import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.DasSourceBrowser;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import uk.ac.ebi.picr.model.UPEntry;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
/**
* Implements a runnable for validating a sequence against external databases
void finished();
}
- private List<FetchFinishedListenerI> listeners;
-
SequenceI[] dataset;
IProgressIndicator progressWindow;
*/
uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
- // /This will be a collection of Vectors of sequenceI refs.
+ // This will be a collection of Vectors of sequenceI refs.
// The key will be the seq name or accession id of the seq
- Hashtable seqRefs;
+ Hashtable<String, Vector<SequenceI>> seqRefs;
DbSourceProxy[] dbSources;
SequenceFetcher sfetcher;
+ private List<FetchFinishedListenerI> listeners;
+
private SequenceI[] alseqs;
- /**
+ /*
* when true - retrieved sequences will be trimmed to cover longest derived
* alignment sequence
*/
trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
if (sources == null)
{
- // af.featureSettings_actionPerformed(null);
- String[] defdb = null, otherdb = sfetcher
- .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
- List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
- .getSelectedSources() : new jalview.gui.DasSourceBrowser()
- .getSelectedSources();
- Enumeration<jalviewSourceI> en = dasselsrc.elements();
- while (en.hasMoreElements())
+ setDatabaseSources(featureSettings, isNucleotide);
+ }
+ else
+ {
+ // we assume the caller knows what they're doing and ensured that all the
+ // db source names are valid
+ dbSources = sources;
+ }
+ }
+
+ /**
+ * Helper method to configure the list of database sources to query
+ *
+ * @param featureSettings
+ * @param forNucleotide
+ */
+ void setDatabaseSources(FeatureSettings featureSettings,
+ boolean forNucleotide)
+ {
+ // af.featureSettings_actionPerformed(null);
+ String[] defdb = null;
+ List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+ Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
+ .getSelectedSources() : new DasSourceBrowser()
+ .getSelectedSources();
+
+ for (jalviewSourceI src : dasselsrc)
+ {
+ List<DbSourceProxy> sp = src.getSequenceSourceProxies();
+ if (sp != null)
{
- jalviewSourceI src = en.nextElement();
- List<DbSourceProxy> sp = src.getSequenceSourceProxies();
- if (sp != null)
+ selsources.addAll(sp);
+ if (sp.size() > 1)
{
- selsources.addAll(sp);
- if (sp.size() > 1)
- {
- Cache.log.debug("Added many Db Sources for :" + src.getTitle());
- }
+ Cache.log.debug("Added many Db Sources for :" + src.getTitle());
}
}
- // select appropriate databases based on alignFrame context.
- if (isNucleotide)
- {
- defdb = DBRefSource.DNACODINGDBS;
- }
- else
- {
- defdb = DBRefSource.PROTEINDBS;
- }
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
- for (String ddb : defdb)
+ }
+ // select appropriate databases based on alignFrame context.
+ if (forNucleotide)
+ {
+ defdb = DBRefSource.DNACODINGDBS;
+ }
+ else
+ {
+ defdb = DBRefSource.PROTEINDBS;
+ }
+ List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ for (String ddb : defdb)
+ {
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+ if (srcesfordb != null)
{
- List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
- if (srcesfordb != null)
+ for (DbSourceProxy src : srcesfordb)
{
- srces.addAll(srcesfordb);
+ if (!srces.contains(src))
+ {
+ srces.addAll(srcesfordb);
+ }
}
}
- // append the PDB data source, since it is 'special', catering for both
- // nucleotide and protein
- srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
-
- // append the selected sequence sources to the default dbs
- srces.addAll(selsources);
- dbSources = srces.toArray(new DbSourceProxy[0]);
- }
- else
- {
- // we assume the caller knows what they're doing and ensured that all the
- // db source names are valid
- dbSources = sources;
}
+ // append the PDB data source, since it is 'special', catering for both
+ // nucleotide and protein
+ // srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
+
+ srces.addAll(selsources);
+ dbSources = srces.toArray(new DbSourceProxy[srces.size()]);
}
/**
}
// append additional sources
DbSourceProxy[] otherdb = sfetcher
- .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ .getDbSourceProxyInstances(DasSequenceSource.class);
if (otherdb != null && otherdb.length > 0)
{
DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
*/
public void fetchDBRefs(boolean waitTillFinished)
{
+ // TODO can we not simply write
+ // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
+
Thread thread = new Thread(this);
thread.start();
running = true;
{
key = key.toUpperCase();
- Vector seqs;
+ Vector<SequenceI> seqs;
if (seqRefs.containsKey(key))
{
- seqs = (Vector) seqRefs.get(key);
+ seqs = seqRefs.get(key);
if (seqs != null && !seqs.contains(seq))
{
}
else if (seqs == null)
{
- seqs = new Vector();
+ seqs = new Vector<SequenceI>();
seqs.addElement(seq);
}
}
else
{
- seqs = new Vector();
+ seqs = new Vector<SequenceI>();
seqs.addElement(seq);
}
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
{
- picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+ picrClient = new AccessionMapperServiceLocator()
.getAccessionMapperPort();
}
} catch (Exception e)
System.err.println("Couldn't locate PICR service instance.\n");
e.printStackTrace();
}
+
+ Vector<SequenceI> sdataset = new Vector<SequenceI>(
+ Arrays.asList(dataset));
+
int db = 0;
- Vector sdataset = new Vector();
- for (int s = 0; s < dataset.length; s++)
- {
- sdataset.addElement(dataset[s]);
- }
while (sdataset.size() > 0 && db < dbSources.length)
{
- int maxqlen = 1; // default number of queries made to at one time
- System.err.println("Verifying against " + dbSources[db].getDbName());
- boolean dn = false;
+ int maxqlen = 1; // default number of queries made at one time
+ System.out.println("Verifying against " + dbSources[db].getDbName());
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
sdataset.copyInto(currSeqs);// seqs that are to be validated against
// dbSources[db]
- Vector queries = new Vector(); // generated queries curSeq
- seqRefs = new Hashtable();
+ Vector<String> queries = new Vector<String>(); // generated queries curSeq
+ seqRefs = new Hashtable<String, Vector<SequenceI>>();
int seqIndex = 0;
- jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
+ DbSourceProxy dbsource = dbSources[db];
+ // for moment, we dumbly iterate over all retrieval sources for a
+ // particular database
+ // TODO: introduce multithread multisource queries and logic to remove a
+ // query from other sources if any source for a database returns a
+ // record
+ maxqlen = dbsource.getMaximumQueryCount();
+
+ while (queries.size() > 0 || seqIndex < currSeqs.length)
{
- // for moment, we dumbly iterate over all retrieval sources for a
- // particular database
- // TODO: introduce multithread multisource queries and logic to remove a
- // query from other sources if any source for a database returns a
- // record
- maxqlen = dbsource.getMaximumQueryCount();
-
- while (queries.size() > 0 || seqIndex < currSeqs.length)
+ if (queries.size() > 0)
{
- if (queries.size() > 0)
- {
- // Still queries to make for current seqIndex
- StringBuffer queryString = new StringBuffer("");
- int numq = 0, nqSize = (maxqlen > queries.size()) ? queries
- .size() : maxqlen;
+ // Still queries to make for current seqIndex
+ StringBuffer queryString = new StringBuffer("");
+ int numq = 0;
+ int nqSize = (maxqlen > queries.size()) ? queries
+ .size() : maxqlen;
- while (queries.size() > 0 && numq < nqSize)
- {
- String query = (String) queries.elementAt(0);
- if (dbsource.isValidReference(query))
- {
- queryString.append((numq == 0) ? "" : dbsource
- .getAccessionSeparator());
- queryString.append(query);
- numq++;
- }
- // remove the extracted query string
- queries.removeElementAt(0);
- }
- // make the queries and process the response
- AlignmentI retrieved = null;
- try
- {
- if (jalview.bin.Cache.log.isDebugEnabled())
- {
- jalview.bin.Cache.log.debug("Querying "
- + dbsource.getDbName() + " with : '"
- + queryString.toString() + "'");
- }
- retrieved = dbsource.getSequenceRecords(queryString
- .toString());
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } catch (OutOfMemoryError err)
+ while (queries.size() > 0 && numq < nqSize)
+ {
+ String query = queries.elementAt(0);
+ if (dbsource.isValidReference(query))
{
- new OOMWarning("retrieving database references ("
- + queryString.toString() + ")", err);
+ queryString.append((numq == 0) ? "" : dbsource
+ .getAccessionSeparator());
+ queryString.append(query);
+ numq++;
}
- if (retrieved != null)
+ // remove the extracted query string
+ queries.removeElementAt(0);
+ }
+ // make the queries and process the response
+ AlignmentI retrieved = null;
+ try
+ {
+ if (Cache.log.isDebugEnabled())
{
- transferReferences(sdataset, dbsource.getDbSource(),
- retrieved, trimDsSeqs);
+ Cache.log.debug("Querying " + dbsource.getDbName()
+ + " with : '" + queryString.toString() + "'");
}
+ retrieved = dbsource.getSequenceRecords(queryString.toString());
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } catch (OutOfMemoryError err)
+ {
+ new OOMWarning("retrieving database references ("
+ + queryString.toString() + ")", err);
+ }
+ if (retrieved != null)
+ {
+ transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+ trimDsSeqs);
}
- else
+ }
+ else
+ {
+ // make some more strings for use as queries
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
{
- // make some more strings for use as queries
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ SequenceI sequence = dataset[seqIndex];
+ DBRefEntry[] uprefs = DBRefUtils.selectRefs(
+ sequence.getDBRefs(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ // });
+ // check for existing dbrefs to use
+ if (uprefs != null && uprefs.length > 0)
{
- SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRefs(),
- new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
- // });
- // check for existing dbrefs to use
- if (uprefs != null && uprefs.length > 0)
+ for (int j = 0; j < uprefs.length; j++)
{
- for (int j = 0; j < uprefs.length; j++)
- {
- addSeqId(sequence, uprefs[j].getAccessionId());
- queries.addElement(uprefs[j].getAccessionId()
- .toUpperCase());
- }
+ addSeqId(sequence, uprefs[j].getAccessionId());
+ queries.addElement(uprefs[j].getAccessionId().toUpperCase());
}
- else
+ }
+ else
+ {
+ // generate queries from sequence ID string
+ StringTokenizer st = new StringTokenizer(sequence.getName(),
+ "|");
+ while (st.hasMoreTokens())
{
- // generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(
- sequence.getName(), "|");
- while (st.hasMoreTokens())
+ String token = st.nextToken();
+ UPEntry[] presp = null;
+ if (picrClient != null)
{
- String token = st.nextToken();
- UPEntry[] presp = null;
- if (picrClient != null)
+ // resolve the string against PICR to recover valid IDs
+ try
{
- // resolve the string against PICR to recover valid IDs
- try
- {
- presp = picrClient.getUPIForAccession(token, null,
- picrClient.getMappedDatabaseNames(), null,
- true);
- } catch (Exception e)
- {
- System.err.println("Exception with Picr for '"
- + token + "'\n");
- e.printStackTrace();
- }
- }
- if (presp != null && presp.length > 0)
+ presp = picrClient
+ .getUPIForAccession(token, null,
+ picrClient.getMappedDatabaseNames(),
+ null, true);
+ } catch (Exception e)
{
- for (int id = 0; id < presp.length; id++)
- {
- // construct sequences from response if sequences are
- // present, and do a transferReferences
- // otherwise transfer non sequence x-references directly.
- }
- System.out
- .println("Validated ID against PICR... (for what its worth):"
- + token);
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ System.err.println("Exception with Picr for '" + token
+ + "'\n");
+ e.printStackTrace();
}
- else
+ }
+ if (presp != null && presp.length > 0)
+ {
+ for (int id = 0; id < presp.length; id++)
{
- // if ()
- // System.out.println("Not querying source with token="+token+"\n");
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ // construct sequences from response if sequences are
+ // present, and do a transferReferences
+ // otherwise transfer non sequence x-references directly.
}
+ System.out
+ .println("Validated ID against PICR... (for what its worth):"
+ + token);
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase());
+ }
+ else
+ {
+ // if ()
+ // System.out.println("Not querying source with token="+token+"\n");
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase());
}
}
}
}
// advance to next database
db++;
- } // all databases have been queries.
+ } // all databases have been queried
if (sbuffer.length() > 0)
{
output.setText(MessageManager
* @param trimDatasetSeqs
*
*/
- void transferReferences(Vector sdataset, String dbSource,
- AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
- // file)
+ void transferReferences(Vector<SequenceI> sdataset, String dbSource,
+ AlignmentI retrievedAl, boolean trimDatasetSeqs)
{
- System.out.println("trimming ? " + trimDatasetSeqs);
+ // System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return;
.getSequencesArray());
SequenceI sequence = null;
boolean transferred = false;
- StringBuffer messages = new StringBuffer();
+ StringBuilder messages = new StringBuilder(64);
- // Vector entries = new Uniprot().getUniprotEntries(file);
-
- int i, iSize = retrieved.length; // entries == null ? 0 : entries.size();
- // UniprotEntry entry;
- for (i = 0; i < iSize; i++)
+ for (SequenceI entry : retrieved)
{
- SequenceI entry = retrieved[i]; // (UniprotEntry) entries.elementAt(i);
-
// Work out which sequences this sequence matches,
// taking into account all accessionIds and names in the file
- Vector sequenceMatches = new Vector();
+ Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
entry.getDBRefs(), new String[] { dbSource });
}
for (int j = 0; j < entryRefs.length; j++)
{
- String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
+ String accessionId = entryRefs[j].getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase()))
{
- Vector seqs = (Vector) seqRefs.get(accessionId);
+ Vector<SequenceI> seqs = seqRefs.get(accessionId);
for (int jj = 0; jj < seqs.size(); jj++)
{
- sequence = (SequenceI) seqs.elementAt(jj);
+ sequence = seqs.elementAt(jj);
if (!sequenceMatches.contains(sequence))
{
sequenceMatches.addElement(sequence);
}
}
}
- if (sequenceMatches.size() == 0)
+ if (sequenceMatches.isEmpty())
{
// failed to match directly on accessionId==query so just compare all
// sequences to entry
- Enumeration e = seqRefs.keys();
+ Enumeration<String> e = seqRefs.keys();
while (e.hasMoreElements())
{
- Vector sqs = (Vector) seqRefs.get(e.nextElement());
+ Vector<SequenceI> sqs = seqRefs.get(e.nextElement());
if (sqs != null && sqs.size() > 0)
{
- Enumeration sqe = sqs.elements();
+ Enumeration<SequenceI> sqe = sqs.elements();
while (sqe.hasMoreElements())
{
sequenceMatches.addElement(sqe.nextElement());
String entrySeq = entry.getSequenceAsString().toUpperCase();
for (int m = 0; m < sequenceMatches.size(); m++)
{
- sequence = (SequenceI) sequenceMatches.elementAt(m);
+ sequence = sequenceMatches.elementAt(m);
// only update start and end positions and shift features if there are
// no existing references
// TODO: test for legacy where uniprot or EMBL refs exist but no
// verification failed. couldn't find any relationship between
// entrySeq and local sequence
messages.append(sequence.getName()
- + " SEQUENCE NOT %100 MATCH \n");
+ + " Sequence not 100% match with " + entry.getName()
+ + "\n");
continue;
}
/*
* sequence's reference frame.
*/
transferred = true;
- sbuffer.append(sequence.getName() + " HAS " + absStart
- + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
+ sbuffer.append(sequence.getName() + " has " + absStart
+ + " prefixed residues compared to " + entry.getName()
+ + "\n");
/*
* So create a mapping to the external entry from the matching region of
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- Vector nseq = new Vector();
+ Vector<SequenceI> nseq = new Vector<SequenceI>();
for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
{
nseq.addElement(sequencesArray[i]);
- DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
- jalview.datamodel.Mapping map = null;
+ DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
+ Mapping map = null;
for (int r = 0; (dbr != null) && r < dbr.length; r++)
{
if ((map = dbr[r].getMap()) != null)
git://source.jalview.org / jalview.git / commitdiff