-package jalview.ws;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.ws.seqfetcher.ASequenceFetcher;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-\r
-/**\r
- * prototype of abstract sequence retrieval interface\r
- * \r
- */\r
-public class SequenceFetcher extends ASequenceFetcher\r
-{\r
- /**\r
- * Thread safe construction of database proxies TODO: extend to a configurable\r
- * database plugin mechanism where classes are instantiated by reflection and\r
- * queried for their DbRefSource and version association.\r
- * \r
- */\r
- public SequenceFetcher()\r
- {\r
- FETCHABLEDBS = new Hashtable();\r
- FETCHABLEDBS.put(DBRefSource.EMBL,\r
- new jalview.ws.dbsources.EmblSource());\r
- FETCHABLEDBS.put(DBRefSource.EMBLCDS,\r
- new jalview.ws.dbsources.EmblCdsSouce());\r
- FETCHABLEDBS.put(DBRefSource.UNIPROT,\r
- new jalview.ws.dbsources.Uniprot());\r
- FETCHABLEDBS.put(DBRefSource.UP_NAME,\r
- new jalview.ws.dbsources.Uniprot());\r
- FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());\r
- FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());\r
- };\r
- \r
- public static void main(String[] argv)\r
- {\r
- AlignmentI ds = null;\r
- Vector noProds = new Vector();\r
- if (argv != null && argv.length > 0)\r
- {\r
- System.out\r
- .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");\r
- }\r
- SequenceFetcher sfetcher = new SequenceFetcher();\r
- Enumeration e = sfetcher.FETCHABLEDBS.keys();\r
- while (e.hasMoreElements())\r
- {\r
- String db = (String) e.nextElement();\r
- // skip me\r
- if (db.equals(DBRefSource.PDB))\r
- continue;\r
- DbSourceProxy sp = sfetcher.getSourceProxy(db);\r
- System.out\r
- .println("" + db + ": retrieving test:" + sp.getTestQuery());\r
- AlignmentI al = null;\r
- try\r
- {\r
- al = sp.getSequenceRecords(sp.getTestQuery());\r
- if (al != null && al.getHeight() > 0)\r
- {\r
- boolean dna = sp.getDbSourceProperties().containsKey(\r
- DBRefSource.DNACODINGSEQDB)\r
- || sp.getDbSourceProperties().containsKey(\r
- DBRefSource.DNASEQDB)\r
- || sp.getDbSourceProperties().containsKey(\r
- DBRefSource.CODINGSEQDB);\r
- // try and find products\r
- String types[] = jalview.analysis.CrossRef.findSequenceXrefTypes(\r
- dna, al.getSequencesArray());\r
- if (types != null)\r
- {\r
- System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));\r
- for (int t = 0; t < types.length; t++)\r
- {\r
- System.out.println("Type: " + types[t]);\r
- SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
- .getSequencesArray(), dna, types[t]).getSequencesArray();\r
- System.out.println("Found "\r
- + ((prod == null) ? "no" : "" + prod.length)\r
- + " products");\r
- if (prod!=null)\r
- {\r
- for (int p=0; p<prod.length; p++)\r
- {\r
- System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
- } else {\r
- noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); \r
- }\r
-\r
- }\r
- } catch (Exception ex)\r
- {\r
- System.out.println("ERROR:Failed to retrieve test query.");\r
- ex.printStackTrace(System.out);\r
- }\r
- if (al == null)\r
- {\r
- System.out.println("ERROR:No alignment retrieved.");\r
- StringBuffer raw = sp.getRawRecords();\r
- if (raw != null)\r
- System.out.println(raw.toString());\r
- else\r
- System.out.println("ERROR:No Raw results.");\r
- }\r
- else\r
- {\r
- System.out.println("Retrieved " + al.getHeight() + " sequences.");\r
- for (int s = 0; s < al.getHeight(); s++)\r
- {\r
- SequenceI sq = al.getSequenceAt(s);\r
- while (sq.getDatasetSequence() != null)\r
- {\r
- sq = sq.getDatasetSequence();\r
-\r
- }\r
- if (ds == null)\r
- {\r
- ds = new Alignment(new SequenceI[]\r
- { sq });\r
-\r
- }\r
- else\r
- {\r
- ds.addSequence(sq);\r
- }\r
- }\r
- }\r
- System.out.flush();\r
- System.err.flush();\r
-\r
- }\r
- if (noProds.size()>0)\r
- {\r
- Enumeration ts = noProds.elements();\r
- while (ts.hasMoreElements())\r
- \r
- {\r
- Object[] typeSq = (Object[]) ts.nextElement();\r
- boolean dna = (typeSq.length>1);\r
- AlignmentI al = (AlignmentI) typeSq[0];\r
- System.out.println("Trying getProducts for "+al.getSequenceAt(0).getDisplayId(true));\r
- System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));\r
- // have a bash at finding the products amongst all the retrieved sequences.\r
- SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
- .getSequencesArray(), dna, null, ds).getSequencesArray(); // note should test rather than throw away codon mapping (if present)\r
- System.out.println("Found "\r
- + ((prod == null) ? "no" : "" + prod.length)\r
- + " products");\r
- if (prod!=null)\r
- {\r
- for (int p=0; p<prod.length; p++)\r
- {\r
- System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-}\r
+/*
+ * 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.ext.ensembl.EnsemblGene;
+import jalview.ext.ensembl.EnsemblGenomes;
+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.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+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()
+ {
+ this(true);
+ }
+
+ public SequenceFetcher(boolean addDas)
+ {
+ 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);
+
+ if (addDas)
+ {
+ registerDasSequenceSources();
+ }
+ }
+
+ /**
+ * return an ordered list of database sources where non-das database classes
+ * appear before das database classes
+ */
+ public String[] getOrderedSupportedSources()
+ {
+ String[] srcs = this.getSupportedDb();
+ ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+ for (int i = 0; i < srcs.length; i++)
+ {
+ boolean das = false, skip = false;
+ String nm;
+ 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())
+ {
+ 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]);
+ }
+ }
+ String[] tosort = nondas.toArray(new String[0]), sorted = nondas
+ .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;
+ }
+
+ /**
+ * 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