAnnotation annotation)
+ private IdentityHashMap mapValuesToString(IdentityHashMap jv2vobj2)
{
- return annotation.label.equals("Quality")
- || annotation.label.equals("Conservation")
- || annotation.label.equals("Consensus");
+ 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;
}
/**
- * 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
+ * translate the Vobject values to strings for use in Jalview2XML
+ *
+ * @param vobj2jv2
+ * @return hashtable with string values
*/
- public AlignFrame getAlignFrameFor(AlignViewport av)
+ private Hashtable mapKeysToString(Hashtable vobj2jv2)
{
- if (Desktop.desktop != null)
+ Hashtable mapped = new Hashtable();
+ Iterator keys = vobj2jv2.keySet().iterator();
+ while (keys.hasNext())
{
- 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() == av)
- {
- return (AlignFrame) frames[t];
- }
- }
- }
+ Object key = keys.next();
+ mapped.put(key.toString(), vobj2jv2.get(key));
}
- return null;
+ return mapped;
}
- public void updateToJalview()
+ /**
+ * synchronize Jalview from the vamsas document
+ *
+ * @return number of new views from document
+ */
+ public int updateToJalview()
{
VAMSAS _roots[] = cdoc.getVamsasRoots();
@@ -954,9 +1605,8 @@ public class VamsasAppDatastore
// ///LOAD DATASET
DataSet dataset = root.getDataSet(_ds);
int i, iSize = dataset.getSequenceCount();
- Vector dsseqs;
- jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment)
- getvObj2jv(dataset);
+ List dsseqs;
+ jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
int jremain = 0;
if (jdataset == null)
{
@@ -977,26 +1627,12 @@ public class VamsasAppDatastore
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)
@@ -1004,19 +1640,10 @@ public class VamsasAppDatastore
DbRef[] dbref = vdseq.getDbRef();
for (int db = 0; db < dbref.length; db++)
{
- jalview.datamodel.DBRefEntry dbr = (jalview.datamodel.DBRefEntry)
- getvObj2jv(dbref[db]);
- if (dbr == null)
- {
- // add new dbref
- dsseq.addDBRef(dbr = new jalview.datamodel.DBRefEntry
- (
- dbref[db].getSource().toString(),
- dbref[db].getVersion().toString(),
- dbref[db].getAccessionId().toString()));
- bindjvvobj(dbr, dbref[db]);
- }
+ new jalview.io.vamsas.Dbref(this, dbref[db], vdseq, dsseq);
+
}
+ dsseq.updatePDBIds();
}
}
@@ -1025,8 +1652,8 @@ public class VamsasAppDatastore
SequenceI[] seqs = new SequenceI[dsseqs.size()];
for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
{
- seqs[i] = (SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
+ seqs[i] = dsseqs.get(i);
+ dsseqs.set(i, null);
}
jdataset = new jalview.datamodel.Alignment(seqs);
Cache.log.debug("New vamsas dataset imported into jalview.");
@@ -1039,57 +1666,71 @@ public class VamsasAppDatastore
for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
{
DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
- SequenceI dsSeq = (SequenceI) getvObj2jv( (Vobject) dseta.getSeqRef());
- if (dsSeq == null)
- {
- jalview.bin.Cache.log.warn(
- "Couldn't resolve jalview sequenceI for dataset object reference " +
- ( (Vobject) dataset.getDataSetAnnotations(dsa).getSeqRef()).
- getVorbaId().getId());
- }
- else
+ // TODO: deal with group annotation on datset sequences.
+ if (dseta.getSeqRefCount() == 1)
{
- if (dseta.getAnnotationElementCount() == 0)
+ SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta
+ .getSeqRef(0)); // TODO: deal with group dataset
+ // annotations
+ if (dsSeq == null)
{
- jalview.datamodel.SequenceFeature sf = (jalview.datamodel.
- SequenceFeature) getvObj2jv(dseta);
- if (sf == null)
- {
- dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dseta));
- bindjvvobj(sf, dseta);
- }
+ jalview.bin.Cache.log
+ .warn("Couldn't resolve jalview sequenceI for dataset object reference "
+ + ((Vobject) dataset.getDataSetAnnotations(
+ dsa).getSeqRef(0)).getVorbaId()
+ .getId());
}
else
{
- // TODO: deal with alignmentAnnotation style annotation
- // appearing on dataset sequences.
- // JBPNote: we could just add them to all alignments but
- // that may complicate cross references in the jalview
- // datamodel
- Cache.log.warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
+ if (dseta.getAnnotationElementCount() == 0)
+ {
+ new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
+
+ }
+ else
+ {
+ // TODO: deal with alignmentAnnotation style annotation
+ // appearing on dataset sequences.
+ // JBPNote: we could just add them to all alignments but
+ // that may complicate cross references in the jalview
+ // datamodel
+ Cache.log
+ .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.");
+ }
}
}
-
if (dataset.getAlignmentCount() > 0)
{
// LOAD ALIGNMENTS from DATASET
for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
{
- uk.ac.vamsas.objects.core.Alignment alignment = dataset.getAlignment(
- al);
- AlignViewport av = (AlignViewport) getvObj2jv(alignment);
+ uk.ac.vamsas.objects.core.Alignment alignment = dataset
+ .getAlignment(al);
+ // TODO check this handles multiple views properly
+ AlignmentViewport 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
+ char gapChar = ' '; // default for new alignments read in from the
+ // document
if (jal != null)
{
dsseqs = jal.getSequences(); // for merge/update
@@ -1103,73 +1744,64 @@ public class VamsasAppDatastore
for (i = 0; i < iSize; i++)
{
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
- jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq);
- if (alseq != null)
+ jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
+ if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
+ dsseqs) && alseq != null)
{
- //TODO: upperCase/LowerCase situation here ? do we allow it ?
- //if (!alseq.getSequence().equals(valseq.getSequence())) {
- // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence.");
- if (Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Updating apparently edited sequence " +
- alseq.getName());
- }
- // this might go *horribly* wrong
- alseq.setSequence(new String(valseq.getSequence()).replace(
- valGapchar, gapChar));
+
+ // updated to sequence from the document
jremain--;
- }
- else
- {
- alseq = new jalview.datamodel.Sequence(
- valseq.getName(),
- valseq.getSequence().replace(valGapchar, gapChar),
- (int)valseq.getStart(),
- (int)valseq.getEnd());
-
- Vobject datsetseq = (Vobject) valseq.getRefid();
- if (datsetseq != null)
- {
- alseq.setDatasetSequence( (SequenceI) getvObj2jv(datsetseq)); // exceptions if AlignemntSequence reference isn't a simple SequenceI
- }
- else
- {
- Cache.log.error(
- "Invalid dataset sequence id (null) for alignment sequence " +
- valseq.getVorbaId());
- }
- bindjvvobj(alseq, valseq);
- alseq.setVamsasId(valseq.getVorbaId().getId());
- dsseqs.add(alseq);
+ refreshal = true;
}
if (valseq.getAlignmentSequenceAnnotationCount() > 0)
{
- AlignmentSequenceAnnotation[] vasannot = valseq.
- getAlignmentSequenceAnnotation();
+ AlignmentSequenceAnnotation[] vasannot = valseq
+ .getAlignmentSequenceAnnotation();
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
+ jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
+ // 1:many
+ // jalview
+ // alignment
+ // sequence
+ // annotations
if (asa == null)
{
int se[] = getBounds(vasannot[a]);
asa = getjAlignmentAnnotation(jal, vasannot[a]);
- asa.sequenceRef = alseq;
- asa.createSequenceMapping(alseq, alseq.getStart() + se[0], false); // TODO: verify that positions in alseqAnnotation correspond to ungapped residue positions.
+ asa.setSequenceRef(alseq);
+ asa.createSequenceMapping(alseq, se[0], false); // TODO:
+ // 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)
+ if (vasannot[a].getModifiable() == null) // TODO: USE
+ // VAMSAS LIBRARY
+ // OBJECT LOCK
+ // METHODS)
{
- Cache.log.info(
- "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
- // TODO: should at least replace with new one - otherwise things will break
+ Cache.log
+ .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
+ // TODO: should at least replace with new one - otherwise
+ // things will break
// basically do this:
// int se[] = getBounds(vasannot[a]);
- // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); // update from another annotation object in place.
+ // asa.update(getjAlignmentAnnotation(jal, vasannot[a]));
+ // // update from another annotation object in place.
// asa.createSequenceMapping(alseq, se[0], false);
}
@@ -1182,12 +1814,12 @@ public class VamsasAppDatastore
SequenceI[] seqs = new SequenceI[dsseqs.size()];
for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
{
- seqs[i] = (SequenceI) dsseqs.elementAt(i);
- dsseqs.setElementAt(null, i);
+ seqs[i] = dsseqs.get(i);
+ dsseqs.set(i, null);
}
jal = new jalview.datamodel.Alignment(seqs);
- Cache.log.debug("New vamsas alignment imported into jalview " +
- alignment.getVorbaId().getId());
+ Cache.log.debug("New vamsas alignment imported into jalview "
+ + alignment.getVorbaId().getId());
jal.setDataset(jdataset);
}
if (newasAnnots != null && newasAnnots.size() > 0)
@@ -1195,9 +1827,10 @@ public class VamsasAppDatastore
// Add the new sequence annotations in to the alignment.
for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
{
- jal.addAnnotation( (AlignmentAnnotation) newasAnnots.elementAt(
- an));
- // TODO: check if anything has to be done - like calling adjustForAlignment or something.
+ jal.addAnnotation((AlignmentAnnotation) newasAnnots
+ .elementAt(an));
+ // TODO: check if anything has to be done - like calling
+ // adjustForAlignment or something.
newasAnnots.setElementAt(null, an);
}
newasAnnots = null;
@@ -1207,26 +1840,31 @@ public class VamsasAppDatastore
// ////////////////////////////////////
if (alignment.getAlignmentAnnotationCount() > 0)
{
- uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment.
- getAlignmentAnnotation();
+ uk.ac.vamsas.objects.core.AlignmentAnnotation[] an = alignment
+ .getAlignmentAnnotation();
for (int j = 0; j < an.length; j++)
{
- jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.
- AlignmentAnnotation) getvObj2jv(an[j]);
+ jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
if (jan != null)
{
// update or stay the same.
- // TODO: should at least replace with a new one - otherwise things will break
+ // TODO: should at least replace with a new one - otherwise
+ // things will break
// basically do this:
- // jan.update(getjAlignmentAnnotation(jal, an[a])); // update from another annotation object in place.
-
- 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)
+ // jan.update(getjAlignmentAnnotation(jal, an[a])); // update
+ // from another annotation object in place.
+
+ 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)
{
- // TODO: user defined annotation is totally mutable... - so load it up or throw away if locally edited.
- Cache.log.info(
- "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
+ // TODO: user defined annotation is totally mutable... - so
+ // load it up or throw away if locally edited.
+ Cache.log
+ .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
// TODO: compare props.
@@ -1234,46 +1872,64 @@ public class VamsasAppDatastore
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;
}
}
}
AlignFrame alignFrame;
if (av == null)
{
- Cache.log.debug("New alignframe for alignment " +
- alignment.getVorbaId());
+ Cache.log.debug("New alignframe for alignment "
+ + alignment.getVorbaId());
// ///////////////////////////////
// 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).getAction();
+ 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(
- "jalview:AlTitle"))
+ if (alignment.getProperty(p).getName().equals("title"))
{
title = alignment.getProperty(p).getContent();
}
}
}
- // TODO: automatically create meaningful title for a vamsas alignment using its provenance.
- jalview.gui.Desktop.addInternalFrame(alignFrame,
- title + "(" + alignment.getVorbaId() + ")",
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- bindjvvobj(av, alignment);
+ // TODO: automatically create meaningful title for a vamsas
+ // alignment using its provenance.
+ if (Cache.log.isDebugEnabled())
+ {
+ title = title + "(" + alignment.getVorbaId() + ")";
+
+ }
+ jalview.gui.Desktop.addInternalFrame(alignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ bindjvvobj(av.getSequenceSetId(), alignment);
}
else
{
// find the alignFrame for jal.
- // TODO: fix this so we retrieve the alignFrame handing av *directly*
- alignFrame = getAlignFrameFor(av);
+ // TODO: fix this so we retrieve the alignFrame handing 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
// /////////////////////////////////////
@@ -1282,84 +1938,118 @@ public class VamsasAppDatastore
for (int t = 0; t < alignment.getTreeCount(); t++)
{
- Tree tree = alignment.getTree(t);
- TreePanel tp = (TreePanel) getvObj2jv(tree);
- if (tp != null)
+ jalview.io.vamsas.Tree vstree = new jalview.io.vamsas.Tree(
+ this, alignFrame, alignment.getTree(t));
+ TreePanel tp = null;
+ if (vstree.isValidTree())
{
- Cache.log.info(
- "Update from vamsas document to alignment associated tree not implemented yet.");
+ tp = alignFrame.ShowNewickTree(vstree.getNewickTree(),
+ vstree.getTitle(), vstree.getInputData(), 600,
+ 500, t * 20 + 50, t * 20 + 50);
+
}
- else
+ if (tp != null)
{
- // make a new tree
- Object[] idata = this.recoverInputData(tree.getProvenance());
+ bindjvvobj(tp, alignment.getTree(t));
try
{
- AlignmentView inputData = null;
- if (idata != null && idata[0] != null)
- {
- inputData = (AlignmentView) idata[0];
- }
- tp = alignFrame.ShowNewickTree(
- new jalview.io.NewickFile(tree.getNewick(0).getContent()),
- tree.getNewick(0).getTitle() + " (" + tree.getVorbaId() +
- ")", inputData,
- 600, 500,
- t * 20 + 50, t * 20 + 50);
- bindjvvobj(tp, tree);
- }
- catch (Exception e)
+ vstree.UpdateSequenceTreeMap(tp);
+ } catch (RuntimeException e)
{
- Cache.log.warn("Problems parsing treefile '" +
- tree.getNewick(0).getContent() + "'", 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());
+ }
+
}
}
-
}
}
}
+ // we do sequenceMappings last because they span all datasets in a vamsas
+ // root
+ for (int _ds = 0, _nds = root.getDataSetCount(); _ds < _nds; _ds++)
+ {
+ DataSet dataset = root.getDataSet(_ds);
+ if (dataset.getSequenceMappingCount() > 0)
+ {
+ for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++)
+ {
+ Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
+ dataset.getSequenceMapping(sm));
+ }
+ }
+ }
+ }
+ return newAlignmentViews.size();
+ }
+
+ public AlignmentViewport findViewport(Alignment alignment)
+ {
+ AlignmentViewport av = null;
+ AlignmentViewport[] avs = Desktop
+ .getViewports((String) getvObj2jv(alignment));
+ if (avs != null)
+ {
+ av = avs[0];
}
+ return av;
}
// bitfields - should be a template in j1.5
private static int HASSECSTR = 0;
+
private static int HASVALS = 1;
+
private static int HASHPHOB = 2;
+
private static int HASDC = 3;
+
private static int HASDESCSTR = 4;
+
private static int HASTWOSTATE = 5; // not used yet.
+
/**
- * parses the AnnotationElements - if they exist - into jalview.datamodel.Annotation[] rows
- * Two annotation rows are made if there are distinct annotation for both at 'pos' and 'after pos' at any particular site.
+ * parses the AnnotationElements - if they exist - into
+ * jalview.datamodel.Annotation[] rows Two annotation rows are made if there
+ * are distinct annotation for both at 'pos' and 'after pos' at any particular
+ * site.
+ *
* @param annotation
- * @return { boolean[static int constants ], int[ae.length] - map to annotated object frame, jalview.datamodel.Annotation[], jalview.datamodel.Annotation[] (after)}
+ * @return { boolean[static int constants ], int[ae.length] - map to annotated
+ * object frame, jalview.datamodel.Annotation[],
+ * jalview.datamodel.Annotation[] (after)}
*/
- private Object[] parseRangeAnnotation(uk.ac.vamsas.objects.core.RangeAnnotation
- annotation)
+ private Object[] parseRangeAnnotation(
+ uk.ac.vamsas.objects.core.RangeAnnotation annotation)
{
- // set these attributes by looking in the annotation to decide what kind of alignment annotation rows will be made
- // TODO: potentially we might make several annotation rows from one vamsas alignment annotation. the jv2Vobj binding mechanism
- // may not quite cope with this (without binding an array of annotations to a vamsas alignment annotation)
+ // set these attributes by looking in the annotation to decide what kind of
+ // alignment annotation rows will be made
+ // TODO: potentially we might make several annotation rows from one vamsas
+ // alignment annotation. the jv2Vobj binding mechanism
+ // may not quite cope with this (without binding an array of annotations to
+ // a vamsas alignment annotation)
// summary flags saying what we found over the set of annotation rows.
- boolean[] AeContent = new boolean[]
- {
- false, false, false, false, false};
+ boolean[] AeContent = new boolean[] { false, false, false, false, false };
int[] rangeMap = getMapping(annotation);
jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
- {
- 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.
+ { 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.
if (annotation.getAnnotationElementCount() > 0)
{
AnnotationElement ae[] = annotation.getAnnotationElement();
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)
+ int pos = (int) ae[aa].getPosition() - 1; // pos counts from 1 to
+ // (|seg.start-seg.end|+1)
if (pos >= 0 && pos < rangeMap.length)
{
int row = ae[aa].getAfter() ? 1 : 0;
@@ -1383,43 +2073,46 @@ public class VamsasAppDatastore
AeContent[HASDESCSTR] = true;
}
}
- String dc = null; //ae[aa].getDisplayCharacter()==null ? "dc" : ae[aa].getDisplayCharacter();
- String ss = null; //ae[aa].getSecondaryStructure()==null ? "ss" : ae[aa].getSecondaryStructure();
+ String dc = null; // ae[aa].getDisplayCharacter()==null ? "dc" :
+ // ae[aa].getDisplayCharacter();
+ String ss = null; // ae[aa].getSecondaryStructure()==null ? "ss" :
+ // ae[aa].getSecondaryStructure();
java.awt.Color colour = null;
if (ae[aa].getGlyphCount() > 0)
{
Glyph[] glyphs = ae[aa].getGlyph();
for (int g = 0; g < glyphs.length; g++)
{
- if (glyphs[g].getDict().equals(uk.ac.vamsas.objects.utils.
- GlyphDictionary.PROTEIN_SS_3STATE))
+ if (glyphs[g]
+ .getDict()
+ .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))
+ else if (glyphs[g]
+ .getDict()
+ .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
Cache.log.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
char c = (dc = glyphs[g].getContent()).charAt(0);
// dc may get overwritten - but we still set the colour.
colour = new java.awt.Color(c == '+' ? 255 : 0,
- c == '.' ? 255 : 0,
- c == '-' ? 255 : 0);
+ c == '.' ? 255 : 0, c == '-' ? 255 : 0);
}
- else if (glyphs[g].getDict().equals(uk.ac.vamsas.objects.utils.
- GlyphDictionary.DEFAULT))
+ else if (glyphs[g].getDict().equals(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.DEFAULT))
{
dc = glyphs[g].getContent();
AeContent[HASDC] = true;
}
else
{
- Cache.log.debug("Ignoring unknown glyph type " +
- glyphs[g].getDict());
+ Cache.log
+ .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ + glyphs[g].getDict());
}
}
}
@@ -1429,27 +2122,29 @@ public class VamsasAppDatastore
AeContent[HASVALS] = true;
if (ae[aa].getValueCount() > 1)
{
- Cache.log.warn("ignoring additional " +
- (ae[aa].getValueCount() - 1) +
- "values in annotation element.");
+ Cache.log.warn("ignoring additional "
+ + (ae[aa].getValueCount() - 1)
+ + " 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);
+ anot[row][pos] = new jalview.datamodel.Annotation(
+ (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);
+ anot[row][pos] = new jalview.datamodel.Annotation(
+ (dc != null) ? dc : "", desc,
+ (ss != null) ? ss.charAt(0) : ' ', val, colour);
}
}
else
{
- Cache.log.warn("Ignoring out of bound annotation element " + aa +
- " in " + annotation.getVorbaId().getId());
+ Cache.log.warn("Ignoring out of bound annotation element " + aa
+ + " in " + annotation.getVorbaId().getId());
}
}
// decide on how many annotation rows are needed.
@@ -1461,7 +2156,8 @@ public class VamsasAppDatastore
{
anot[0][i] = anot[1][i];
anot[0][i].description = anot[0][i].description + " (after)";
- AeContent[HASDESCSTR] = true; // we have valid description string data
+ AeContent[HASDESCSTR] = true; // we have valid description string
+ // data
anot[1][i] = null;
}
}
@@ -1474,43 +2170,95 @@ public class VamsasAppDatastore
anot[1][i].description = anot[1][i].description + " (after)";
}
}
- return new Object[]
- {
- AeContent, rangeMap, anot[0], anot[1]};
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
else
{
- // no annotations to parse. Just return an empty annotationElement[] array.
- return new Object[]
- {
- AeContent, rangeMap, anot[0], anot[1]};
+ // no annotations to parse. Just return an empty annotationElement[]
+ // array.
+ return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
}
// return null;
}
/**
- * @param jal the jalview alignment to which the annotation will be attached (ideally - freshly updated from corresponding vamsas alignment)
+ * @param jal
+ * the jalview alignment to which the annotation will be attached
+ * (ideally - freshly updated from corresponding vamsas alignment)
* @param annotation
* @return unbound jalview alignment annotation object.
*/
- private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(jalview.
- datamodel.AlignmentI jal,
- uk.ac.vamsas.objects.core.RangeAnnotation annotation)
+ private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(
+ jalview.datamodel.AlignmentI jal,
+ uk.ac.vamsas.objects.core.RangeAnnotation annotation)
{
- jalview.datamodel.AlignmentAnnotation jan = null;
if (annotation == null)
{
return null;
}
- // boolean hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
- //boolean hasProvenance=hasSequenceRef || (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
- /*int se[] = getBounds(annotation);
- if (se==null)
- se=new int[] {0,jal.getWidth()-1};
+ // boolean
+ // hasSequenceRef=annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.class);
+ // boolean hasProvenance=hasSequenceRef ||
+ // (annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class));
+ /*
+ * int se[] = getBounds(annotation); if (se==null) se=new int[]
+ * {0,jal.getWidth()-1};
*/
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
+ // 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();
+ 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))
+ {
+ type = AlignmentAnnotation.LINE_GRAPH;
+ }
+ else if (props[p].getName().equalsIgnoreCase(THRESHOLD))
+ {
+ Float val = null;
+ try
+ {
+ val = new Float(props[p].getContent());
+ } 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();
+ }
+ }
+ }
+ else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
+ {
+ if (gl == null)
+ {
+ gl = new GraphLine(0, "", java.awt.Color.black);
+ }
+ gl.label = props[p].getContent();
+ }
+ }
+ }
+ jalview.datamodel.AlignmentAnnotation jan = null;
if (a_label == null || a_label.length() == 0)
{
a_label = annotation.getType();
@@ -1525,27 +2273,45 @@ public class VamsasAppDatastore
}
if (parsedRangeAnnotation == null)
{
- Cache.log.debug(
- "Inserting empty annotation row elements for a whole-alignment annotation.");
-
+ Cache.log
+ .debug("Inserting empty annotation row elements for a whole-alignment annotation.");
}
else
{
if (parsedRangeAnnotation[3] != null)
{
- Cache.log.warn("Ignoring 'After' annotation row in " +
- annotation.getVorbaId());
+ Cache.log.warn("Ignoring 'After' annotation row in "
+ + annotation.getVorbaId());
}
- jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[])
- parsedRangeAnnotation[2];
+ jalview.datamodel.Annotation[] arow = (jalview.datamodel.Annotation[]) parsedRangeAnnotation[2];
boolean[] has = (boolean[]) parsedRangeAnnotation[0];
- // VAMSAS: getGraph is only on derived annotation for alignments - in this 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())) {
+ // VAMSAS: getGraph is only on derived annotation for alignments - in this
+ // 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 (has[HASVALS])
{
- // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)
+ if (type == 0)
+ {
+ type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
+ // type of
+ // value
+ // annotation
+ if (has[HASHPHOB])
+ {
+ // no hints - so we ensure HPHOB display is like this.
+ type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
+ }
+ }
+ // make bounds and automatic description strings for jalview user's
+ // benefit (these shouldn't be written back to vamsas document)
boolean first = true;
float min = 0, max = 1;
int lastval = 0;
@@ -1553,7 +2319,7 @@ public class VamsasAppDatastore
{
if (arow[i] != null)
{
- if (i - lastval > 1)
+ if (i - lastval > 1 && interp)
{
// do some interpolation *between* points
if (arow[lastval] != null)
@@ -1564,13 +2330,15 @@ public class VamsasAppDatastore
for (int ip = lastval + 1, np = 0; ip < i; np++, ip++)
{
arow[ip] = new jalview.datamodel.Annotation("", "", ' ',
- interval * np + base);
- // NB - Interpolated points don't get a tooltip and description.
+ interval * np + base);
+ // NB - Interpolated points don't get a tooltip and
+ // description.
}
}
}
lastval = i;
- // check range - shouldn't we have a min and max property in the annotation object ?
+ // check range - shouldn't we have a min and max property in the
+ // annotation object ?
if (first)
{
min = max = arow[i].value;
@@ -1594,68 +2362,71 @@ public class VamsasAppDatastore
}
if (!has[HASDC])
{
- arow[i].displayCharacter = arow[i].value + "";
+ if (!interp)
+ {
+ 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.
+ arow[i].displayCharacter = arow[i].value + "";
+ }
}
}
}
- int type = jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
- if (has[HASHPHOB])
- {
- type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
- }
- jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow,
- min, max, type);
+ jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
+ arow, min, max, type);
}
else
{
- jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
+ 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.
+ }
+ 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.");
+ 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.getPropertyCount() > 0)
+ try
{
- // look for special jalview properties
- uk.ac.vamsas.objects.core.Property[] props = annotation.getProperty();
- for (int p = 0; p < props.length; p++)
+ if (annotation.getGroup() != null
+ && annotation.getGroup().length() > 0)
{
- if (props[p].getName().equalsIgnoreCase("jalview:graphType"))
- {
- try
- {
- // probably a jalview annotation graph so recover the visualization hints.
- jan.graph = jalview.datamodel.AlignmentAnnotation.
- getGraphValueFromString(props[p].getContent());
- }
- catch (Exception e)
- {
- Cache.log.debug(
- "Invalid graph type value in jalview:graphType property.");
- }
- try
- {
- if (annotation.getGroup() != null &&
- annotation.getGroup().length() > 0)
- {
- jan.graphGroup = Integer.parseInt(annotation.getGroup());
- }
- }
- catch (Exception e)
- {
- Cache.log.info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
- }
- }
+ jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
+ // group
+ // similarly
+ // named
+ // annotation
+ // together
+ // ?
}
+ } catch (Exception e)
+ {
+ Cache.log
+ .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
-
return jan;
}
@@ -1663,27 +2434,11 @@ 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
- * inclusive range within which all segments and positions lie.
- * TODO: refactor to vamsas utils
+ * inclusive range within which all segments and positions lie. TODO: refactor
+ * to vamsas utils
+ *
* @param dseta
* @return int[] { start, end}
*/
@@ -1694,7 +2449,9 @@ public class VamsasAppDatastore
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
@@ -1714,11 +2471,10 @@ public class VamsasAppDatastore
}
if (dseta.getPosCount() > 0)
{
- // could do a polarity for pos range too. and pass back indication of discontinuities.
+ // could do a polarity for pos range too. and pass back indication of
+ // discontinuities.
int pos = dseta.getPos(0).getI();
- se = new int[]
- {
- pos, pos};
+ se = new int[] { pos, pos };
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
@@ -1738,7 +2494,9 @@ public class VamsasAppDatastore
}
/**
- * map from a rangeType's internal frame to the referenced object's coordinate frame.
+ * map from a rangeType's internal frame to the referenced object's coordinate
+ * frame.
+ *
* @param dseta
* @return int [] { ref(pos)...} for all pos in rangeType's frame.
*/
@@ -1750,7 +2508,9 @@ public class VamsasAppDatastore
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
@@ -1780,7 +2540,7 @@ public class VamsasAppDatastore
int[] range = new int[posList.size()];
for (int i = 0; i < range.length; i++)
{
- range[i] = ( (Integer) posList.elementAt(i)).intValue();
+ range[i] = ((Integer) posList.elementAt(i)).intValue();
}
posList.clear();
return range;
@@ -1788,48 +2548,89 @@ public class VamsasAppDatastore
return null;
}
- /* not needed now.
- * Provenance getVamsasProvenance(jalview.datamodel.Provenance jprov) {
- jalview.datamodel.ProvenanceEntry[] entries = null;
- // TODO: fix App and Action here.
- Provenance prov = new Provenance();
- org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
- new java.util.Date());
- Entry provEntry;
+ /**
+ *
+ * @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
+ * @return MapList
+ */
+ private jalview.util.MapList parsemapType(MapType maprange, int localu,
+ int mappedu)
+ {
+ jalview.util.MapList ml = null;
+ int[] localRange = getMapping(maprange.getLocal());
+ int[] mappedRange = getMapping(maprange.getMapped());
+ long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
+ : localu;
+ long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
+ .getUnit() : mappedu;
+ ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
+ (int) mu);
+ return ml;
+ }
- if (jprov != null)
+ /**
+ * initialise a range type object from a set of start/end inclusive intervals
+ *
+ * @param mrt
+ * @param ranges
+ */
+ private void initRangeType(RangeType mrt, List ranges)
+ {
+ for (int[] range : ranges)
{
- 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();
-
- date = new org.exolab.castor.types.Date(entries[i].getDate());
- }
- provEntry.setDate(date);
- provEntry.setUser(entries[i].getUser());
- provEntry.setAction(entries[i].getAction());
- prov.addEntry(provEntry);
- }
+ Seg vSeg = new Seg();
+ vSeg.setStart(range[0]);
+ vSeg.setEnd(range[1]);
+ mrt.addSeg(vSeg);
}
- else
+ }
+
+ /**
+ * initialise a MapType object from a MapList object.
+ *
+ * @param maprange
+ * @param ml
+ * @param setUnits
+ */
+ private void initMapType(MapType maprange, jalview.util.MapList ml,
+ boolean setUnits)
+ {
+ maprange.setLocal(new Local());
+ maprange.setMapped(new Mapped());
+ initRangeType(maprange.getLocal(), ml.getFromRanges());
+ initRangeType(maprange.getMapped(), ml.getToRanges());
+ if (setUnits)
{
- provEntry = new Entry();
- provEntry.setDate(date);
- provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
- provEntry.setApp("JVAPP"); // TODO: ext string
- provEntry.setAction(action);
- prov.addEntry(provEntry);
+ maprange.getLocal().setUnit(ml.getFromRatio());
+ maprange.getLocal().setUnit(ml.getToRatio());
}
+ }
- return prov;
- }
+ /*
+ * not needed now. Provenance getVamsasProvenance(jalview.datamodel.Provenance
+ * jprov) { jalview.datamodel.ProvenanceEntry[] entries = null; // TODO: fix
+ * App and Action here. Provenance prov = new Provenance();
+ * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new
+ * java.util.Date()); Entry provEntry;
+ *
+ * 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();
+ *
+ * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
+ * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
+ * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } }
+ * else { provEntry = new Entry(); provEntry.setDate(date);
+ * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
+ * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action);
+ * prov.addEntry(provEntry); }
+ *
+ * return prov; }
*/
jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
{
@@ -1837,16 +2638,16 @@ public class VamsasAppDatastore
jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
for (int i = 0; i < prov.getEntryCount(); i++)
{
- jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i).getAction(),
- prov.getEntry(i).getDate().toDate(),
- prov.getEntry(i).getId());
+ jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
+ .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
+ .getId());
}
return jprov;
}
/**
- *
+ *
* @return default initial provenance list for a Jalview created vamsas
* object.
*/
@@ -1867,7 +2668,7 @@ public class VamsasAppDatastore
{
entry.setAction("created.");
}
- entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+ entry.setDate(new java.util.Date());
entry.setUser(this.provEntry.getUser());
return entry;
}
@@ -1879,9 +2680,131 @@ public class VamsasAppDatastore
return prov;
}
- void addProvenance(Provenance p, String action)
+ Entry addProvenance(Provenance p, String action)
+ {
+ Entry dentry = dummyPEntry(action);
+ p.addEntry(dentry);
+ return dentry;
+ }
+
+ public Entry getProvEntry()
+ {
+ return provEntry;
+ }
+
+ public IClientDocument getClientDocument()
+ {
+ return cdoc;
+ }
+
+ public IdentityHashMap getJvObjectBinding()
+ {
+ return jv2vobj;
+ }
+
+ public Hashtable getVamsasObjectBinding()
+ {
+ return vobj2jv;
+ }
+
+ public void storeSequenceMappings(AlignmentViewport viewport, String title)
+ throws Exception
+ {
+ AlignmentViewport av = viewport;
+ try
+ {
+ jalview.datamodel.AlignmentI jal = av.getAlignment();
+ // /////////////////////////////////////////
+ // SAVE THE DATASET
+ DataSet dataset = null;
+ if (jal.getDataset() == null)
+ {
+ Cache.log.warn("Creating new dataset for an alignment.");
+ jal.setDataset(null);
+ }
+ 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.
+ Set cframes = av.getAlignment().getCodonFrames();
+ if (cframes != null)
+ {
+ for (AlignedCodonFrame acf : cframes)
+ {
+ if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
+ {
+ jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] mps = acf.getProtMappings();
+ for (int smp = 0; smp < mps.length; smp++)
+ {
+ uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
+ if (mfrom != null)
+ {
+ new jalview.io.vamsas.Sequencemapping(this, mps[smp],
+ mfrom, dataset);
+ }
+ else
+ {
+ Cache.log
+ .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
+ + dmps[smp].getDisplayId(true)
+ + " to "
+ + mps[smp].getTo().getName());
+ }
+ }
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ throw new Exception(MessageManager.formatMessage(
+ "exception.couldnt_store_sequence_mappings",
+ new String[] { title }), 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)
{
- p.addEntry(dummyPEntry(action));
+ this.skipList = skipList;
}
+ /**
+ * registry for datastoreItems
+ */
+ DatastoreRegistry dsReg = new DatastoreRegistry();
+
+ public DatastoreRegistry getDatastoreRegisty()
+ {
+ if (dsReg == null)
+ {
+ dsReg = new DatastoreRegistry();
+ }
+ return dsReg;
+ }
}