From a814169959613691aa08823a9fc53374b26aea5b Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 18 May 2007 11:03:18 +0000 Subject: [PATCH] update to and from document (and remove deprecated classes) --- src/jalview/gui/VamsasApplication.java | 23 +- src/jalview/gui/VamsasClient.java | 275 ----- src/jalview/io/VamsasDatastore.java | 1900 -------------------------------- 3 files changed, 16 insertions(+), 2182 deletions(-) delete mode 100755 src/jalview/gui/VamsasClient.java delete mode 100755 src/jalview/io/VamsasDatastore.java diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 62e2d21..2b208ba 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -18,7 +18,6 @@ import javax.swing.JInternalFrame; import jalview.bin.Cache; import jalview.io.VamsasAppDatastore; -import jalview.io.VamsasDatastore; import uk.ac.vamsas.client.*; import uk.ac.vamsas.*; @@ -116,7 +115,7 @@ public class VamsasApplication addDocumentUpdateHandler(); startSession(); Cache.log.debug("Jalview loading the Vamsas Session for the first time."); - dealWithDocumentUpdate(); + dealWithDocumentUpdate(false); // we don't push an update out to the document yet. Cache.log.debug("... finished update for the first time."); } /** @@ -155,7 +154,7 @@ public class VamsasApplication public void push_update() { Cache.log.info("Jalview updating to the Vamsas Session."); - dealWithDocumentUpdate(); + dealWithDocumentUpdate(true); /* IClientDocument cdoc=null; try @@ -268,15 +267,25 @@ public class VamsasApplication pentry.setAction("created"); return pentry; } - protected void dealWithDocumentUpdate() + /** + * do a vamsas document update or update jalview from the vamsas document + * @param fromJalview true to update from jalview to the vamsas document + */ + protected void dealWithDocumentUpdate(boolean fromJalview) { // called by update handler for document update. Cache.log.debug("Updating jalview from changed vamsas document."); disableGui(true); try { IClientDocument cdoc = vclient.getClientDocument(); - updateJalview(cdoc); - // cdoc.setVamsasRoots(cdoc.getVamsasRoots()); + if (fromJalview) + { + this.updateVamsasDocument(cdoc); + cdoc.setVamsasRoots(cdoc.getVamsasRoots()); + } else + { + updateJalview(cdoc); + } vclient.updateDocument(cdoc); cdoc=null; } catch (Exception ee) { @@ -293,7 +302,7 @@ public class VamsasApplication public void propertyChange(PropertyChangeEvent evt) { Cache.log.debug("Dealing with document update event."); - client.dealWithDocumentUpdate(); + client.dealWithDocumentUpdate(false); Cache.log.debug("finished dealing with event."); } }); diff --git a/src/jalview/gui/VamsasClient.java b/src/jalview/gui/VamsasClient.java deleted file mode 100755 index de62c6d..0000000 --- a/src/jalview/gui/VamsasClient.java +++ /dev/null @@ -1,275 +0,0 @@ -/** - * - */ -package jalview.gui; - -import java.io.File; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Vector; -import java.util.jar.JarOutputStream; - -import javax.swing.JInternalFrame; - -import jalview.bin.Cache; -import jalview.io.VamsasDatastore; - -import uk.ac.vamsas.client.UserHandle; -import uk.ac.vamsas.client.simpleclient.FileWatcher; -import uk.ac.vamsas.client.simpleclient.VamsasArchive; -import uk.ac.vamsas.client.simpleclient.VamsasFile; -import uk.ac.vamsas.objects.core.Entry; -import uk.ac.vamsas.objects.core.VamsasDocument; -import uk.ac.vamsas.test.simpleclient.ArchiveClient; -import uk.ac.vamsas.test.simpleclient.ClientDoc; - -/** - * @author jimp - * - */ -public class VamsasClient - extends ArchiveClient -{ - // Cache.preferences for vamsas client session arena - // preferences for check for default session at startup. - // user and organisation stuff. - public VamsasClient(Desktop jdesktop, - File sessionPath) - { - super(System.getProperty("user.name"), System.getProperty("host.name"), - "jalview", "2.7", - sessionPath); - } - - public void initial_update() - { - Cache.log.info("Jalview loading the Vamsas Session."); - // load in the vamsas archive for the first time - ClientDoc cdoc = this.getUpdateable(); - updateJalview(cdoc); - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - if (frames == null) - { - return; - } - - try - { - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) - { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; - af.alignPanel.alignmentChanged(); - } - } - } - catch (Exception e) - { - Cache.log.warn( - "Exception whilst refreshing jalview windows after a vamsas document update.", - e); - } - doUpdate(cdoc); - cdoc.closeDoc(); - } - - /** - * this will close all windows currently in Jalview. - * - - protected void closeWindows() { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - if (frames == null) - { - return; - } - - try - { - for (int i = frames.length - 1; i > -1; i--) { - frames[i].dispose(); - } - } catch (Exception e) { - Cache.log.error("Whilst closing windows",e); - } - - } - - public void get_update(VamsasArchive doc) { - // Close windows - load update. - Cache.log.info("Jalview updating from Vamsas Session."); - } - */ - VamsasClientWatcher watcher = null; - public void push_update() - { - watchForChange = false; - try - { - Thread.sleep(WATCH_SLEEP); - } - catch (Exception e) - { - - } - ; - ClientDoc cdoc = getUpdateable(); - updateVamsasDocument(cdoc); - doUpdate(cdoc); - cdoc.closeDoc(); - cdoc = null; - watchForChange = true; - if (watcher != null) - { - startWatcher(); /// TODO: check this works... must recreate watcher to start it... - } - // collect all uncached alignments and put them into the vamsas dataset. - // store them. - Cache.log.info("Jalview updating the Vamsas Session."); - } - - public void end_session() - { - // stop any update/watcher thread. - watchForChange = false; // this makes any watch(long) loops return. - // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped. - try - { - Thread.sleep(WATCH_SLEEP); - } - catch (Exception e) - { - - } - ; - Cache.log.info("Jalview disconnecting from the Vamsas Session."); - } - - public void updateJalview(ClientDoc cdoc) - { - ensureJvVamsas(); - VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, - baseProvEntry()); - vds.updateToJalview(); - } - - private void ensureJvVamsas() - { - if (jv2vobj == null) - { - jv2vobj = new IdentityHashMap(); - vobj2jv = new Hashtable(); - } - } - - /** - * jalview object binding to VorbaIds - */ - IdentityHashMap jv2vobj = null; - Hashtable vobj2jv = null; - public void updateVamsasDocument(ClientDoc doc) - { - ensureJvVamsas(); - VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, - baseProvEntry()); - // wander through frames - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - if (frames == null) - { - return; - } - - try - { - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) - { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; - - // update alignment and root from frame. - vds.storeVAMSAS(af.getViewport(), af.getTitle()); - } - } - } - catch (Exception e) - { - Cache.log.error("Vamsas Document store exception", e); - } - } - - private Entry baseProvEntry() - { - uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry(); - pentry.setUser(this.getProvenanceUser()); - pentry.setApp(this.getClientHandle().getClientName()); - pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date())); - pentry.setAction("created"); - return pentry; - } - - protected class VamsasClientWatcher - extends Thread - { - /* (non-Javadoc) - * @see java.lang.Thread#run() - */ - VamsasClient client = null; - VamsasClientWatcher(VamsasClient client) - { - this.client = client; - } - - boolean running = false; - public void run() - { - running = true; - while (client.watchForChange) - { - ClientDoc docio = client.watch(0); - if (docio != null) - { - client.disableGui(true); - Cache.log.debug("Updating jalview from changed vamsas document."); - client.updateJalview(docio); - Cache.log.debug("Finished updating from document change."); - docio.closeDoc(); - docio = null; - client.disableGui(false); - } - } - running = false; - - } - - } - - public void disableGui(boolean b) - { - Desktop.instance.setVamsasUpdate(b); - } - - public void startWatcher() - { - if (watcher == null) - { - watcher = new VamsasClientWatcher(this); - } - Thread thr = new Thread() - { - public void run() - { - watcher.start(); - } - }; - thr.start(); - } -} diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java deleted file mode 100755 index aca86c6..0000000 --- a/src/jalview/io/VamsasDatastore.java +++ /dev/null @@ -1,1900 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.io; - -import jalview.bin.Cache; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.AlignmentView; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.gui.AlignFrame; -import jalview.gui.AlignViewport; -import jalview.gui.Desktop; -import jalview.gui.TreePanel; - -import java.util.HashMap; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Vector; - -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.Input; -import uk.ac.vamsas.objects.core.Link; -import uk.ac.vamsas.objects.core.Newick; -import uk.ac.vamsas.objects.core.Param; -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.Tree; -import uk.ac.vamsas.objects.core.VAMSAS; -import uk.ac.vamsas.test.simpleclient.ClientDoc; - -/* - * - * static { - * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty( - * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } - * - */ - -public class VamsasDatastore -{ - Entry provEntry = null; - - // AlignViewport av; - - org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( - new java.util.Date()); - - ClientDoc cdoc; - - Hashtable vobj2jv; - - IdentityHashMap jv2vobj; - - public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv, - IdentityHashMap jv2vobj, Entry provEntry) - { - this.cdoc = cdoc; - this.vobj2jv = vobj2jv; - this.jv2vobj = jv2vobj; - this.provEntry = provEntry; - } - - /* - * 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(); } } - * - * - */ - /** - * @return the Vobject bound to Jalview datamodel object - */ - protected Vobject getjv2vObj(Object jvobj) - { - if (jv2vobj.containsKey(jvobj)) - { - return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj)); - } - return null; - } - - /** - * - * @param vobj - * @return Jalview datamodel object bound to the vamsas document object - */ - protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) - { - VorbaId id = vobj.getVorbaId(); - if (id == null) - { - id = cdoc.registerObject(vobj); - Cache.log - .debug("Registering new object and returning null for getvObj2jv"); - return null; - } - if (vobj2jv.containsKey(vobj.getVorbaId())) - { - return vobj2jv.get(vobj.getVorbaId()); - } - return null; - } - - protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) - { - VorbaId id = vobj.getVorbaId(); - if (id == null) - { - id = cdoc.registerObject(vobj); - if (id == null || vobj.getVorbaId() == null) - { - 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)) - { - Cache.log.debug("Warning? Overwriting existing vamsas id binding for " + - vobj.getVorbaId(), - new Exception("Overwriting vamsas id binding.")); - } - 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.")); - } - /* 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! - vobj2jv.put(vobj.getVorbaId(), jvobj); - // JBPNote - better implementing a hybrid invertible hash. - jv2vobj.put(jvobj, vobj.getVorbaId()); - } - - /** - * put the alignment viewed by AlignViewport into cdoc. - * - * @param av alignViewport to be stored - * @param aFtitle title for alignment - */ - public void storeVAMSAS(AlignViewport av, String aFtitle) - { - try - { - jalview.datamodel.AlignmentI jal = av.getAlignment(); - boolean nw = false; - VAMSAS root = null; // will be resolved based on Dataset Parent. - // ///////////////////////////////////////// - // SAVE THE DATASET - if (jal.getDataset() == null) - { - Cache.log.warn("Creating new dataset for an alignment."); - jal.setDataset(null); - } - DataSet dataset = (DataSet) getjv2vObj(jal.getDataset()); - if (dataset == null) - { - root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying. - dataset = new DataSet(); - root.addDataSet(dataset); - bindjvvobj(jal.getDataset(), dataset); - dataset.setProvenance(dummyProvenance()); - dataset.getProvenance().addEntry(provEntry); - nw = true; - } - else - { - root = (VAMSAS) dataset.getV_parent(); - } - // 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; - 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) - { - 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."); - } - } - } - - if (sq.getDBRef() != null) - { - 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."); - } - } - - } - } - // dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance())); - // //////////////////////////////////////////// - - // //////////////////////////////////////////// - // 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); - if (alignment.getProvenance() == null) - { - alignment.setProvenance(new Provenance()); - } - addProvenance(alignment.getProvenance(), "added"); // TODO: insert some - // sensible source - // here - dataset.addAlignment(alignment); - { - Property title = new Property(); - title.setName("jalview:AlTitle"); - 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()); - alseq.setRefid(getjv2vObj(jal.getSequenceAt(i).getDatasetSequence())); - alignment.addAlignmentSequence(alseq); - bindjvvobj(jal.getSequenceAt(i), alseq); - } - } - else - { - // todo: verify and update mutable alignment props. - if (alignment.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS - { - System.out.println("update alignment in document."); - } - else - { - System.out - .println("update edited alignment to new alignment in document."); - } - } - // //////////////////////////////////////////// - // SAVE Alignment Sequence Features - for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; - i++) - { - AlignmentSequence valseq; - SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment - .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); - } - } - - } - } - } - - // //////////////////////////////////////////// - // SAVE ANNOTATIONS - if (jal.getAlignmentAnnotation() != null) - { - jalview.datamodel.AlignmentAnnotation[] aa = jal - .getAlignmentAnnotation(); - java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from - // alignment columns to - // sequence positions. - for (int i = 0; i < aa.length; i++) - { - if (aa[i] == null || isJalviewOnly(aa[i])) - { - 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)) - { - gapMap = (int[]) AlSeqMaps.get(aa[i].sequenceRef); - } - 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) - { - 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) - { - 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); - } - 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]); - if (an == null) - { - an = new uk.ac.vamsas.objects.core.AlignmentAnnotation(); - an.setType("jalview:AnnotationRow"); - an.setDescription(aa[i].description); - alignment.addAlignmentAnnotation(an); - Seg vSeg = new Seg(); - vSeg.setStart(1); - vSeg.setInclusive(true); - vSeg.setEnd(jal.getWidth()); - an.addSeg(vSeg); - if (aa[i].graph > 0) - { - an.setGraph(true); // aa[i].graph); - } - an.setLabel(aa[i].label); - an.setProvenance(dummyProvenance()); - if (aa[i].graph != aa[i].NO_GRAPH) - { - an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote - - // originally we - // were going to - // store - // graphGroup in - // the Jalview - // specific - // bits. - an.setGraph(true); - } - else - { - an.setGraph(false); - } - AnnotationElement ae; - - for (int a = 0; a < aa[i].annotations.length; a++) - { - if ( (aa[i] == null) || (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 - ae.addValue(aa[i].annotations[a].value); - ae.setPosition(a + 1); - if (aa[i].annotations[a].secondaryStructure != ' ') - { - Glyph ss = new Glyph(); - ss - .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary. - PROTEIN_SS_3STATE); - ss.setContent(String - .valueOf(aa[i].annotations[a]. - secondaryStructure)); - 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. - } - 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); - */ - - } - } - else - { - 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."); - } - else - { - // verify annotation - update (perhaps) - Cache.log.info("updated alignment sequence annotation added."); - } - } - } - } - } - // ///////////////////////////////////////////////////// - - // ////////////////////////////////////////////// - // /SAVE THE TREES - // ///////////////////////////////// - // FIND ANY ASSOCIATED TREES - if (Desktop.desktop != null) - { - javax.swing.JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof TreePanel) - { - TreePanel tp = (TreePanel) frames[t]; - - if (tp.getAlignment() == jal) - { - 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."); - } - } - } - } - } - } - // Store Jalview specific stuff in the Jalview appData - // not implemented in the SimpleDoc interface. - } - - catch (Exception ex) - { - ex.printStackTrace(); - } - - } - - private Property newProperty(String name, String type, String content) - { - Property vProperty = new Property(); - vProperty.setName(name); - if (type != null) - { - vProperty.setType(type); - } - else - { - vProperty.setType("String"); - } - vProperty.setContent(content); - return vProperty; - } - - /** - * correctly create a RangeAnnotation from a jalview sequence feature - * - * @param dsa - * (typically DataSetAnnotations or AlignmentSequenceAnnotation) - * @param feature - * (the feature to be mapped from) - * @return - */ - private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa, - SequenceFeature feature) - { - dsa.setType(feature.getType()); - Seg vSeg = new Seg(); - vSeg.setStart(feature.getBegin()); - vSeg.setEnd(feature.getEnd()); - vSeg.setInclusive(true); - dsa.addSeg(vSeg); - dsa.setDescription(feature.getDescription()); - dsa.setStatus(feature.getStatus()); - if (feature.links != null && feature.links.size() > 0) - { - for (int i = 0, iSize = feature.links.size(); i < iSize; i++) - { - String link = (String) feature.links.elementAt(i); - int sep = link.indexOf('|'); - if (sep > -1) - { - Link vLink = new Link(); - if (sep > 0) - { - vLink.setContent(link.substring(0, sep - 1)); - } - else - { - vLink.setContent(""); - } - vLink.setHref(link.substring(sep + 1)); // TODO: validate href. - dsa.addLink(vLink); - } - } - } - dsa.setGroup(feature.getFeatureGroup()); - return dsa; - } - - /** - * correctly creates provenance for trees calculated on an alignment by - * jalview. - * - * @param jal - * @param tp - * @return - */ - private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) - { - 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); - } - } - return prov; - } - - /** - * - * @param tp - * @return Object[] { AlignmentView, AlignmentI - reference alignment for - * input } - */ - private Object[] recoverInputData(Provenance tp) - { - for (int pe = 0; pe < tp.getEntryCount(); pe++) - { - if (tp.getEntry(pe).getInputCount() > 0) - { - if (tp.getEntry(pe).getInputCount() > 1) - { - Cache.log.warn("Ignoring additional input spec in provenance entry " - + tp.getEntry(pe).toString()); - } - // LATER: deal sensibly with multiple inputs. - Input vInput = tp.getEntry(pe).getInput(0); - if (vInput.getObjRef() instanceof uk.ac.vamsas.objects.core.Alignment) - { - // 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++) - { - 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; - } - } - 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}; - } - } - } - Cache.log.debug("Returning null for input data recovery from provenance."); - return null; - } - - /** - * get start 0) - { - 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]); - } - } - } - } - - if (newds) - { - 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); - } - jdataset = new jalview.datamodel.Alignment(seqs); - Cache.log.debug("New vamsas dataset imported into jalview."); - bindjvvobj(jdataset, dataset); - } - // //////// - // add any new dataset sequence feature annotations - if (dataset.getDataSetAnnotations() != null) - { - 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 - { - if (dseta.getAnnotationElementCount() == 0) - { - jalview.datamodel.SequenceFeature sf = (jalview.datamodel. - SequenceFeature) getvObj2jv(dseta); - if (sf == null) - { - dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dseta)); - bindjvvobj(sf, dseta); - } - } - 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 (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); - jalview.datamodel.AlignmentI jal = null; - if (av != null) - { - jal = av.getAlignment(); - } - iSize = alignment.getAlignmentSequenceCount(); - boolean newal = (jal == null) ? true : false; - Vector newasAnnots = new Vector(); - char gapChar = ' '; // default for new alignments read in from the document - if (jal != null) - { - dsseqs = jal.getSequences(); // for merge/update - gapChar = jal.getGapCharacter(); - } - else - { - dsseqs = new Vector(); - } - char valGapchar = alignment.getGapChar().charAt(0); - for (i = 0; i < iSize; i++) - { - AlignmentSequence valseq = alignment.getAlignmentSequence(i); - jalview.datamodel.SequenceI alseq = (SequenceI) getvObj2jv(valseq); - if (alseq != null) - { - //TODO: upperCase/LowerCase situation here ? do we allow it ? - //if (!alseq.getSequence().equals(valseq.getSequence())) { - // throw new Error("Broken! - mismatch of dataset sequence and jalview internal dataset sequence."); - if (Cache.log.isDebugEnabled()) - { - Cache.log.debug("Updating apparently edited sequence " + - alseq.getName()); - } - // this might go *horribly* wrong - alseq.setSequence(new String(valseq.getSequence()).replace( - valGapchar, gapChar)); - jremain--; - } - else - { - 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); - } - if (valseq.getAlignmentSequenceAnnotationCount() > 0) - { - 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 - 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. - bindjvvobj(asa, vasannot[a]); - newasAnnots.add(asa); - } - else - { - // update existing annotation - can do this in place - 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 - // basically do this: - // int se[] = getBounds(vasannot[a]); - // asa.update(getjAlignmentAnnotation(jal, vasannot[a])); // update from another annotation object in place. - // asa.createSequenceMapping(alseq, se[0], false); - - } - } - } - } - } - if (jal == null) - { - 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); - } - jal = new jalview.datamodel.Alignment(seqs); - Cache.log.debug("New vamsas alignment imported into jalview " + - alignment.getVorbaId().getId()); - jal.setDataset(jdataset); - } - if (newasAnnots != null && newasAnnots.size() > 0) - { - // 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. - newasAnnots.setElementAt(null, an); - } - newasAnnots = null; - } - // ////////////////////////////////////////// - // //LOAD ANNOTATIONS FOR THE ALIGNMENT - // //////////////////////////////////// - if (alignment.getAlignmentAnnotationCount() > 0) - { - 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]); - if (jan != null) - { - // update or stay the same. - // 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) - { - // 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. - } - else - { - jan = getjAlignmentAnnotation(jal, an[j]); - jal.addAnnotation(jan); - bindjvvobj(jan, an[j]); - } - } - } - AlignFrame alignFrame; - if (av == null) - { - Cache.log.debug("New alignframe for alignment " + - alignment.getVorbaId()); - // /////////////////////////////// - // construct alignment view - alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - av = alignFrame.getViewport(); - 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")) - { - 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); - } - else - { - // find the alignFrame for jal. - // TODO: fix this so we retrieve the alignFrame handing av *directly* - alignFrame = getAlignFrameFor(av); - } - // LOAD TREES - // ///////////////////////////////////// - if (alignment.getTreeCount() > 0) - { - - for (int t = 0; t < alignment.getTreeCount(); t++) - { - Tree tree = alignment.getTree(t); - TreePanel tp = (TreePanel) getvObj2jv(tree); - if (tp != null) - { - Cache.log.info( - "Update from vamsas document to alignment associated tree not implemented yet."); - } - else - { - // make a new tree - Object[] idata = this.recoverInputData(tree.getProvenance()); - 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) - { - Cache.log.warn("Problems parsing treefile '" + - tree.getNewick(0).getContent() + "'", e); - } - } - } - } - - } - } - } - } - } - - // 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. - * @param annotation - * @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) - { - // 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}; - 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. - - 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) - if (pos >= 0 && pos < rangeMap.length) - { - int row = ae[aa].getAfter() ? 1 : 0; - if (anot[row][pos] != null) - { - // only time this should happen is if the After flag is set. - Cache.log.debug("Ignoring duplicate annotation site at " + pos); - continue; - } - if (anot[1 - row][pos] != null) - { - mergeable = false; - } - String desc = ""; - if (ae[aa].getDescription() != null) - { - desc = ae[aa].getDescription(); - if (desc.length() > 0) - { - // have imported valid description string - 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(); - 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)) - { - ss = glyphs[g].getContent(); - AeContent[HASSECSTR] = true; - } - 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); - - } - 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()); - } - } - } - float val = 0; - if (ae[aa].getValueCount() > 0) - { - AeContent[HASVALS] = true; - if (ae[aa].getValueCount() > 1) - { - 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); - } - else - { - 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()); - } - } - // decide on how many annotation rows are needed. - if (mergeable) - { - for (int i = 0; i < anot[0].length; i++) - { - if (anot[1][i] != null) - { - anot[0][i] = anot[1][i]; - anot[0][i].description = anot[0][i].description + " (after)"; - AeContent[HASDESCSTR] = true; // we have valid description string data - anot[1][i] = null; - } - } - anot[1] = null; - } - else - { - for (int i = 0; i < anot[0].length; i++) - { - anot[1][i].description = anot[1][i].description + " (after)"; - } - } - 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]}; - } - // return null; - } - - /** - * @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) - { - 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}; - */ - Object[] parsedRangeAnnotation = parseRangeAnnotation(annotation); - String a_label = annotation.getLabel(); - String a_descr = annotation.getDescription(); - if (a_label == null || a_label.length() == 0) - { - a_label = annotation.getType(); - if (a_label.length() == 0) - { - a_label = "Unamed annotation"; - } - } - if (a_descr == null || a_descr.length() == 0) - { - a_descr = "Annotation of type '" + annotation.getType() + "'"; - } - if (parsedRangeAnnotation == null) - { - 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()); - } - 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())) { - */ - if (has[HASVALS]) - { - // 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; - for (int i = 0; i < arow.length; i++) - { - if (arow[i] != null) - { - if (i - lastval > 1) - { - // do some interpolation *between* points - if (arow[lastval] != null) - { - float interval = arow[i].value - arow[lastval].value; - interval /= i - lastval; - float base = arow[lastval].value; - 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. - } - } - } - lastval = i; - // check range - shouldn't we have a min and max property in the annotation object ? - if (first) - { - min = max = arow[i].value; - first = false; - } - else - { - if (arow[i].value < min) - { - min = arow[i].value; - } - else if (arow[i].value > max) - { - max = arow[i].value; - } - } - // make tooltip and display char value - if (!has[HASDESCSTR]) - { - arow[i].description = arow[i].value + ""; - } - if (!has[HASDC]) - { - 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); - } - else - { - jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow); - jan.setThreshold(null); - } - if (annotation.getLinkCount() > 0) - { - Cache.log.warn("Ignoring " + annotation.getLinkCount() + - "links added to AlignmentAnnotation."); - } - if (annotation.getModifiable()==null) // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS) - { - jan.editable = true; - } - - 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("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."); - } - } - } - } - - return jan; - - } - - 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 - * @param dseta - * @return int[] { start, end} - */ - private int[] getBounds(RangeType dseta) - { - if (dseta != null) - { - 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!"); - } - if (dseta.getSegCount() > 0) - { - se = getSegRange(dseta.getSeg(0), true); - for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) - { - int nse[] = getSegRange(dseta.getSeg(s), true); - if (se[0] > nse[0]) - { - se[0] = nse[0]; - } - if (se[1] < nse[1]) - { - se[1] = nse[1]; - } - } - } - if (dseta.getPosCount() > 0) - { - // 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}; - for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) - { - pos = dseta.getPos(p).getI(); - if (se[0] > pos) - { - se[0] = pos; - } - if (se[1] < pos) - { - se[1] = pos; - } - } - } - return se; - } - return null; - } - - /** - * 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. - */ - private int[] getMapping(RangeType dseta) - { - Vector posList = new Vector(); - if (dseta != null) - { - 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!"); - } - if (dseta.getSegCount() > 0) - { - for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) - { - se = getSegRange(dseta.getSeg(s), false); - int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1); - for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) - { - posList.add(new Integer(p)); - } - } - } - else if (dseta.getPosCount() > 0) - { - int pos = dseta.getPos(0).getI(); - - for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) - { - pos = dseta.getPos(p).getI(); - posList.add(new Integer(pos)); - } - } - } - if (posList != null && posList.size() > 0) - { - int[] range = new int[posList.size()]; - for (int i = 0; i < range.length; i++) - { - range[i] = ( (Integer) posList.elementAt(i)).intValue(); - } - posList.clear(); - return range; - } - 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; - - 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) - { - // TODO: fix App and Action entries and check use of provenance in jalview. - 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()); - } - - return jprov; - } - - /** - * - * @return default initial provenance list for a Jalview created vamsas - * object. - */ - Provenance dummyProvenance() - { - return dummyProvenance(null); - } - - Entry dummyPEntry(String action) - { - Entry entry = new Entry(); - entry.setApp(this.provEntry.getApp()); - if (action != null) - { - entry.setAction(action); - } - else - { - entry.setAction("created."); - } - entry.setDate(new org.exolab.castor.types.Date(new java.util.Date())); - entry.setUser(this.provEntry.getUser()); - return entry; - } - - Provenance dummyProvenance(String action) - { - Provenance prov = new Provenance(); - prov.addEntry(dummyPEntry(action)); - return prov; - } - - void addProvenance(Provenance p, String action) - { - p.addEntry(dummyPEntry(action)); - } - -} -- 1.7.10.2