+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws;
-
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.FeatureSettings;
-import jalview.gui.JvOptionPane;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.util.UrlLink;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import org.biodas.jdas.client.FeaturesClient;
-import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
-import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
-import org.biodas.jdas.client.threads.FeaturesClientMultipleSources;
-import org.biodas.jdas.schema.features.ERRORSEGMENT;
-import org.biodas.jdas.schema.features.FEATURE;
-import org.biodas.jdas.schema.features.LINK;
-import org.biodas.jdas.schema.features.SEGMENT;
-import org.biodas.jdas.schema.features.TYPE;
-import org.biodas.jdas.schema.features.UNKNOWNFEATURE;
-import org.biodas.jdas.schema.features.UNKNOWNSEGMENT;
-import org.biodas.jdas.schema.sources.COORDINATES;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class DasSequenceFeatureFetcher
-{
- SequenceI[] sequences;
-
- AlignFrame af;
-
- FeatureSettings fsettings;
-
- StringBuffer sbuffer = new StringBuffer();
-
- List<jalviewSourceI> selectedSources;
-
- boolean cancelled = false;
-
- private void debug(String mesg)
- {
- debug(mesg, null);
- }
-
- private void debug(String mesg, Exception e)
- {
- if (Cache.log != null)
- {
- Cache.log.debug(mesg, e);
- }
- else
- {
- System.err.println(mesg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
- long startTime;
-
- private DasSourceRegistryI sourceRegistry;
-
- private boolean useJDASMultiThread = true;
-
- /**
- * Creates a new SequenceFeatureFetcher object. Uses default
- *
- * @param align
- * DOCUMENT ME!
- * @param ap
- * DOCUMENT ME!
- */
- public DasSequenceFeatureFetcher(SequenceI[] sequences,
- FeatureSettings fsettings, Vector selectedSources)
- {
- this(sequences, fsettings, selectedSources, true, true, true);
- }
-
- public DasSequenceFeatureFetcher(SequenceI[] oursequences,
- FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,
- boolean checkDbrefs, boolean promptFetchDbrefs)
- {
- this(oursequences, fsettings, selectedSources2, checkDbrefs,
- promptFetchDbrefs, true);
- }
-
- public DasSequenceFeatureFetcher(SequenceI[] oursequences,
- FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,
- boolean checkDbrefs, boolean promptFetchDbrefs,
- boolean useJDasMultiThread)
- {
- this.useJDASMultiThread = useJDasMultiThread;
- this.selectedSources = new ArrayList<>();
- // filter both sequences and sources to eliminate duplicates
- for (jalviewSourceI src : selectedSources2)
- {
- if (!selectedSources.contains(src))
- {
- selectedSources.add(src);
- }
- ;
- }
- Vector sqs = new Vector();
- for (int i = 0; i < oursequences.length; i++)
- {
- if (!sqs.contains(oursequences[i]))
- {
- sqs.addElement(oursequences[i]);
- }
- }
- sequences = new SequenceI[sqs.size()];
- for (int i = 0; i < sequences.length; i++)
- {
- sequences[i] = (SequenceI) sqs.elementAt(i);
- }
- if (fsettings != null)
- {
- this.fsettings = fsettings;
- this.af = fsettings.af;
- af.setShowSeqFeatures(true);
- }
- int uniprotCount = 0;
- for (jalviewSourceI source : selectedSources)
- {
- for (COORDINATES coords : source.getVersion().getCOORDINATES())
- {
- // TODO: match UniProt coord system canonically (?) - does
- // UniProt==uniprot==UNIPROT ?
- if (coords.getAuthority().toLowerCase().equals("uniprot"))
- {
- uniprotCount++;
- break;
- }
- }
- }
-
- int refCount = 0;
- for (int i = 0; i < sequences.length; i++)
- {
- DBRefEntry[] dbref = sequences[i].getDBRefs();
- if (dbref != null)
- {
- for (int j = 0; j < dbref.length; j++)
- {
- if (dbref[j].getSource().equals(DBRefSource.UNIPROT))
- {
- refCount++;
- break;
- }
- }
- }
- }
-
- if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
- {
-
- int reply = JvOptionPane.YES_OPTION;
- if (promptFetchDbrefs)
- {
- reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString(
- "info.you_want_jalview_to_find_uniprot_accessions"),
- MessageManager
- .getString("label.find_uniprot_accession_ids"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.QUESTION_MESSAGE);
- }
-
- if (reply == JvOptionPane.YES_OPTION)
- {
- Thread thread = new Thread(new FetchDBRefs());
- thread.start();
- }
- else
- {
- _startFetching();
- }
- }
- else
- {
- _startFetching();
- }
-
- }
-
- private void _startFetching()
- {
- running = true;
- new Thread(new FetchSeqFeatures()).start();
- }
-
- class FetchSeqFeatures implements Runnable
- {
- @Override
- public void run()
- {
- startFetching();
- setGuiFetchComplete();
- }
- }
-
- class FetchDBRefs implements Runnable
- {
- @Override
- public void run()
- {
- running = true;
- boolean isNucleotide = af.getViewport().getAlignment().isNucleotide();
- new DBRefFetcher(sequences, af, null, af.featureSettings,
- isNucleotide).fetchDBRefs(true);
-
- startFetching();
- setGuiFetchComplete();
- }
- }
-
- /**
- * Spawns Fetcher threads to add features to sequences in the dataset
- */
- void startFetching()
- {
- running = true;
- cancelled = false;
- startTime = System.currentTimeMillis();
- if (af != null)
- {
- af.setProgressBar(MessageManager.getString(
- "status.fetching_das_sequence_features"), startTime);
- }
- if (sourceRegistry == null)
- {
- sourceRegistry = Cache.getDasSourceRegistry();
- }
- if (selectedSources == null || selectedSources.size() == 0)
- {
- try
- {
- jalviewSourceI[] sources = sourceRegistry.getSources()
- .toArray(new jalviewSourceI[0]);
- String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
- StringTokenizer st = new StringTokenizer(active, "\t");
- selectedSources = new Vector();
- String token;
- while (st.hasMoreTokens())
- {
- token = st.nextToken();
- for (int i = 0; i < sources.length; i++)
- {
- if (sources[i].getTitle().equals(token))
- {
- selectedSources.add(sources[i]);
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- debug("Exception whilst setting default feature sources from registry and local preferences.",
- ex);
- }
- }
-
- if (selectedSources == null || selectedSources.size() == 0)
- {
- System.out.println("No DAS Sources active");
- cancelled = true;
- setGuiNoDassourceActive();
- return;
- }
-
- sourcesRemaining = selectedSources.size();
- FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();
- fc.setConnProps(sourceRegistry.getSessionHandler());
- // Now sending requests one at a time to each server
- ArrayList<jalviewSourceI> srcobj = new ArrayList<>();
- ArrayList<String> src = new ArrayList<>();
- List<List<String>> ids = new ArrayList<>();
- List<List<DBRefEntry>> idobj = new ArrayList<>();
- List<Map<String, SequenceI>> sqset = new ArrayList<>();
- for (jalviewSourceI _sr : selectedSources)
- {
-
- Map<String, SequenceI> slist = new HashMap<>();
- List<DBRefEntry> idob = new ArrayList<>();
- List<String> qset = new ArrayList<>();
-
- for (SequenceI seq : sequences)
- {
- Object[] idset = nextSequence(_sr, seq);
- if (idset != null)
- {
- List<DBRefEntry> _idob = (List<DBRefEntry>) idset[0];
- List<String> _qset = (List<String>) idset[1];
- if (_idob.size() > 0)
- {
- // add sequence's ref for each id derived from it
- // (space inefficient, but most unambiguous)
- // could replace with hash with _qset values as keys.
- Iterator<DBRefEntry> dbobj = _idob.iterator();
- for (String q : _qset)
- {
- SequenceI osq = slist.get(q);
- DBRefEntry dr = dbobj.next();
- if (osq != null && osq != seq)
- {
- // skip - non-canonical query
- }
- else
- {
- idob.add(dr);
- qset.add(q);
- slist.put(q, seq);
- }
- }
- }
- }
- }
- if (idob.size() > 0)
- {
- srcobj.add(_sr);
- src.add(_sr.getSourceURL());
- ids.add(qset);
- idobj.add(idob);
- sqset.add(slist);
- }
- }
- Map<String, Map<List<String>, Exception>> errors = new HashMap<>();
- Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<>();
- if (!useJDASMultiThread)
- {
- Iterator<String> sources = src.iterator();
- // iterate over each query for each source and do each one individually
- for (List<String> idl : ids)
- {
- String source = sources.next();
- FeaturesClient featuresc = new FeaturesClient(
- sourceRegistry.getSessionHandler()
- .getConnectionPropertyProviderFor(source));
- for (String id : idl)
- {
- List<String> qid = Arrays.asList(new String[] { id });
- try
- {
- DasGFFAdapter dga = featuresc.fetchData(source, qid);
- Map<List<String>, DasGFFAdapter> ers = results.get(source);
- if (ers == null)
- {
- results.put(source,
- ers = new HashMap<>());
- }
- ers.put(qid, dga);
- } catch (Exception ex)
- {
- Map<List<String>, Exception> ers = errors.get(source);
- if (ers == null)
- {
- errors.put(source,
- ers = new HashMap<>());
- }
- ers.put(qid, ex);
- }
- }
- }
- }
- else
- {
- // pass them all at once
- fc.fetchData(src, ids, false, results, errors);
- fc.shutDown();
- while (!fc.isTerminated())
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
-
- }
- }
- }
- Iterator<List<String>> idset = ids.iterator();
- Iterator<List<DBRefEntry>> idobjset = idobj.iterator();
- Iterator<Map<String, SequenceI>> seqset = sqset.iterator();
- for (jalviewSourceI source : srcobj)
- {
- processResponse(seqset.next(), source, idset.next(), idobjset.next(),
- results.get(source.getSourceURL()),
- errors.get(source.getSourceURL()));
- }
- }
-
- private void processResponse(Map<String, SequenceI> sequencemap,
- jalviewSourceI jvsource, List<String> ids, List<DBRefEntry> idobj,
- Map<List<String>, DasGFFAdapter> results,
- Map<List<String>, Exception> errors)
- {
- Set<SequenceI> sequences = new HashSet<>();
- String source = jvsource.getSourceURL();
- // process features
- DasGFFAdapter result = (results == null) ? null : results.get(ids);
- Exception error = (errors == null) ? null : errors.get(ids);
- if (result == null)
- {
- debug("das source " + source + " could not be contacted. "
- + (error == null ? "" : error.toString()));
- }
- else
- {
-
- GFFAdapter gff = result.getGFF();
- List<SEGMENT> segments = gff.getSegments();
- List<ERRORSEGMENT> errorsegs = gff.getErrorSegments();
- List<UNKNOWNFEATURE> unkfeats = gff.getUnknownFeatures();
- List<UNKNOWNSEGMENT> unksegs = gff.getUnknownSegments();
- debug("das source " + source + " returned " + gff.getTotal()
- + " responses. " + (errorsegs != null ? errorsegs.size() : 0)
- + " were incorrect segment queries, "
- + (unkfeats != null ? unkfeats.size() : 0)
- + " were unknown features "
- + (unksegs != null ? unksegs.size() : 0)
- + " were unknown segments and "
- + (segments != null ? segments.size() : 0)
- + " were segment responses.");
- Iterator<DBRefEntry> dbr = idobj.iterator();
- if (segments != null)
- {
- for (SEGMENT seg : segments)
- {
- String id = seg.getId();
- if (ids.indexOf(id) == -1)
- {
- id = id.toUpperCase();
- }
- DBRefEntry dbref = idobj.get(ids.indexOf(id));
- SequenceI sequence = sequencemap.get(id);
- boolean added = false;
- sequences.add(sequence);
-
- for (FEATURE feat : seg.getFEATURE())
- {
- // standard DAS feature-> jalview sequence feature transformation
- SequenceFeature f = newSequenceFeature(feat,
- jvsource.getTitle());
- if (!parseSeqFeature(sequence, f, feat, jvsource))
- {
- if (dbref.getMap() != null && f.getBegin() > 0
- && f.getEnd() > 0)
- {
- debug("mapping from " + f.getBegin() + " - " + f.getEnd());
- SequenceFeature vf[] = null;
-
- try
- {
- vf = dbref.getMap().locateFeature(f);
- } catch (Exception ex)
- {
- Cache.log.warn(
- "Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
- Cache.log.warn("Mapping feature from " + f.getBegin()
- + " to " + f.getEnd() + " in dbref "
- + dbref.getAccessionId() + " in "
- + dbref.getSource());
- Cache.log.warn("using das Source " + source);
- Cache.log.warn("Exception", ex);
- }
-
- if (vf != null)
- {
- for (int v = 0; v < vf.length; v++)
- {
- debug("mapping to " + v + ": " + vf[v].getBegin()
- + " - " + vf[v].getEnd());
- sequence.addSequenceFeature(vf[v]);
- }
- }
- }
- else
- {
- sequence.addSequenceFeature(f);
- }
- }
- }
- }
- featuresAdded(sequences);
- }
- else
- {
- // System.out.println("No features found for " + seq.getName()
- // + " from: " + e.getDasSource().getNickname());
- }
- }
- }
-
- private void setGuiNoDassourceActive()
- {
-
- if (af != null)
- {
- af.setProgressBar(
- MessageManager.getString("status.no_das_sources_active"),
- startTime);
- }
- if (getFeatSettings() != null)
- {
- fsettings.noDasSourceActive();
- }
- }
-
- /**
- * Update our fsettings dialog reference if we didn't have one when we were
- * first initialised.
- *
- * @return fsettings
- */
- private FeatureSettings getFeatSettings()
- {
- if (fsettings == null)
- {
- if (af != null)
- {
- fsettings = af.featureSettings;
- }
- }
- return fsettings;
- }
-
- public void cancel()
- {
- if (af != null)
- {
- af.setProgressBar(MessageManager.getString(
- "status.das_feature_fetching_cancelled"), startTime);
- }
- cancelled = true;
- }
-
- int sourcesRemaining = 0;
-
- private boolean running = false;
-
- private void setGuiFetchComplete()
- {
- running = false;
- if (!cancelled && af != null)
- {
- // only update the progress bar if we've completed the fetch normally
- af.setProgressBar(MessageManager.getString(
- "status.das_feature_fetching_complete"), startTime);
- }
-
- if (af != null && af.featureSettings != null)
- {
- af.featureSettings.discoverAllFeatureData();
- }
-
- if (getFeatSettings() != null)
- {
- fsettings.complete();
- }
- }
-
- void featuresAdded(Set<SequenceI> seqs)
- {
- if (af == null)
- {
- // no gui to update with features.
- return;
- }
- af.getFeatureRenderer().featuresAdded();
-
- int start = af.getViewport().getRanges().getStartSeq();
- int end = af.getViewport().getRanges().getEndSeq();
- int index;
- for (index = start; index < end; index++)
- {
- for (SequenceI seq : seqs)
- {
- if (seq == af.getViewport().getAlignment().getSequenceAt(index)
- .getDatasetSequence())
- {
- af.alignPanel.paintAlignment(true, true);
- index = end;
- break;
- }
- }
- }
- }
-
- Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)
- {
- if (cancelled)
- {
- return null;
- }
- DBRefEntry[] uprefs = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[]
- {
- // jalview.datamodel.DBRefSource.PDB,
- DBRefSource.UNIPROT,
- // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
- // sys sources
- });
- // TODO: minimal list of DAS queries to make by querying with untyped ID if
- // distinct from any typed IDs
-
- List<DBRefEntry> ids = new ArrayList<>();
- List<String> qstring = new ArrayList<>();
- boolean dasCoordSysFound = false;
-
- if (uprefs != null)
- {
- // do any of these ids match the source's coordinate system ?
- for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)
- {
-
- for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
- {
- if (DBRefUtils.isDasCoordinateSystem(csys.getAuthority(),
- uprefs[j]))
- {
- debug("Launched fetcher for coordinate system "
- + csys.getAuthority());
- // Will have to pass any mapping information to the fetcher
- // - the start/end for the DBRefEntry may not be the same as the
- // sequence's start/end
-
- System.out.println(
- seq.getName() + " " + (seq.getDatasetSequence() == null)
- + " " + csys.getUri());
-
- dasCoordSysFound = true; // break's out of the loop
- ids.add(uprefs[j]);
- qstring.add(uprefs[j].getAccessionId());
- }
- else
- {
- System.out.println("IGNORE " + csys.getAuthority());
- }
- }
- }
- }
-
- if (!dasCoordSysFound)
- {
- String id = null;
- // try and use the name as the sequence id
- if (seq.getName().indexOf("|") > -1)
- {
- id = seq.getName().substring(seq.getName().lastIndexOf("|") + 1);
- if (id.trim().length() < 4)
- {
- // hack - we regard a significant ID as being at least 4
- // non-whitespace characters
- id = seq.getName().substring(0, seq.getName().lastIndexOf("|"));
- if (id.indexOf("|") > -1)
- {
- id = id.substring(id.lastIndexOf("|") + 1);
- }
- }
- }
- else
- {
- id = seq.getName();
- }
- if (id != null)
- {
- DBRefEntry dbre = new DBRefEntry();
- dbre.setAccessionId(id);
- // Should try to call a general feature fetcher that
- // queries many sources with name to discover applicable ID references
- ids.add(dbre);
- qstring.add(dbre.getAccessionId());
- }
- }
-
- return new Object[] { ids, qstring };
- }
-
- /**
- * examine the given sequence feature to determine if it should actually be
- * turned into sequence annotation or database cross references rather than a
- * simple sequence feature.
- *
- * @param seq
- * the sequence to annotate
- * @param f
- * the jalview sequence feature generated from the DAS feature
- * @param map
- * the sequence feature attributes
- * @param source
- * the source that emitted the feature
- * @return true if feature was consumed as another kind of annotation.
- */
- protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,
- FEATURE feature, jalviewSourceI source)
- {
- SequenceI mseq = seq;
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- if (f.getType() != null)
- {
- String type = f.getType();
- if (type.equalsIgnoreCase("protein_name"))
- {
- // parse name onto the alignment sequence or the dataset sequence.
- if (seq.getDescription() == null
- || seq.getDescription().trim().length() == 0)
- {
- // could look at the note series to pick out the first long name, for
- // the moment just use the whole description string
- seq.setDescription(f.getDescription());
- }
- if (mseq.getDescription() == null
- || mseq.getDescription().trim().length() == 0)
- {
- // could look at the note series to pick out the first long name, for
- // the moment just use the whole description string
- mseq.setDescription(f.getDescription());
- }
- return true;
- }
- // check if source has biosapiens or other sequence ontology label
- if (type.equalsIgnoreCase("DBXREF") || type.equalsIgnoreCase("DBREF"))
- {
- // try to parse the accession out
-
- DBRefEntry dbr = new DBRefEntry();
- dbr.setVersion(source.getTitle());
- StringTokenizer st = new StringTokenizer(f.getDescription(), ":");
- if (st.hasMoreTokens())
- {
- dbr.setSource(st.nextToken());
- }
- if (st.hasMoreTokens())
- {
- dbr.setAccessionId(st.nextToken());
- }
- seq.addDBRef(dbr);
-
- if (f.links != null && f.links.size() > 0)
- {
- // feature is also appended to enable links to be seen.
- // TODO: consider extending dbrefs to have their own links ?
- // TODO: new feature: extract dbref links from DAS servers and add the
- // URL pattern to the list of DB name associated links in the user's
- // preferences ?
- // for the moment - just fix up the existing feature so it displays
- // correctly.
- // f.setType(dbr.getSource());
- // f.setDescription();
- f.setValue("linkonly", Boolean.TRUE);
- // f.setDescription("");
- Vector newlinks = new Vector();
- Enumeration it = f.links.elements();
- while (it.hasMoreElements())
- {
- String elm;
- UrlLink urllink = new UrlLink(elm = (String) it.nextElement());
- if (urllink.isValid())
- {
- urllink.setLabel(f.getDescription());
- newlinks.addElement(urllink.toString());
- }
- else
- {
- // couldn't parse the link properly. Keep it anyway - just in
- // case.
- debug("couldn't parse link string - " + elm);
- newlinks.addElement(elm);
- }
- }
- f.links = newlinks;
- seq.addSequenceFeature(f);
- }
- return true;
- }
- }
- return false;
- }
-
- /**
- * creates a jalview sequence feature from a das feature document
- *
- * @param feat
- * @return sequence feature object created using dasfeature information
- */
- SequenceFeature newSequenceFeature(FEATURE feat, String nickname)
- {
- if (feat == null)
- {
- return null;
- }
- try
- {
- /**
- * Different qNames for a DAS Feature - are string keys to the HashMaps in
- * features "METHOD") || qName.equals("TYPE") || qName.equals("START") ||
- * qName.equals("END") || qName.equals("NOTE") || qName.equals("LINK") ||
- * qName.equals("SCORE")
- */
- String desc = new String();
- if (feat.getNOTE() != null)
- {
- for (String note : feat.getNOTE())
- {
- desc += note;
- }
- }
-
- int start = 0, end = 0;
- float score = 0f;
-
- try
- {
- start = Integer.parseInt(feat.getSTART().toString());
- } catch (Exception ex)
- {
- }
- try
- {
- end = Integer.parseInt(feat.getEND().toString());
- } catch (Exception ex)
- {
- }
- try
- {
- Object scr = feat.getSCORE();
- if (scr != null)
- {
- score = (float) Double.parseDouble(scr.toString());
-
- }
- } catch (Exception ex)
- {
- }
-
- SequenceFeature f = new SequenceFeature(getTypeString(feat.getTYPE()),
- desc, start, end, score, nickname);
-
- if (feat.getLINK() != null)
- {
- for (LINK link : feat.getLINK())
- {
- // Do not put feature extent in link text for non-positional features
- if (f.begin == 0 && f.end == 0)
- {
- f.addLink(f.getType() + " " + link.getContent() + "|"
- + link.getHref());
- }
- else
- {
- f.addLink(f.getType() + " " + f.begin + "_" + f.end + " "
- + link.getContent() + "|" + link.getHref());
- }
- }
- }
-
- return f;
- } catch (Exception e)
- {
- System.out.println("ERRR " + e);
- e.printStackTrace();
- System.out.println("############");
- debug("Failed to parse " + feat.toString(), e);
- return null;
- }
- }
-
- private String getTypeString(TYPE type)
- {
- return type.getContent();
- }
-
- public boolean isRunning()
- {
- return running;
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff