/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ext.ensembl.EnsemblGene;
+import jalview.ws.dbsources.EmblCdsSource;
+import jalview.ws.dbsources.EmblSource;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.PfamFull;
+import jalview.ws.dbsources.PfamSeed;
+import jalview.ws.dbsources.RfamSeed;
+import jalview.ws.dbsources.Uniprot;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
/**
- * This is the the concrete implementation of the sequence retrieval interface
- * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clients, and provides a hardwired main for
- * testing all registered handlers.
+ * This implements the run-time discovery of sequence database clients.
*
*/
public class SequenceFetcher extends ASequenceFetcher
*/
public SequenceFetcher()
{
- this(true);
- }
-
- public SequenceFetcher(boolean addDas)
- {
- addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
- addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);
- addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
- addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
- addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
- addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
- addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class);
- // ensures Seed alignment is 'default' for PFAM
- addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
- addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
- if (addDas)
- {
- registerDasSequenceSources();
- }
+ addDBRefSourceImpl(EnsemblGene.class);
+ // addDBRefSourceImpl(EnsemblGenomes.class);
+ addDBRefSourceImpl(EmblSource.class);
+ addDBRefSourceImpl(EmblCdsSource.class);
+ addDBRefSourceImpl(Uniprot.class);
+ addDBRefSourceImpl(Pdb.class);
+ addDBRefSourceImpl(PfamFull.class);
+ addDBRefSourceImpl(PfamSeed.class);
+ addDBRefSourceImpl(RfamSeed.class);
}
/**
- * return an ordered list of database sources where non-das database classes
- * appear before das database classes
+ * return an ordered list of database sources excluding alignment only databases
*/
public String[] getOrderedSupportedSources()
{
String[] srcs = this.getSupportedDb();
- ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+ ArrayList<String> src = new ArrayList<>();
+
for (int i = 0; i < srcs.length; i++)
{
- boolean das = false, skip = false;
- String nm;
+ boolean skip = false;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
// Skip the alignment databases for the moment - they're not useful for
// verifying a single sequence against its reference source
- if (dbs.isA(DBRefSource.ALIGNMENTDB))
+ if (dbs.isAlignmentSource())
{
skip = true;
}
- else
- {
- nm = dbs.getDbName();
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- if (nm.startsWith("das:"))
- {
- nm = nm.substring(4);
- das = true;
- }
- break;
- }
- }
}
if (skip)
{
continue;
}
- if (das)
- {
- dassrc.add(srcs[i]);
- }
- else
{
- nondas.add(srcs[i]);
+ src.add(srcs[i]);
}
}
- String[] tosort = nondas.toArray(new String[0]), sorted = nondas
- .toArray(new String[0]);
+ String[] tosort = src.toArray(new String[0]),
+ sorted = src.toArray(new String[0]);
for (int j = 0, jSize = sorted.length; j < jSize; j++)
{
tosort[j] = tosort[j].toLowerCase();
}
jalview.util.QuickSort.sort(tosort, sorted);
// construct array with all sources listed
-
- srcs = new String[sorted.length + dassrc.size()];
int i = 0;
for (int j = sorted.length - 1; j >= 0; j--, i++)
{
srcs[i] = sorted[j];
- sorted[j] = null;
- }
-
- sorted = dassrc.toArray(new String[0]);
- tosort = dassrc.toArray(new String[0]);
- for (int j = 0, jSize = sorted.length; j < jSize; j++)
- {
- tosort[j] = tosort[j].toLowerCase();
- }
- jalview.util.QuickSort.sort(tosort, sorted);
- for (int j = sorted.length - 1; j >= 0; j--, i++)
- {
- srcs[i] = sorted[j];
- }
- return srcs;
- }
-
- /**
- * return plaintext databse list suitable for using in a GUI element
- */
- public String[] _getOrderedSupportedSources()
- {
- String[] srcs = this.getSupportedDb();
- ArrayList dassrc = new ArrayList(), nondas = new ArrayList();
- for (int i = 0; i < srcs.length; i++)
- {
- for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
- {
- String nm = dbs.getDbName();
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- if (nm.startsWith("das:"))
- {
- nm = nm.substring(4);
- }
- dassrc.add(new String[] { srcs[i], nm.toUpperCase() });
- }
- else
- {
- nondas.add(new String[] { srcs[i], nm.toUpperCase() });
- }
- }
- }
- Object[] sorted = nondas.toArray();
- String[] tosort = new String[sorted.length];
- nondas.clear();
- for (int j = 0; j < sorted.length; j++)
- {
- tosort[j] = ((String[]) sorted[j])[1];
- }
- jalview.util.QuickSort.sort(tosort, sorted);
- int i = 0;
- // construct array with all sources listed
- srcs = new String[sorted.length + dassrc.size()];
- for (int j = sorted.length - 1; j >= 0; j--, i++)
- {
- srcs[i] = ((String[]) sorted[j])[0];
- sorted[j] = null;
- }
-
- sorted = dassrc.toArray();
- tosort = new String[sorted.length];
- dassrc.clear();
- for (int j = 0; j < sorted.length; j++)
- {
- tosort[j] = ((String[]) sorted[j])[1];
- }
- jalview.util.QuickSort.sort(tosort, sorted);
- for (int j = sorted.length - 1; j >= 0; j--, i++)
- {
- srcs[i] = ((String[]) sorted[j])[0];
- sorted[j] = null;
}
return srcs;
}
-
- /**
- * simple run method to test dbsources.
- *
- * @param argv
- */
- public static void main(String[] argv)
- {
- AlignmentI ds = null;
- Vector noProds = new Vector();
- String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
- + "With no arguments, all DbSources will be queried with their test Accession number.\n"
- + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
- + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
- boolean withDas = true;
- if (argv != null && argv.length > 0
- && argv[0].toLowerCase().startsWith("-nodas"))
- {
- withDas = false;
- String targs[] = new String[argv.length - 1];
- System.arraycopy(argv, 1, targs, 0, targs.length);
- argv = targs;
- }
- if (argv != null && argv.length > 0)
- {
- List<DbSourceProxy> sps = new SequenceFetcher(withDas)
- .getSourceProxy(argv[0]);
-
- if (sps != null)
- {
- for (DbSourceProxy sp : sps)
- {
- AlignmentI al = null;
- try
- {
- al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
- .getTestQuery());
- } catch (Exception e)
- {
- e.printStackTrace();
- System.err.println("Error when retrieving "
- + (argv.length > 1 ? argv[1] : sp.getTestQuery())
- + " from " + argv[0] + "\nUsage: " + usage);
- }
- SequenceI[] prod = al.getSequencesArray();
- if (al != null)
- {
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true) + " : "
- + prod[p].getDescription());
- }
- }
- }
- return;
- }
- else
- {
- System.err.println("Can't resolve " + argv[0]
- + " as a database name. Allowed values are :\n"
- + new SequenceFetcher().getSupportedDb());
- }
- System.out.println(usage);
- return;
- }
- ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
- String[] dbSources = sfetcher.getSupportedDb();
- for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
- {
- String db = dbSources[dbsource];
- // skip me
- if (db.equals(DBRefSource.PDB))
- {
- continue;
- }
- for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
- {
- System.out.println("Source: " + sp.getDbName() + " (" + db
- + "): retrieving test:" + sp.getTestQuery());
- AlignmentI al = null;
- try
- {
- al = sp.getSequenceRecords(sp.getTestQuery());
- if (al != null && al.getHeight() > 0
- && sp.getDbSourceProperties() != null)
- {
- boolean dna = sp.getDbSourceProperties().containsKey(
- DBRefSource.DNACODINGSEQDB)
- || sp.getDbSourceProperties().containsKey(
- DBRefSource.DNASEQDB)
- || sp.getDbSourceProperties().containsKey(
- DBRefSource.CODINGSEQDB);
- // try and find products
- String types[] = jalview.analysis.CrossRef
- .findSequenceXrefTypes(dna, al.getSequencesArray());
- if (types != null)
- {
- System.out.println("Xref Types for: "
- + (dna ? "dna" : "prot"));
- for (int t = 0; t < types.length; t++)
- {
- System.out.println("Type: " + types[t]);
- SequenceI[] prod = jalview.analysis.CrossRef
- .findXrefSequences(al.getSequencesArray(), dna,
- types[t]).getSequencesArray();
- System.out.println("Found "
- + ((prod == null) ? "no" : "" + prod.length)
- + " products");
- if (prod != null)
- {
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
- }
- }
- }
- }
- else
- {
- noProds.addElement((dna ? new Object[] { al, al }
- : new Object[] { al }));
- }
-
- }
- } catch (Exception ex)
- {
- System.out.println("ERROR:Failed to retrieve test query.");
- ex.printStackTrace(System.out);
- }
-
- if (al == null)
- {
- System.out.println("ERROR:No alignment retrieved.");
- StringBuffer raw = sp.getRawRecords();
- if (raw != null)
- {
- System.out.println(raw.toString());
- }
- else
- {
- System.out.println("ERROR:No Raw results.");
- }
- }
- else
- {
- System.out.println("Retrieved " + al.getHeight() + " sequences.");
- for (int s = 0; s < al.getHeight(); s++)
- {
- SequenceI sq = al.getSequenceAt(s);
- while (sq.getDatasetSequence() != null)
- {
- sq = sq.getDatasetSequence();
-
- }
- if (ds == null)
- {
- ds = new Alignment(new SequenceI[] { sq });
-
- }
- else
- {
- ds.addSequence(sq);
- }
- }
- }
- System.out.flush();
- System.err.flush();
-
- }
- if (noProds.size() > 0)
- {
- Enumeration ts = noProds.elements();
- while (ts.hasMoreElements())
-
- {
- Object[] typeSq = (Object[]) ts.nextElement();
- boolean dna = (typeSq.length > 1);
- AlignmentI al = (AlignmentI) typeSq[0];
- System.out.println("Trying getProducts for "
- + al.getSequenceAt(0).getDisplayId(true));
- System.out.println("Search DS Xref for: "
- + (dna ? "dna" : "prot"));
- // have a bash at finding the products amongst all the retrieved
- // sequences.
- SequenceI[] seqs = al.getSequencesArray();
- Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
- seqs, dna, null, ds);
- System.out.println("Found "
- + ((prodal == null) ? "no" : "" + prodal.getHeight())
- + " products");
- if (prodal != null)
- {
- SequenceI[] prod = prodal.getSequencesArray(); // note
- // should
- // test
- // rather
- // than
- // throw
- // away
- // codon
- // mapping
- // (if
- // present)
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
- }
- }
- }
-
- }
-
- }
- }
-
- /**
- * query the currently defined DAS source registry for sequence sources and
- * add a DasSequenceSource instance for each source to the SequenceFetcher
- * source list.
- */
- public void registerDasSequenceSources()
- {
- // TODO: define a context as a registry provider (either desktop,
- // jalview.bin.cache, or something else).
- for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
- .getSources())
- {
- if (source.isSequenceSource())
- {
- List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
- for (DbSourceProxy seqsrc : dassources)
- {
- addDbRefSourceImpl(seqsrc);
- }
- }
- }
- }
-
}
git://source.jalview.org / jalview.git / blobdiff