+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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.ArrayList;\r
import java.util.Enumeration;\r
-import java.util.Hashtable;\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.dbsources.DasSequenceSource;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
/**\r
- * prototype of abstract sequence retrieval interface\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
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
+ 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
- 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
- SequenceFetcher sfetcher = new SequenceFetcher();\r
- Enumeration e = sfetcher.FETCHABLEDBS.keys();\r
- while (e.hasMoreElements())\r
+ ASequenceFetcher sfetcher = new SequenceFetcher();\r
+ String[] dbSources = sfetcher.getSupportedDb();\r
+ for (int dbsource = 0; dbsource < dbSources.length; dbsource++)\r
{\r
- String db = (String) e.nextElement();\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
dna, al.getSequencesArray());\r
if (types != null)\r
{\r
- System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));\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
+ 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
+ if (prod != null)\r
{\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+": "+prod[p].getDisplayId(true));\r
+ System.out.println("Prod " + p + ": "\r
+ + prod[p].getDisplayId(true));\r
}\r
}\r
}\r
- } else {\r
- noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); \r
+ }\r
+ else\r
+ {\r
+ noProds.addElement((dna ? new Object[]\r
+ { al, al } : new Object[]\r
+ { al }));\r
}\r
\r
}\r
System.err.flush();\r
\r
}\r
- if (noProds.size()>0)\r
+ if (noProds.size() > 0)\r
{\r
Enumeration ts = noProds.elements();\r
while (ts.hasMoreElements())\r
- \r
+\r
{\r
Object[] typeSq = (Object[]) ts.nextElement();\r
- boolean dna = (typeSq.length>1);\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("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
- + ((prod == null) ? "no" : "" + prod.length)\r
+ + ((prodal == null) ? "no" : "" + prodal.getHeight())\r
+ " products");\r
- if (prod!=null)\r
+ if (prodal != null)\r
{\r
- for (int p=0; p<prod.length; p++)\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+": "+prod[p].getDisplayId(true));\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
+ if (sources != null)\r
+ {\r
+ for (int s = 0; sources != null && s < sources.length; s++)\r
+ {\r
+ addDasSequenceSource(sources[s]);\r
+ }\r
+ }\r
+\r
+ Vector localsources = jalview.bin.Cache.getLocalDasSources();\r
+ if (localsources != null)\r
+ {\r
+ for (Enumeration ls = localsources.elements(); ls.hasMoreElements();)\r
+ {\r
+ addDasSequenceSource((DasSource) ls.nextElement());\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Try to create and add a DasSequenceSource to the list of sources.\r
+ * \r
+ * @param source\r
+ * @return null if no source was added, or the new DasSequenceSource created\r
+ */\r
+ DasSequenceSource addDasSequenceSource(DasSource source)\r
+ {\r
+ DasSequenceSource ds = null;\r
+ Das1Source d1s = null;\r
+ if (source.hasCapability("sequence"))\r
+ {\r
+ if (source instanceof Das2Source)\r
+ {\r
+ if (((Das2Source) source).hasDas1Capabilities())\r
+ {\r
+ try\r
+ {\r
+ d1s = org.biojava.dasobert.das2.DasSourceConverter\r
+ .toDas1Source((Das2Source) source);\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Ignoring DAS2 sequence source "\r
+ + source.getNickname()\r
+ + " - couldn't map to Das1Source.\n");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (source instanceof Das1Source)\r
+ {\r
+ d1s = (Das1Source) source;\r
+ }\r
+ }\r
+ }\r
+ if (d1s != null)\r
+ {\r
+ DasCoordinateSystem[] css = d1s.getCoordinateSystem();\r
+ if (css == null || css.length == 0)\r
+ {\r
+ // TODO: query das source directly to identify coordinate system... or\r
+ // have to make up a coordinate system\r
+ css = new DasCoordinateSystem[]\r
+ { new DasCoordinateSystem() };\r
+ css[0].setName(d1s.getNickname());\r
+ css[0].setUniqueId(d1s.getNickname());\r
+ }\r
+ for (int c = 0; c < css.length; c++)\r
+ {\r
+ try\r
+ {\r
+ addDbRefSourceImpl(ds = new DasSequenceSource("das:"\r
+ + 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 " + d1s.getNickname()\r
+ + "- threw exception when constructing fetcher.\n");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ return ds;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff