-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.ws;\r
-\r
-import java.util.ArrayList;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-\r
-import org.biojava.dasobert.das2.Das2Source;\r
-import org.biojava.dasobert.dasregistry.Das1Source;\r
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
-import org.biojava.dasobert.dasregistry.DasSource;\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
- * This is the the concrete implementation of the sequence retrieval interface\r
- * and abstract class in jalview.ws.seqfetcher. This implements the run-time\r
- * discovery of sequence database clients, and provides a hardwired main for\r
- * testing all registered handlers.\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
- addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed\r
- // alignment is\r
- // 'default' for\r
- // PFAM\r
- registerDasSequenceSources();\r
- }\r
-\r
- /**\r
- * return an ordered list of database sources suitable for using in a GUI\r
- * element\r
- */\r
- public String[] getOrderedSupportedSources()\r
- {\r
- String[] srcs = this.getSupportedDb();\r
- ArrayList dassrc = new ArrayList(), nondas = new ArrayList();\r
- for (int i = 0; i < srcs.length; i++)\r
- {\r
- String nm = getSourceProxy(srcs[i]).getDbName();\r
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)\r
- {\r
- if (nm.startsWith("das:"))\r
- {\r
- nm = nm.substring(4);\r
- }\r
- dassrc.add(new String[]\r
- { srcs[i], nm.toUpperCase() });\r
- }\r
- else\r
- {\r
- nondas.add(new String[]\r
- { srcs[i], nm.toUpperCase() });\r
- }\r
- }\r
- Object[] sorted = nondas.toArray();\r
- String[] tosort = new String[sorted.length];\r
- nondas.clear();\r
- for (int j = 0; j < sorted.length; j++)\r
- {\r
- tosort[j] = ((String[]) sorted[j])[1];\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- int i = 0;\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = ((String[]) sorted[j])[0];\r
- sorted[j] = null;\r
- }\r
-\r
- sorted = dassrc.toArray();\r
- tosort = new String[sorted.length];\r
- dassrc.clear();\r
- for (int j = 0; j < sorted.length; j++)\r
- {\r
- tosort[j] = ((String[]) sorted[j])[1];\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = ((String[]) sorted[j])[0];\r
- sorted[j] = null;\r
- }\r
- return srcs;\r
- }\r
-\r
- /**\r
- * simple run method to test dbsources.\r
- * \r
- * @param argv\r
- */\r
- public static void main(String[] argv)\r
- {\r
- AlignmentI ds = null;\r
- Vector noProds = new Vector();\r
- String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"\r
- + "With no arguments, all DbSources will be queried with their test Accession number.\n"\r
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";\r
- if (argv != null && argv.length > 0)\r
- {\r
- DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);\r
- if (sp != null)\r
- {\r
- AlignmentI al = null;\r
- try\r
- {\r
- al = sp.getSequenceRecords(argv[1]);\r
- } catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- System.err.println("Error when retrieving " + argv[1] + " from "\r
- + argv[0] + "\nUsage: " + usage);\r
- }\r
- SequenceI[] prod = al.getSequencesArray();\r
- if (al != null)\r
- {\r
- for (int p = 0; p < prod.length; p++)\r
- {\r
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true) + " : "\r
- + prod[p].getDescription());\r
- }\r
- }\r
- return;\r
- }\r
- else\r
- {\r
- System.err.println("Can't resolve " + argv[0]\r
- + " as a database name. Allowed values are :\n"\r
- + new SequenceFetcher().getSupportedDb());\r
- }\r
- System.out.println(usage);\r
- }\r
- ASequenceFetcher sfetcher = new SequenceFetcher();\r
- String[] dbSources = sfetcher.getSupportedDb();\r
- for (int dbsource = 0; dbsource < dbSources.length; dbsource++)\r
- {\r
- String db = dbSources[dbsource];\r
- // skip me\r
- if (db.equals(DBRefSource.PDB))\r
- continue;\r
- DbSourceProxy sp = sfetcher.getSourceProxy(db);\r
- System.out.println("Source: " + sp.getDbName() + " (" + db\r
- + "): 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
- && sp.getDbSourceProperties() != null)\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\r
- .findXrefSequences(al.getSequencesArray(), dna,\r
- 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 + ": "\r
- + prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- noProds.addElement((dna ? new Object[]\r
- { al, al } : new Object[]\r
- { 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 "\r
- + 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\r
- // sequences.\r
- SequenceI[] seqs = al.getSequencesArray();\r
- Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(\r
- seqs, dna, null, ds);\r
- System.out.println("Found "\r
- + ((prodal == null) ? "no" : "" + prodal.getHeight())\r
- + " products");\r
- if (prodal != null)\r
- {\r
- SequenceI[] prod = prodal.getSequencesArray(); // note\r
- // should\r
- // test\r
- // rather\r
- // than\r
- // throw\r
- // away\r
- // codon\r
- // mapping\r
- // (if\r
- // present)\r
- for (int p = 0; p < prod.length; p++)\r
- {\r
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true));\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
- /**\r
- * query the currently defined DAS source registry for sequence sources and\r
- * add a DasSequenceSource instance for each source to the SequenceFetcher\r
- * source list.\r
- */\r
- public void registerDasSequenceSources()\r
- {\r
- DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher\r
- .getDASSources();\r
- for (int s = 0; s < sources.length; s++)\r
- {\r
- Das1Source d1s = null;\r
- if (sources[s].hasCapability("sequence"))\r
- {\r
- if (sources[s] instanceof Das2Source)\r
- {\r
- if (((Das2Source) sources[s]).hasDas1Capabilities())\r
- {\r
- try\r
- {\r
- d1s = org.biojava.dasobert.das2.DasSourceConverter\r
- .toDas1Source((Das2Source) sources[s]);\r
- } catch (Exception e)\r
- {\r
- System.err.println("Ignoring DAS2 sequence source "\r
- + sources[s].getNickname()\r
- + " - couldn't map to Das1Source.\n");\r
- e.printStackTrace();\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (sources[s] instanceof Das1Source)\r
- {\r
- d1s = (Das1Source) sources[s];\r
- }\r
- }\r
- }\r
- if (d1s != null)\r
- {\r
- DasCoordinateSystem[] css = d1s.getCoordinateSystem();\r
- for (int c = 0; c < css.length; c++)\r
- {\r
- try\r
- {\r
- addDbRefSourceImpl(new jalview.ws.dbsources.DasSequenceSource(\r
- "das:" + d1s.getNickname() + " (" + css[c].getName()\r
- + ")", css[c].getName(), d1s, css[c]));\r
- } catch (Exception e)\r
- {\r
- System.err.println("Ignoring sequence coord system " + c + " ("\r
- + css[c].getName() + ") for source "\r
- + d1s.getNickname()\r
- + "- threw exception when constructing fetcher.\n");\r
- e.printStackTrace();\r
- }\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