/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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;\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.dbsources.das.api.jalviewSourceI;\r
-import jalview.ws.seqfetcher.ASequenceFetcher;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-\r
-import java.util.ArrayList;\r
-import java.util.Enumeration;\r
-import java.util.List;\r
-import java.util.Vector;\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
- this(true);\r
- }\r
- public SequenceFetcher(boolean addDas)\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
- addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);\r
- addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);\r
- if (addDas) {\r
- registerDasSequenceSources();\r
- }\r
- }\r
-\r
- /**\r
- * return an ordered list of database sources where non-das database classes\r
- * appear before das database classes\r
- */\r
- public String[] getOrderedSupportedSources()\r
- {\r
- String[] srcs = this.getSupportedDb();\r
- ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();\r
- for (int i = 0; i < srcs.length; i++)\r
- {\r
- boolean das = false, skip = false;\r
- String nm;\r
- for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
- {\r
- // Skip the alignment databases for the moment - they're not useful for\r
- // verifying a single sequence against its reference source\r
- if (dbs.isA(DBRefSource.ALIGNMENTDB))\r
- {\r
- skip = true;\r
- }\r
- else\r
- {\r
- nm = dbs.getDbName();\r
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
- {\r
- if (nm.startsWith("das:"))\r
- {\r
- nm = nm.substring(4);\r
- das = true;\r
- }\r
- break;\r
- }\r
- }\r
- }\r
- if (skip)\r
- {\r
- continue;\r
- }\r
- if (das)\r
- {\r
- dassrc.add(srcs[i]);\r
- }\r
- else\r
- {\r
- nondas.add(srcs[i]);\r
- }\r
- }\r
- String[] tosort = nondas.toArray(new String[0]), sorted = nondas\r
- .toArray(new String[0]);\r
- for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
- {\r
- tosort[j] = tosort[j].toLowerCase();\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- // construct array with all sources listed\r
-\r
- srcs = new String[sorted.length + dassrc.size()];\r
- int i = 0;\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = sorted[j];\r
- sorted[j] = null;\r
- }\r
-\r
- sorted = dassrc.toArray(new String[0]);\r
- tosort = dassrc.toArray(new String[0]);\r
- for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
- {\r
- tosort[j] = tosort[j].toLowerCase();\r
- }\r
- jalview.util.QuickSort.sort(tosort, sorted);\r
- for (int j = sorted.length - 1; j >= 0; j--, i++)\r
- {\r
- srcs[i] = sorted[j];\r
- }\r
- return srcs;\r
- }\r
-\r
- /**\r
- * return plaintext databse list suitable for using in a GUI 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
- for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
- {\r
- String nm = dbs.getDbName();\r
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.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
- }\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
- // construct array with all sources listed\r
- srcs = new String[sorted.length + dassrc.size()];\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 [-nodas] [<DBNAME> [<ACCNO>]]\n"\r
- + "With no arguments, all DbSources will be queried with their test Accession number.\n"\r
- + "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"\r
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"\r
- + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";\r
- boolean withDas=true;\r
- if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))\r
- {\r
- withDas=false;\r
- String targs[] = new String[argv.length-1];\r
- System.arraycopy(argv, 1, targs, 0, targs.length);\r
- argv=targs;\r
- }\r
- if (argv != null && argv.length > 0)\r
- {\r
- List<DbSourceProxy> sps = new SequenceFetcher(withDas)\r
- .getSourceProxy(argv[0]);\r
-\r
- if (sps != null)\r
- {\r
- for (DbSourceProxy sp : sps)\r
- {\r
- AlignmentI al = null;\r
- try\r
- {\r
- al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());\r
- } catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())\r
- + " from " + 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
- }\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
- return;\r
- }\r
- ASequenceFetcher sfetcher = new SequenceFetcher(withDas);\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
- for (DbSourceProxy sp : sfetcher.getSourceProxy(db))\r
- {\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\r
- .findSequenceXrefTypes(dna, al.getSequencesArray());\r
- if (types != null)\r
- {\r
- System.out.println("Xref Types for: "\r
- + (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
-\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: "\r
- + (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
-\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
- // TODO: define a context as a registry provider (either desktop,\r
- // jalview.bin.cache, or something else).\r
- for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()\r
- .getSources())\r
- {\r
- if (source.isSequenceSource())\r
- {\r
- List<DbSourceProxy> dassources = source.getSequenceSourceProxies();\r
- for (DbSourceProxy seqsrc : dassources)\r
- {\r
- addDbRefSourceImpl(seqsrc);\r
- }\r
- }\r
- }\r
- }\r
-\r
-}\r
+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()
+ {
+ 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();
+ }
+ }
+
+ /**
+ * 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.isA(DBRefSource.ALIGNMENTDB))
+ {
+ 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;
+ }
+
+ /**
+ * 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