X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=518e7c6025ca2f57f65829e248cf9a3f1c626911;hb=115a611d005faab33f978a469578bcacbcecc112;hp=8c9e08f499bc925046d4b6ae532543d0febe468b;hpb=9d2628ef9266d6c7a953c8fd6e5539069e5997b3;p=jalview.git
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 8c9e08f..518e7c6 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,330 +1,99 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-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.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.
- *
- */
-public class SequenceFetcher extends ASequenceFetcher
-{
- /**
- * Thread safe construction of database proxies TODO: extend to a configurable
- * database plugin mechanism where classes are instantiated by reflection and
- * queried for their DbRefSource and version association.
- *
- */
- public SequenceFetcher()
- {
- 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
- registerDasSequenceSources();
- }
-
- /**
- * return an ordered list of database sources 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++)
- {
- String nm = getSourceProxy(srcs[i]).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;
- 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 [ ]\n"
- + "With no arguments, all DbSources will be queried with their test Accession number.\n"
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to and retrieve from it.";
- if (argv != null && argv.length > 0)
- {
- DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);
- if (sp != null)
- {
- AlignmentI al = null;
- try
- {
- al = sp.getSequenceRecords(argv[1]);
- } catch (Exception e)
- {
- e.printStackTrace();
- System.err.println("Error when retrieving " + argv[1] + " 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);
- }
- ASequenceFetcher sfetcher = new SequenceFetcher();
- String[] dbSources = sfetcher.getSupportedDb();
- for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
- {
- String db = dbSources[dbsource];
- // skip me
- if (db.equals(DBRefSource.PDB))
- continue;
- 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 dassources = source.getSequenceSourceProxies();
- for (DbSourceProxy seqsrc : dassources)
- {
- addDbRefSourceImpl(seqsrc);
- }
- }
- }
- }
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws;
+
+import jalview.ext.ensembl.EnsemblGene;
+import jalview.ws.dbsources.EBIAlfaFold;
+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.TDBeacons;
+import jalview.ws.dbsources.Uniprot;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * This implements the run-time discovery of sequence database clients.
+ *
+ */
+public class SequenceFetcher extends ASequenceFetcher
+{
+ /**
+ * Thread safe construction of database proxies TODO: extend to a configurable
+ * database plugin mechanism where classes are instantiated by reflection and
+ * queried for their DbRefSource and version association.
+ *
+ */
+ public SequenceFetcher()
+ {
+ addDBRefSourceImpl(EnsemblGene.class);
+ // addDBRefSourceImpl(EnsemblGenomes.class);
+ addDBRefSourceImpl(EmblSource.class);
+ addDBRefSourceImpl(EmblCdsSource.class);
+ addDBRefSourceImpl(Uniprot.class);
+ // not a sequence source yet
+ // addDBRefSourceImpl(TDBeacons.class);
+ addDBRefSourceImpl(Pdb.class);
+ addDBRefSourceImpl(PfamFull.class);
+ addDBRefSourceImpl(PfamSeed.class);
+ addDBRefSourceImpl(RfamSeed.class);
+ addDBRefSourceImpl(EBIAlfaFold.class);
+ }
+
+ /**
+ * return an ordered list of database sources excluding alignment only
+ * databases
+ */
+ public String[] getNonAlignmentSources()
+ {
+ String[] srcs = this.getSupportedDb();
+ List src = new ArrayList<>();
+
+ for (int i = 0; i < srcs.length; i++)
+ {
+ boolean accept = true;
+ 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.isAlignmentSource())
+ {
+ accept = false;
+ break;
+ }
+ }
+ if (accept)
+ {
+ src.add(srcs[i]);
+ }
+ }
+
+ Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+ return src.toArray(new String[src.size()]);
+ }
+}