+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
package jalview.ws;\r
\r
-import java.util.Enumeration;\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.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 testing all registered handlers. \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
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.Pfam.class);\r
- };\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
+ 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.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
+ 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
- System.out\r
- .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");\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
+ 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\r
- .println("" + db + ": retrieving test:" + sp.getTestQuery());\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
+ if (al != null && al.getHeight() > 0\r
+ && sp.getDbSourceProperties() != null)\r
{\r
boolean dna = sp.getDbSourceProperties().containsKey(\r
DBRefSource.DNACODINGSEQDB)\r
Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(\r
seqs, dna, null, ds);\r
System.out.println("Found "\r
- + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");\r
+ + ((prodal == null) ? "no" : "" + prodal.getHeight())\r
+ + " products");\r
if (prodal != null)\r
{\r
SequenceI[] prod = prodal.getSequencesArray(); // note\r
// mapping\r
// (if\r
// present)\r
- for (int p = 0; p < prod.length; p++)\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
+ * 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().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