/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.ws;\r
\r
-import java.net.*;\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-import org.biojava.dasobert.das.*;\r
-import org.biojava.dasobert.das2.*;\r
-import org.biojava.dasobert.das2.io.*;\r
-import org.biojava.dasobert.dasregistry.*;\r
-import org.biojava.dasobert.eventmodel.*;\r
import jalview.bin.Cache;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.gui.AlignFrame;\r
+import jalview.gui.Desktop;\r
+import jalview.gui.FeatureSettings;\r
+import jalview.util.UrlLink;\r
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;\r
+import jalview.ws.dbsources.das.api.jalviewSourceI;\r
+\r
+import java.util.ArrayList;\r
+import java.util.Arrays;\r
+import java.util.Enumeration;\r
+import java.util.HashMap;\r
+import java.util.HashSet;\r
+import java.util.Iterator;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
+import javax.swing.JOptionPane;\r
+\r
+import org.biodas.jdas.client.FeaturesClient;\r
+import org.biodas.jdas.client.adapters.features.DasGFFAdapter;\r
+import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;\r
+import org.biodas.jdas.client.threads.FeaturesClientMultipleSources;\r
+import org.biodas.jdas.schema.features.ERRORSEGMENT;\r
+import org.biodas.jdas.schema.features.FEATURE;\r
+import org.biodas.jdas.schema.features.LINK;\r
+import org.biodas.jdas.schema.features.SEGMENT;\r
+import org.biodas.jdas.schema.features.TYPE;\r
+import org.biodas.jdas.schema.features.UNKNOWNFEATURE;\r
+import org.biodas.jdas.schema.features.UNKNOWNSEGMENT;\r
+import org.biodas.jdas.schema.sources.COORDINATES;\r
\r
/**\r
* DOCUMENT ME!\r
\r
StringBuffer sbuffer = new StringBuffer();\r
\r
- Vector selectedSources;\r
+ List<jalviewSourceI> selectedSources;\r
\r
boolean cancelled = false;\r
\r
\r
long startTime;\r
\r
+ private DasSourceRegistryI sourceRegistry;\r
+ private boolean useJDASMultiThread=true;\r
/**\r
* Creates a new SequenceFeatureFetcher object. Uses default\r
* \r
* @param align\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
* @param ap\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
*/\r
public DasSequenceFeatureFetcher(SequenceI[] sequences,\r
FeatureSettings fsettings, Vector selectedSources)\r
{\r
- this(sequences, fsettings, selectedSources, true, true);\r
+ this(sequences, fsettings, selectedSources, true, true, true);\r
}\r
\r
- public DasSequenceFeatureFetcher(SequenceI[] sequences,\r
- FeatureSettings fsettings, Vector selectedSources,\r
+ public DasSequenceFeatureFetcher(SequenceI[] oursequences,\r
+ FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,\r
boolean checkDbrefs, boolean promptFetchDbrefs)\r
{\r
- this.selectedSources = selectedSources;\r
- this.sequences = sequences;\r
+ this(oursequences,fsettings,selectedSources2,checkDbrefs,promptFetchDbrefs,true);\r
+ }\r
+ public DasSequenceFeatureFetcher(SequenceI[] oursequences,\r
+ FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,\r
+ boolean checkDbrefs, boolean promptFetchDbrefs, boolean useJDasMultiThread)\r
+ {\r
+ this.useJDASMultiThread=useJDasMultiThread;\r
+ this.selectedSources = new ArrayList<jalviewSourceI>();\r
+ // filter both sequences and sources to eliminate duplicates\r
+ for (jalviewSourceI src : selectedSources2)\r
+ {\r
+ if (!selectedSources.contains(src))\r
+ {\r
+ selectedSources.add(src);\r
+ }\r
+ ;\r
+ }\r
+ Vector sqs = new Vector();\r
+ for (int i = 0; i < oursequences.length; i++)\r
+ {\r
+ if (!sqs.contains(oursequences[i]))\r
+ {\r
+ sqs.addElement(oursequences[i]);\r
+ }\r
+ }\r
+ sequences = new SequenceI[sqs.size()];\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ sequences[i] = (SequenceI) sqs.elementAt(i);\r
+ }\r
if (fsettings != null)\r
{\r
this.fsettings = fsettings;\r
this.af = fsettings.af;\r
- af.getViewport().setShowSequenceFeatures(true);\r
+ af.setShowSeqFeatures(true);\r
}\r
int uniprotCount = 0;\r
- for (int i = 0; i < selectedSources.size(); i++)\r
+ for (jalviewSourceI source : selectedSources)\r
{\r
- DasSource source = (DasSource) selectedSources.elementAt(i);\r
- DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
- for (int c = 0; c < coords.length; c++)\r
+ for (COORDINATES coords : source.getVersion().getCOORDINATES())\r
{\r
// TODO: match UniProt coord system canonically (?) - does\r
// UniProt==uniprot==UNIPROT ?\r
- if (coords[c].getName().indexOf("UniProt") > -1)\r
+ if (coords.getAuthority().toLowerCase().equals("uniprot"))\r
{\r
uniprotCount++;\r
break;\r
}\r
else\r
{\r
- startFetching();\r
+ _startFetching();\r
}\r
}\r
else\r
{\r
- startFetching();\r
+ _startFetching();\r
}\r
\r
}\r
-\r
+ private void _startFetching()\r
+ {\r
+ running=true;\r
+ new Thread(new FetchSeqFeatures()).start();\r
+ }\r
+ class FetchSeqFeatures implements Runnable\r
+ {\r
+ public void run()\r
+ {\r
+ startFetching();\r
+ setGuiFetchComplete();\r
+ }\r
+ }\r
class FetchDBRefs implements Runnable\r
{\r
public void run()\r
{\r
+ running=true;\r
new DBRefFetcher(sequences, af).fetchDBRefs(true);\r
startFetching();\r
+ setGuiFetchComplete();\r
}\r
}\r
\r
/**\r
- * Spawns a number of dasobert Fetcher threads to add features to sequences in\r
- * the dataset\r
+ * Spawns Fetcher threads to add features to sequences in the dataset\r
*/\r
void startFetching()\r
{\r
+ running=true;\r
cancelled = false;\r
startTime = System.currentTimeMillis();\r
if (af != null)\r
{\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
}\r
-\r
- DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
-\r
+ if (sourceRegistry == null)\r
+ {\r
+ sourceRegistry = Cache.getDasSourceRegistry();\r
+ }\r
if (selectedSources == null || selectedSources.size() == 0)\r
{\r
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
- "uniprot");\r
- StringTokenizer st = new StringTokenizer(active, "\t");\r
- Vector selectedSources = new Vector();\r
- String token;\r
- while (st.hasMoreTokens())\r
+ try\r
{\r
- token = st.nextToken();\r
- for (int i = 0; i < sources.length; i++)\r
+ jalviewSourceI[] sources = sourceRegistry.getSources().toArray(\r
+ new jalviewSourceI[0]);\r
+ String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
+ "uniprot");\r
+ StringTokenizer st = new StringTokenizer(active, "\t");\r
+ selectedSources = new Vector();\r
+ String token;\r
+ while (st.hasMoreTokens())\r
{\r
- if (sources[i].getNickname().equals(token))\r
+ token = st.nextToken();\r
+ for (int i = 0; i < sources.length; i++)\r
{\r
- selectedSources.addElement(sources[i]);\r
- break;\r
+ if (sources[i].getTitle().equals(token))\r
+ {\r
+ selectedSources.add(sources[i]);\r
+ break;\r
+ }\r
}\r
}\r
+ } catch (Exception ex)\r
+ {\r
+ debug("Exception whilst setting default feature sources from registry and local preferences.",\r
+ ex);\r
}\r
}\r
\r
}\r
\r
sourcesRemaining = selectedSources.size();\r
+ FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();\r
+ fc.setConnProps(sourceRegistry.getSessionHandler());\r
// Now sending requests one at a time to each server\r
- for (int sourceIndex = 0; sourceIndex < selectedSources.size()\r
- && !cancelled; sourceIndex++)\r
+ ArrayList<jalviewSourceI> srcobj = new ArrayList<jalviewSourceI>();\r
+ ArrayList<String> src = new ArrayList<String>();\r
+ List<List<String>> ids = new ArrayList<List<String>>();\r
+ List<List<DBRefEntry>> idobj = new ArrayList<List<DBRefEntry>>();\r
+ List<Map<String, SequenceI>> sqset = new ArrayList<Map<String, SequenceI>>();\r
+ for (jalviewSourceI _sr : selectedSources)\r
{\r
- DasSource dasSource = (DasSource) selectedSources\r
- .elementAt(sourceIndex);\r
\r
- nextSequence(dasSource, sequences[0]);\r
+ Map<String, SequenceI> slist = new HashMap<String, SequenceI>();\r
+ List<DBRefEntry> idob = new ArrayList<DBRefEntry>();\r
+ List<String> qset = new ArrayList<String>();\r
+\r
+ for (SequenceI seq : sequences)\r
+ {\r
+ Object[] idset = nextSequence(_sr, seq);\r
+ if (idset != null)\r
+ {\r
+ List<DBRefEntry> _idob = (List<DBRefEntry>) idset[0];\r
+ List<String> _qset = (List<String>) idset[1];\r
+ if (_idob.size() > 0)\r
+ {\r
+ // add sequence's ref for each id derived from it\r
+ // (space inefficient, but most unambiguous)\r
+ // could replace with hash with _qset values as keys.\r
+ Iterator<DBRefEntry> dbobj = _idob.iterator();\r
+ for (String q : _qset)\r
+ {\r
+ SequenceI osq = slist.get(q);\r
+ DBRefEntry dr = dbobj.next();\r
+ if (osq != null && osq != seq)\r
+ {\r
+ // skip - non-canonical query\r
+ }\r
+ else\r
+ {\r
+ idob.add(dr);\r
+ qset.add(q);\r
+ slist.put(q, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (idob.size() > 0)\r
+ {\r
+ srcobj.add(_sr);\r
+ src.add(_sr.getSourceURL());\r
+ ids.add(qset);\r
+ idobj.add(idob);\r
+ sqset.add(slist);\r
+ }\r
+ }\r
+ Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();\r
+ Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<String, Map<List<String>, DasGFFAdapter>>();\r
+ if (!useJDASMultiThread)\r
+ {\r
+ Iterator<String> sources=src.iterator();\r
+ // iterate over each query for each source and do each one individually\r
+ for (List<String> idl:ids)\r
+ {\r
+ String source=sources.next();\r
+ FeaturesClient featuresc=new FeaturesClient(sourceRegistry.getSessionHandler().getConnectionPropertyProviderFor(source));\r
+ for (String id:idl)\r
+ {\r
+ List<String> qid=Arrays.asList(new String[] { id});\r
+ try {\r
+ DasGFFAdapter dga=featuresc.fetchData(source, qid);\r
+ Map<List<String>,DasGFFAdapter> ers=results.get(source);\r
+ if (ers==null)\r
+ {\r
+ results.put(source, ers=new HashMap<List<String>,DasGFFAdapter>());\r
+ }\r
+ ers.put(qid, dga);\r
+ } catch (Exception ex)\r
+ {\r
+ Map<List<String>,Exception> ers=errors.get(source);\r
+ if (ers==null)\r
+ {\r
+ errors.put(source, ers=new HashMap<List<String>,Exception>());\r
+ }\r
+ ers.put(qid, ex);\r
+ }\r
+ }\r
+ }\r
+ } else {\r
+ // pass them all at once\r
+ fc.fetchData(src, ids, false, results, errors);\r
+ fc.shutDown();\r
+ while (!fc.isTerminated())\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(200);\r
+ } catch (InterruptedException x)\r
+ {\r
+\r
+ }\r
+ }\r
+ }\r
+ Iterator<List<String>> idset = ids.iterator();\r
+ Iterator<List<DBRefEntry>> idobjset = idobj.iterator();\r
+ Iterator<Map<String, SequenceI>> seqset = sqset.iterator();\r
+ for (jalviewSourceI source : srcobj)\r
+ {\r
+ processResponse(seqset.next(), source, idset.next(), idobjset.next(),\r
+ results.get(source.getSourceURL()),\r
+ errors.get(source.getSourceURL()));\r
+ }\r
+ }\r
+\r
+ private void processResponse(Map<String, SequenceI> sequencemap,\r
+ jalviewSourceI jvsource, List<String> ids,\r
+ List<DBRefEntry> idobj, Map<List<String>, DasGFFAdapter> results,\r
+ Map<List<String>, Exception> errors)\r
+ {\r
+ Set<SequenceI> sequences = new HashSet<SequenceI>();\r
+ String source = jvsource.getSourceURL();\r
+ // process features\r
+ DasGFFAdapter result = (results == null) ? null : results.get(ids);\r
+ Exception error = (errors == null) ? null : errors.get(ids);\r
+ if (result == null)\r
+ {\r
+ debug("das source " + source + " could not be contacted. "\r
+ + (error == null ? "" : error.toString()));\r
+ }\r
+ else\r
+ {\r
+\r
+ GFFAdapter gff = result.getGFF();\r
+ List<SEGMENT> segments = gff.getSegments();\r
+ List<ERRORSEGMENT> errorsegs = gff.getErrorSegments();\r
+ List<UNKNOWNFEATURE> unkfeats = gff.getUnknownFeatures();\r
+ List<UNKNOWNSEGMENT> unksegs = gff.getUnknownSegments();\r
+ debug("das source " + source + " returned " + gff.getTotal()\r
+ + " responses. " + (errorsegs != null ? errorsegs.size() : 0)\r
+ + " were incorrect segment queries, "\r
+ + (unkfeats != null ? unkfeats.size() : 0)\r
+ + " were unknown features "\r
+ + (unksegs != null ? unksegs.size() : 0)\r
+ + " were unknown segments and "\r
+ + (segments != null ? segments.size() : 0)\r
+ + " were segment responses.");\r
+ Iterator<DBRefEntry> dbr = idobj.iterator();\r
+ if (segments != null)\r
+ {\r
+ for (SEGMENT seg : segments)\r
+ {\r
+ String id = seg.getId();\r
+ if (ids.indexOf(id)==-1)\r
+ {\r
+ id=id.toUpperCase();\r
+ }\r
+ DBRefEntry dbref = idobj.get(ids.indexOf(id));\r
+ SequenceI sequence = sequencemap.get(id);\r
+ boolean added = false;\r
+ sequences.add(sequence);\r
+\r
+ for (FEATURE feat : seg.getFEATURE())\r
+ {\r
+ // standard DAS feature-> jalview sequence feature transformation\r
+ SequenceFeature f = newSequenceFeature(feat, jvsource.getTitle());\r
+ if (!parseSeqFeature(sequence, f, feat, jvsource))\r
+ {\r
+ if (dbref.getMap() != null && f.getBegin() > 0\r
+ && f.getEnd() > 0)\r
+ {\r
+ debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
+ SequenceFeature vf[] = null;\r
+\r
+ try\r
+ {\r
+ vf = dbref.getMap().locateFeature(f);\r
+ } catch (Exception ex)\r
+ {\r
+ Cache.log\r
+ .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");\r
+ Cache.log.info("Mapping feature from " + f.getBegin()\r
+ + " to " + f.getEnd() + " in dbref "\r
+ + dbref.getAccessionId() + " in "\r
+ + dbref.getSource());\r
+ Cache.log.info("using das Source " + source);\r
+ Cache.log.info("Exception", ex);\r
+ }\r
+\r
+ if (vf != null)\r
+ {\r
+ for (int v = 0; v < vf.length; v++)\r
+ {\r
+ debug("mapping to " + v + ": " + vf[v].getBegin()\r
+ + " - " + vf[v].getEnd());\r
+ sequence.addSequenceFeature(vf[v]);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sequence.addSequenceFeature(f);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ featuresAdded(sequences);\r
+ }\r
+ else\r
+ {\r
+ // System.out.println("No features found for " + seq.getName()\r
+ // + " from: " + e.getDasSource().getNickname());\r
+ }\r
}\r
}\r
\r
}\r
\r
int sourcesRemaining = 0;\r
-\r
- void responseComplete(DasSource dasSource, SequenceI seq)\r
- {\r
- if (seq != null)\r
- {\r
- for (int seqIndex = 0; seqIndex < sequences.length - 1 && !cancelled; seqIndex++)\r
- {\r
- if (sequences[seqIndex] == seq)\r
- {\r
- nextSequence(dasSource, sequences[++seqIndex]);\r
- return;\r
- }\r
- }\r
- }\r
-\r
- sourcesRemaining--;\r
-\r
- if (sourcesRemaining == 0)\r
- {\r
- System.err.println("Fetching Complete.");\r
- setGuiFetchComplete();\r
- }\r
-\r
- }\r
-\r
+ private boolean running=false;\r
private void setGuiFetchComplete()\r
{\r
-\r
- if (af != null)\r
+ running=false;\r
+ if (!cancelled && af != null)\r
{\r
+ // only update the progress bar if we've completed the fetch normally\r
af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
}\r
\r
}\r
}\r
\r
- void featuresAdded(SequenceI seq)\r
+ void featuresAdded(Set<SequenceI> seqs)\r
{\r
if (af == null)\r
{\r
int index;\r
for (index = start; index < end; index++)\r
{\r
- if (seq == af.getViewport().getAlignment().getSequenceAt(index)\r
- .getDatasetSequence())\r
+ for (SequenceI seq : seqs)\r
{\r
- af.alignPanel.paintAlignment(true);\r
- break;\r
+ if (seq == af.getViewport().getAlignment().getSequenceAt(index)\r
+ .getDatasetSequence())\r
+ {\r
+ af.alignPanel.paintAlignment(true);\r
+ index = end;\r
+ break;\r
+ }\r
}\r
}\r
}\r
\r
- void nextSequence(DasSource dasSource, SequenceI seq)\r
+ Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)\r
{\r
if (cancelled)\r
- return;\r
+ return null;\r
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
seq.getDBRef(), new String[]\r
{\r
// TODO: minimal list of DAS queries to make by querying with untyped ID if\r
// distinct from any typed IDs\r
\r
+ List<DBRefEntry> ids = new ArrayList<DBRefEntry>();\r
+ List<String> qstring = new ArrayList<String>();\r
boolean dasCoordSysFound = false;\r
\r
if (uprefs != null)\r
// do any of these ids match the source's coordinate system ?\r
for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)\r
{\r
- DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
\r
- for (int csIndex = 0; csIndex < cs.length && !dasCoordSysFound; csIndex++)\r
+ for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())\r
{\r
- if (cs.length > 0\r
- && jalview.util.DBRefUtils.isDasCoordinateSystem(\r
- cs[csIndex].getName(), uprefs[j]))\r
+ if (jalview.util.DBRefUtils.isDasCoordinateSystem(\r
+ csys.getAuthority(), uprefs[j]))\r
{\r
debug("Launched fetcher for coordinate system "\r
- + cs[0].getName());\r
+ + csys.getAuthority());\r
// Will have to pass any mapping information to the fetcher\r
// - the start/end for the DBRefEntry may not be the same as the\r
// sequence's start/end\r
\r
System.out.println(seq.getName() + " "\r
+ (seq.getDatasetSequence() == null) + " "\r
- + dasSource.getUrl());\r
+ + csys.getUri());\r
\r
dasCoordSysFound = true; // break's out of the loop\r
- createFeatureFetcher(seq, dasSource, uprefs[j]);\r
+ ids.add(uprefs[j]);\r
+ qstring.add(uprefs[j].getAccessionId());\r
}\r
else\r
- System.out.println("IGNORE " + cs[csIndex].getName());\r
+ System.out.println("IGNORE " + csys.getAuthority());\r
}\r
}\r
}\r
}\r
if (id != null)\r
{\r
+ DBRefEntry dbre = new DBRefEntry();\r
+ dbre.setAccessionId(id);\r
// Should try to call a general feature fetcher that\r
// queries many sources with name to discover applicable ID references\r
- createFeatureFetcher(seq, dasSource, id);\r
+ ids.add(dbre);\r
+ qstring.add(dbre.getAccessionId());\r
}\r
}\r
\r
+ return new Object[]\r
+ { ids, qstring };\r
}\r
\r
/**\r
- * fetch and add das features to a sequence using the given source URL and\r
- * compatible DbRef id. new features are mapped using the DbRef mapping to the\r
- * local coordinate system.\r
+ * examine the given sequence feature to determine if it should actually be\r
+ * turned into sequence annotation or database cross references rather than a\r
+ * simple sequence feature.\r
* \r
* @param seq\r
- * @param SourceUrl\r
- * @param dbref\r
+ * the sequence to annotate\r
+ * @param f\r
+ * the jalview sequence feature generated from the DAS feature\r
+ * @param map\r
+ * the sequence feature attributes\r
+ * @param source\r
+ * the source that emitted the feature\r
+ * @return true if feature was consumed as another kind of annotation.\r
*/\r
- protected void createFeatureFetcher(final SequenceI seq,\r
- final DasSource dasSource, final DBRefEntry dbref)\r
+ protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,\r
+ FEATURE feature, jalviewSourceI source)\r
{\r
-\r
- // ////////////\r
- // / fetch DAS features\r
- final Das1Source source = new Das1Source();\r
- source.setUrl(dasSource.getUrl());\r
- source.setNickname(dasSource.getNickname());\r
- if (dbref == null || dbref.getAccessionId() == null\r
- || dbref.getAccessionId().length() < 1)\r
+ SequenceI mseq = seq;\r
+ while (seq.getDatasetSequence() != null)\r
{\r
- responseComplete(dasSource, seq); // reduce thread count anyhow\r
- return;\r
+ seq = seq.getDatasetSequence();\r
}\r
- debug("new Das Feature Fetcher for " + dbref.getSource() + ":"\r
- + dbref.getAccessionId() + " querying " + dasSource.getUrl());\r
- FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()\r
- // + ":" + start + "," + end,\r
- , source);\r
-\r
- fetcher.addFeatureListener(new FeatureListener()\r
+ if (f.getType() != null)\r
{\r
- public void comeBackLater(FeatureEvent e)\r
+ String type = f.getType();\r
+ if (type.equalsIgnoreCase("protein_name"))\r
{\r
- responseComplete(dasSource, seq);\r
- debug("das source " + e.getSource().getNickname()\r
- + " asked us to come back in " + e.getComeBackLater()\r
- + " secs.");\r
- }\r
-\r
- public void newFeatures(FeatureEvent e)\r
- {\r
-\r
- Das1Source ds = e.getSource();\r
-\r
- Map[] features = e.getFeatures();\r
- // add features to sequence\r
- debug("das source " + ds.getUrl() + " returned " + features.length\r
- + " features");\r
-\r
- if (features.length > 0)\r
+ // parse name onto the alignment sequence or the dataset sequence.\r
+ if (seq.getDescription() == null\r
+ || seq.getDescription().trim().length() == 0)\r
{\r
- for (int i = 0; i < features.length; i++)\r
- {\r
- SequenceFeature f = newSequenceFeature(features[i], source\r
- .getNickname());\r
- if (dbref.getMap() != null && f.getBegin() > 0\r
- && f.getEnd() > 0)\r
- {\r
- debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
- SequenceFeature vf[] = null;\r
-\r
- try\r
- {\r
- vf = dbref.getMap().locateFeature(f);\r
- } catch (Exception ex)\r
- {\r
- Cache.log\r
- .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");\r
- Cache.log.info("Mapping feature from " + f.getBegin()\r
- + " to " + f.getEnd() + " in dbref "\r
- + dbref.getAccessionId() + " in "\r
- + dbref.getSource());\r
- Cache.log.info("using das Source " + ds.getUrl());\r
- Cache.log.info("Exception", ex);\r
- }\r
-\r
- if (vf != null)\r
- {\r
- for (int v = 0; v < vf.length; v++)\r
- {\r
- debug("mapping to " + v + ": " + vf[v].getBegin() + " - "\r
- + vf[v].getEnd());\r
- seq.addSequenceFeature(vf[v]);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- seq.addSequenceFeature(f);\r
- }\r
- }\r
-\r
- featuresAdded(seq);\r
+ // could look at the note series to pick out the first long name, for\r
+ // the moment just use the whole description string\r
+ seq.setDescription(f.getDescription());\r
}\r
- else\r
+ if (mseq.getDescription() == null\r
+ || mseq.getDescription().trim().length() == 0)\r
{\r
- // System.out.println("No features found for " + seq.getName()\r
- // + " from: " + e.getDasSource().getNickname());\r
+ // could look at the note series to pick out the first long name, for\r
+ // the moment just use the whole description string\r
+ mseq.setDescription(f.getDescription());\r
}\r
- responseComplete(dasSource, seq);\r
-\r
+ return true;\r
}\r
- }\r
-\r
- );\r
-\r
- fetcher.start();\r
- }\r
-\r
- protected void createFeatureFetcher(final SequenceI seq,\r
- final DasSource dasSource, String id)\r
- {\r
- // ////////////\r
- // / fetch DAS features\r
- final Das1Source source = new Das1Source();\r
- source.setUrl(dasSource.getUrl());\r
- source.setNickname(dasSource.getNickname());\r
-\r
- if (id != null)\r
- {\r
- id = id.trim();\r
- }\r
- if (id != null && id.length() > 0)\r
- {\r
- debug("new Das Feature Fetcher for " + id + " querying "\r
- + dasSource.getUrl());\r
- FeatureThread fetcher = new FeatureThread(id\r
- // + ":" + start + "," + end,\r
- , source);\r
-\r
- fetcher.addFeatureListener(new FeatureListener()\r
+ // check if source has biosapiens or other sequence ontology label\r
+ if (type.equalsIgnoreCase("DBXREF") || type.equalsIgnoreCase("DBREF"))\r
{\r
- public void comeBackLater(FeatureEvent e)\r
+ // try to parse the accession out\r
+\r
+ DBRefEntry dbr = new DBRefEntry();\r
+ dbr.setVersion(source.getTitle());\r
+ StringTokenizer st = new StringTokenizer(f.getDescription(), ":");\r
+ if (st.hasMoreTokens())\r
{\r
- responseComplete(dasSource, seq);\r
- debug("das source " + e.getSource().getNickname()\r
- + " asked us to come back in " + e.getComeBackLater()\r
- + " secs.");\r
+ dbr.setSource(st.nextToken());\r
}\r
-\r
- public void newFeatures(FeatureEvent e)\r
+ if (st.hasMoreTokens())\r
{\r
+ dbr.setAccessionId(st.nextToken());\r
+ }\r
+ seq.addDBRef(dbr);\r
\r
- Das1Source ds = e.getSource();\r
-\r
- Map[] features = e.getFeatures();\r
- // add features to sequence\r
- debug("das source " + ds.getUrl() + " returned "\r
- + features.length + " features");\r
-\r
- if (features.length > 0)\r
+ if (f.links != null && f.links.size() > 0)\r
+ {\r
+ // feature is also appended to enable links to be seen.\r
+ // TODO: consider extending dbrefs to have their own links ?\r
+ // TODO: new feature: extract dbref links from DAS servers and add the\r
+ // URL pattern to the list of DB name associated links in the user's\r
+ // preferences ?\r
+ // for the moment - just fix up the existing feature so it displays\r
+ // correctly.\r
+ // f.setType(dbr.getSource());\r
+ // f.setDescription();\r
+ f.setValue("linkonly", Boolean.TRUE);\r
+ // f.setDescription("");\r
+ Vector newlinks = new Vector();\r
+ Enumeration it = f.links.elements();\r
+ while (it.hasMoreElements())\r
{\r
- for (int i = 0; i < features.length; i++)\r
+ String elm;\r
+ UrlLink urllink = new UrlLink(elm = (String) it.nextElement());\r
+ if (urllink.isValid())\r
{\r
- SequenceFeature f = newSequenceFeature(features[i], source\r
- .getNickname());\r
-\r
- seq.addSequenceFeature(f);\r
+ urllink.setLabel(f.getDescription());\r
+ newlinks.addElement(urllink.toString());\r
+ }\r
+ else\r
+ {\r
+ // couldn't parse the link properly. Keep it anyway - just in\r
+ // case.\r
+ debug("couldn't parse link string - " + elm);\r
+ newlinks.addElement(elm);\r
}\r
-\r
- featuresAdded(seq);\r
- }\r
- else\r
- {\r
- // System.out.println("No features found for " + seq.getName()\r
- // + " from: " + e.getDasSource().getNickname());\r
}\r
- responseComplete(dasSource, seq);\r
-\r
+ f.links = newlinks;\r
+ seq.addSequenceFeature(f);\r
}\r
+ return true;\r
}\r
-\r
- );\r
-\r
- fetcher.start();\r
- }\r
- else\r
- {\r
- // invalid fetch - indicate it is finished.\r
- debug("Skipping empty ID for querying " + dasSource.getUrl());\r
- responseComplete(dasSource, seq);\r
}\r
+ return false;\r
}\r
\r
/**\r
* creates a jalview sequence feature from a das feature document\r
* \r
- * @param dasfeature\r
+ * @param feat\r
* @return sequence feature object created using dasfeature information\r
*/\r
- SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
+ SequenceFeature newSequenceFeature(FEATURE feat, String nickname)\r
{\r
- if (dasfeature == null)\r
+ if (feat == null)\r
{\r
return null;\r
}\r
* qName.equals("SCORE")\r
*/\r
String desc = new String();\r
- if (dasfeature.containsKey("NOTE"))\r
+ if (feat.getNOTE() != null)\r
{\r
- desc += (String) dasfeature.get("NOTE");\r
+ for (String note : feat.getNOTE())\r
+ {\r
+ desc += (String) note;\r
+ }\r
}\r
\r
int start = 0, end = 0;\r
\r
try\r
{\r
- start = Integer.parseInt(dasfeature.get("START").toString());\r
+ start = Integer.parseInt(feat.getSTART().toString());\r
} catch (Exception ex)\r
{\r
}\r
try\r
{\r
- end = Integer.parseInt(dasfeature.get("END").toString());\r
+ end = Integer.parseInt(feat.getEND().toString());\r
} catch (Exception ex)\r
{\r
}\r
try\r
{\r
- score = (float) Double.parseDouble(dasfeature.get("SCORE").toString());\r
+ Object scr = feat.getSCORE();\r
+ if (scr != null)\r
+ {\r
+ score = (float) Double.parseDouble(scr.toString());\r
+\r
+ }\r
} catch (Exception ex)\r
{\r
}\r
\r
- SequenceFeature f = new SequenceFeature((String) dasfeature\r
- .get("TYPE"), desc, start, end, score, nickname);\r
+ SequenceFeature f = new SequenceFeature(\r
+ getTypeString(feat.getTYPE()), desc, start, end, score,\r
+ nickname);\r
\r
- if (dasfeature.containsKey("LINK"))\r
+ if (feat.getLINK() != null)\r
{\r
- // Do not put feature extent in link text for non-positional features\r
- if (f.begin==0 && f.end==0)\r
- { f.addLink(f.getType()+"|"\r
- + dasfeature.get("LINK"));\r
- } else {\r
- f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"\r
- + dasfeature.get("LINK"));\r
+ for (LINK link : feat.getLINK())\r
+ {\r
+ // Do not put feature extent in link text for non-positional features\r
+ if (f.begin == 0 && f.end == 0)\r
+ {\r
+ f.addLink(f.getType() + " " + link.getContent() + "|"\r
+ + link.getHref());\r
+ }\r
+ else\r
+ {\r
+ f.addLink(f.getType() + " " + f.begin + "_" + f.end + " "\r
+ + link.getContent() + "|" + link.getHref());\r
+ }\r
}\r
}\r
\r
System.out.println("ERRR " + e);\r
e.printStackTrace();\r
System.out.println("############");\r
- debug("Failed to parse " + dasfeature.toString(), e);\r
+ debug("Failed to parse " + feat.toString(), e);\r
return null;\r
}\r
}\r
\r
- /**\r
- * query the default DAS Source Registry for sources. Uses value of jalview\r
- * property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that\r
- * doesn't exist.\r
- * \r
- * @return list of sources\r
- */\r
- public static DasSource[] getDASSources()\r
+ private String getTypeString(TYPE type)\r
{\r
-\r
- String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- DasSourceBrowser.DEFAULT_REGISTRY);\r
- return getDASSources(registryURL);\r
+ return type.getContent();\r
}\r
\r
- /**\r
- * query the given URL for DasSources.\r
- * \r
- * @param registryURL\r
- * return sources from registryURL\r
- */\r
- public static DasSource[] getDASSources(String registryURL)\r
+ public boolean isRunning()\r
{\r
- DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
-\r
- try\r
- {\r
- URL url = new URL(registryURL);\r
-\r
- DasSource[] sources = reader.readDasSource(url);\r
-\r
- List das1sources = new ArrayList();\r
- for (int i = 0; i < sources.length; i++)\r
- {\r
- DasSource ds = sources[i];\r
- if (ds instanceof Das2Source)\r
- {\r
- Das2Source d2s = (Das2Source) ds;\r
- if (d2s.hasDas1Capabilities())\r
- {\r
- Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
- das1sources.add(d1s);\r
- }\r
-\r
- }\r
- else if (ds instanceof Das1Source)\r
- {\r
- das1sources.add((Das1Source) ds);\r
- }\r
- }\r
-\r
- return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources\r
- .size()]);\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- return null;\r
- }\r
+ return running;\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff