import java.lang.reflect.Array;\r
import java.util.Enumeration;\r
import java.util.Hashtable;\r
+import java.util.List;\r
import java.util.StringTokenizer;\r
import java.util.Vector;\r
\r
{\r
int maxqlen = 1; // default number of queries made to at one time\r
System.err.println("Verifying against " + dbSources[db]);\r
- jalview.ws.seqfetcher.DbSourceProxy dbsource = sfetcher\r
+ boolean dn = false;\r
+ List<jalview.ws.seqfetcher.DbSourceProxy> srcs = sfetcher\r
.getSourceProxy(dbSources[db]);\r
- if (dbsource == null)\r
+ if (srcs == null)\r
{\r
System.err.println("No proxy for " + dbSources[db]);\r
db++;\r
continue;\r
}\r
- if (dbsource.getDbSourceProperties()\r
- .containsKey(DBRefSource.MULTIACC))\r
- {\r
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(\r
- DBRefSource.MULTIACC)).intValue();\r
- }\r
- else\r
- {\r
- maxqlen = 1;\r
- }\r
+\r
// iterate through db for each remaining un-verified sequence\r
SequenceI[] currSeqs = new SequenceI[sdataset.size()];\r
sdataset.copyInto(currSeqs);// seqs that are to be validated against\r
\r
int seqIndex = 0;\r
\r
- while (queries.size() > 0 || seqIndex < currSeqs.length)\r
+ for (jalview.ws.seqfetcher.DbSourceProxy dbsource : srcs)\r
{\r
- if (queries.size() > 0)\r
+ // for moment, we dumbly iterate over all retrieval sources for a particular database\r
+ // TODO: introduce multithread multisource queries and logic to remove a query from other sources if any source for a database returns a record\r
+ if (dbsource.getDbSourceProperties().containsKey(\r
+ DBRefSource.MULTIACC))\r
{\r
- // Still queries to make for current seqIndex\r
- StringBuffer queryString = new StringBuffer("");\r
- int numq = 0, nqSize = (maxqlen > queries.size()) ? queries\r
- .size() : maxqlen;\r
-\r
- while (queries.size() > 0 && numq < nqSize)\r
+ maxqlen = ((Integer) dbsource.getDbSourceProperties().get(\r
+ DBRefSource.MULTIACC)).intValue();\r
+ }\r
+ else\r
+ {\r
+ maxqlen = 1;\r
+ }\r
+ while (queries.size() > 0 || seqIndex < currSeqs.length)\r
+ {\r
+ if (queries.size() > 0)\r
{\r
- String query = (String) queries.elementAt(0);\r
- if (dbsource.isValidReference(query))\r
+ // Still queries to make for current seqIndex\r
+ StringBuffer queryString = new StringBuffer("");\r
+ int numq = 0, nqSize = (maxqlen > queries.size()) ? queries\r
+ .size() : maxqlen;\r
+\r
+ while (queries.size() > 0 && numq < nqSize)\r
{\r
- queryString.append((numq == 0) ? "" : dbsource\r
- .getAccessionSeparator());\r
- queryString.append(query);\r
- numq++;\r
+ String query = (String) queries.elementAt(0);\r
+ if (dbsource.isValidReference(query))\r
+ {\r
+ queryString.append((numq == 0) ? "" : dbsource\r
+ .getAccessionSeparator());\r
+ queryString.append(query);\r
+ numq++;\r
+ }\r
+ // remove the extracted query string\r
+ queries.removeElementAt(0);\r
}\r
- // remove the extracted query string\r
- queries.removeElementAt(0);\r
- }\r
- // make the queries and process the response\r
- AlignmentI retrieved = null;\r
- try\r
- {\r
- if (jalview.bin.Cache.log.isDebugEnabled())\r
+ // make the queries and process the response\r
+ AlignmentI retrieved = null;\r
+ try\r
+ {\r
+ if (jalview.bin.Cache.log.isDebugEnabled())\r
+ {\r
+ jalview.bin.Cache.log.debug("Querying "\r
+ + dbsource.getDbName() + " with : '"\r
+ + queryString.toString() + "'");\r
+ }\r
+ retrieved = dbsource.getSequenceRecords(queryString\r
+ .toString());\r
+ } catch (Exception ex)\r
{\r
- jalview.bin.Cache.log.debug("Querying "\r
- + dbsource.getDbName() + " with : '"\r
- + queryString.toString() + "'");\r
+ ex.printStackTrace();\r
+ } catch (OutOfMemoryError err)\r
+ {\r
+ new OOMWarning("retrieving database references ("\r
+ + queryString.toString() + ")", err);\r
+ }\r
+ if (retrieved != null)\r
+ {\r
+ transferReferences(sdataset, dbSources[db], retrieved);\r
}\r
- retrieved = dbsource.getSequenceRecords(queryString.toString());\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- } catch (OutOfMemoryError err)\r
- {\r
- new OOMWarning("retrieving database references ("\r
- + queryString.toString() + ")", err);\r
- }\r
- if (retrieved != null)\r
- {\r
- transferReferences(sdataset, dbSources[db], retrieved);\r
}\r
- }\r
- else\r
- {\r
- // make some more strings for use as queries\r
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)\r
+ else\r
{\r
- SequenceI sequence = dataset[seqIndex];\r
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
- sequence.getDBRef(), new String[]\r
- { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
- // });\r
- // check for existing dbrefs to use\r
- if (uprefs != null && uprefs.length > 0)\r
+ // make some more strings for use as queries\r
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)\r
{\r
- for (int j = 0; j < uprefs.length; j++)\r
+ SequenceI sequence = dataset[seqIndex];\r
+ DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
+ sequence.getDBRef(), new String[]\r
+ { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
+ // });\r
+ // check for existing dbrefs to use\r
+ if (uprefs != null && uprefs.length > 0)\r
{\r
- addSeqId(sequence, uprefs[j].getAccessionId());\r
- queries.addElement(uprefs[j].getAccessionId().toUpperCase());\r
+ for (int j = 0; j < uprefs.length; j++)\r
+ {\r
+ addSeqId(sequence, uprefs[j].getAccessionId());\r
+ queries.addElement(uprefs[j].getAccessionId()\r
+ .toUpperCase());\r
+ }\r
}\r
- }\r
- else\r
- {\r
- // generate queries from sequence ID string\r
- StringTokenizer st = new StringTokenizer(sequence.getName(),\r
- "|");\r
- while (st.hasMoreTokens())\r
+ else\r
{\r
- String token = st.nextToken();\r
- UPEntry[] presp = null;\r
- if (picrClient != null)\r
+ // generate queries from sequence ID string\r
+ StringTokenizer st = new StringTokenizer(\r
+ sequence.getName(), "|");\r
+ while (st.hasMoreTokens())\r
{\r
- // resolve the string against PICR to recover valid IDs\r
- try\r
+ String token = st.nextToken();\r
+ UPEntry[] presp = null;\r
+ if (picrClient != null)\r
{\r
- presp = picrClient\r
- .getUPIForAccession(token, null,\r
- picrClient.getMappedDatabaseNames(),\r
- null, true);\r
- } catch (Exception e)\r
+ // resolve the string against PICR to recover valid IDs\r
+ try\r
+ {\r
+ presp = picrClient.getUPIForAccession(token, null,\r
+ picrClient.getMappedDatabaseNames(), null,\r
+ true);\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Exception with Picr for '"\r
+ + token + "'\n");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ if (presp != null && presp.length > 0)\r
{\r
- System.err.println("Exception with Picr for '" + token\r
- + "'\n");\r
- e.printStackTrace();\r
+ for (int id = 0; id < presp.length; id++)\r
+ {\r
+ // construct sequences from response if sequences are\r
+ // present, and do a transferReferences\r
+ // otherwise transfer non sequence x-references directly.\r
+ }\r
+ System.out\r
+ .println("Validated ID against PICR... (for what its worth):"\r
+ + token);\r
+ addSeqId(sequence, token);\r
+ queries.addElement(token.toUpperCase());\r
}\r
- }\r
- if (presp != null && presp.length > 0)\r
- {\r
- for (int id = 0; id < presp.length; id++)\r
+ else\r
{\r
- // construct sequences from response if sequences are\r
- // present, and do a transferReferences\r
- // otherwise transfer non sequence x-references directly.\r
+ // if ()\r
+ // System.out.println("Not querying source with token="+token+"\n");\r
+ addSeqId(sequence, token);\r
+ queries.addElement(token.toUpperCase());\r
}\r
- System.out\r
- .println("Validated ID against PICR... (for what its worth):"\r
- + token);\r
- addSeqId(sequence, token);\r
- queries.addElement(token.toUpperCase());\r
- }\r
- else\r
- {\r
- // if ()\r
- // System.out.println("Not querying source with token="+token+"\n");\r
- addSeqId(sequence, token);\r
- queries.addElement(token.toUpperCase());\r
}\r
}\r
}\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
+ for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
{\r
- if (nm.startsWith("das:"))\r
+ String nm = dbs.getDbName();\r
+ if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
{\r
- nm = nm.substring(4);\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
- 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
}\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
+ "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
+ List<DbSourceProxy> sps = new SequenceFetcher()\r
+ .getSourceProxy(argv[0]);\r
+\r
+ if (sps != null)\r
{\r
- AlignmentI al = null;\r
- try\r
- {\r
- al = sp.getSequenceRecords(argv[1]);\r
- } catch (Exception e)\r
+ for (DbSourceProxy sp : sps)\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
+ AlignmentI al = null;\r
+ try\r
+ {\r
+ al = sp.getSequenceRecords(argv[1]);\r
+ } catch (Exception e)\r
{\r
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true) + " : "\r
- + prod[p].getDescription());\r
+ e.printStackTrace();\r
+ System.err.println("Error when retrieving " + argv[1]\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
+ new SequenceFetcher().getSupportedDb());\r
}\r
System.out.println(usage);\r
+ return;\r
}\r
ASequenceFetcher sfetcher = new SequenceFetcher();\r
String[] dbSources = sfetcher.getSupportedDb();\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
+ for (DbSourceProxy sp : sfetcher.getSourceProxy(db))\r
{\r
- al = sp.getSequenceRecords(sp.getTestQuery());\r
- if (al != null && al.getHeight() > 0\r
- && sp.getDbSourceProperties() != null)\r
+ System.out.println("Source: " + sp.getDbName() + " (" + db\r
+ + "): retrieving test:" + sp.getTestQuery());\r
+ AlignmentI al = null;\r
+ try\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
+ al = sp.getSequenceRecords(sp.getTestQuery());\r
+ if (al != null && al.getHeight() > 0\r
+ && sp.getDbSourceProperties() != null)\r
{\r
- System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));\r
- for (int t = 0; t < types.length; t++)\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("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
+ System.out.println("Xref Types for: "\r
+ + (dna ? "dna" : "prot"));\r
+ for (int t = 0; t < types.length; t++)\r
{\r
- for (int p = 0; p < prod.length; p++)\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
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true));\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
- else\r
- {\r
- noProds.addElement((dna ? new Object[]\r
- { al, al } : new Object[]\r
- { al }));\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
- } 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
+ System.out.println("Retrieved " + al.getHeight() + " sequences.");\r
+ for (int s = 0; s < al.getHeight(); s++)\r
{\r
- sq = sq.getDatasetSequence();\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
+ if (ds == null)\r
+ {\r
+ ds = new Alignment(new SequenceI[]\r
+ { sq });\r
\r
- }\r
- else\r
- {\r
- ds.addSequence(sq);\r
+ }\r
+ else\r
+ {\r
+ ds.addSequence(sq);\r
+ }\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
+ System.out.flush();\r
+ System.err.flush();\r
\r
+ }\r
+ if (noProds.size() > 0)\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
+ Enumeration ts = noProds.elements();\r
+ while (ts.hasMoreElements())\r
+\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
+ 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
- System.out.println("Prod " + p + ": "\r
- + prod[p].getDisplayId(true));\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
// 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
+ for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()\r
+ .getSources())\r
{\r
if (source.isSequenceSource())\r
{\r
package jalview.ws.seqfetcher;\r
\r
import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.DBRefEntry;\r
import jalview.datamodel.SequenceI;\r
+import jalview.util.DBRefUtils;\r
\r
+import java.util.ArrayList;\r
import java.util.Enumeration;\r
+import java.util.HashSet;\r
import java.util.Hashtable;\r
+import java.util.Iterator;\r
+import java.util.List;\r
+import java.util.Stack;\r
import java.util.Vector;\r
\r
public class ASequenceFetcher\r
/**\r
* set of databases we can retrieve entries from\r
*/\r
- protected Hashtable FETCHABLEDBS;\r
+ protected Hashtable<String, List<DbSourceProxy>> FETCHABLEDBS;\r
\r
public ASequenceFetcher()\r
{\r
public SequenceI[] getSequences(jalview.datamodel.DBRefEntry[] refs)\r
{\r
SequenceI[] ret = null;\r
- Vector rseqs = new Vector();\r
- Hashtable queries = new Hashtable();\r
+ Vector<SequenceI> rseqs = new Vector();\r
+ Hashtable<String, List<String>> queries = new Hashtable();\r
for (int r = 0; r < refs.length; r++)\r
{\r
if (!queries.containsKey(refs[r].getSource()))\r
{\r
- queries.put(refs[r].getSource(), new Vector());\r
+ queries.put(refs[r].getSource(), new ArrayList<String>());\r
}\r
- Vector qset = (Vector) queries.get(refs[r].getSource());\r
+ List<String> qset = queries.get(refs[r].getSource());\r
if (!qset.contains(refs[r].getAccessionId()))\r
{\r
- qset.addElement(refs[r].getAccessionId());\r
+ qset.add(refs[r].getAccessionId());\r
}\r
}\r
- Enumeration e = queries.keys();\r
+ Enumeration<String> e = queries.keys();\r
while (e.hasMoreElements())\r
{\r
- Vector query = null;\r
+ List<String> query = null;\r
String db = null;\r
- try\r
+ db = e.nextElement();\r
+ query = queries.get(db);\r
+ if (!isFetchable(db))\r
{\r
- db = (String) e.nextElement();\r
- query = (Vector) queries.get(db);\r
- if (!isFetchable(db))\r
- throw new Exception(\r
- "Don't know how to fetch from this database :" + db);\r
- DbSourceProxy fetcher = getSourceProxy(db);\r
- boolean doMultiple = fetcher.getAccessionSeparator() != null; // No\r
- // separator\r
- // - no\r
- // Multiple\r
- // Queries\r
- Enumeration qs = query.elements();\r
- while (qs.hasMoreElements())\r
+ reportStdError(db, query, new Exception(\r
+ "Don't know how to fetch from this database :" + db));\r
+ continue;\r
+ }\r
+ Iterator<DbSourceProxy> fetchers = getSourceProxy(db).iterator();\r
+ Stack<String> queriesLeft = new Stack<String>();\r
+// List<String> queriesFailed = new ArrayList<String>();\r
+ queriesLeft.addAll(query);\r
+ while (fetchers.hasNext())\r
+ {\r
+ List<String> queriesMade = new ArrayList<String>();\r
+ HashSet queriesFound = new HashSet<String>();\r
+ try\r
{\r
- StringBuffer qsb = new StringBuffer();\r
- do\r
- {\r
- qsb.append((String) qs.nextElement());\r
- if (qs.hasMoreElements() && doMultiple) // and not reached limit for\r
- // multiple queries at one\r
- // time for this source\r
- {\r
- qsb.append(fetcher.getAccessionSeparator());\r
- }\r
- } while (doMultiple && qs.hasMoreElements());\r
-\r
- AlignmentI seqset = null;\r
- try\r
- {\r
- // create a fetcher and go to it\r
- seqset = fetcher.getSequenceRecords(qsb.toString());\r
- } catch (Exception ex)\r
+ DbSourceProxy fetcher = fetchers.next();\r
+ boolean doMultiple = fetcher.getAccessionSeparator() != null; // No\r
+ // separator\r
+ // - no\r
+ // Multiple\r
+ // Queries\r
+ while (!queriesLeft.isEmpty())\r
{\r
- System.err.println("Failed to retrieve the following from "\r
- + db);\r
- System.err.println(qsb);\r
- ex.printStackTrace(System.err);\r
- }\r
- // TODO: Merge alignment together - perhaps\r
- if (seqset != null)\r
- {\r
- SequenceI seqs[] = seqset.getSequencesArray();\r
- if (seqs != null)\r
+ StringBuffer qsb = new StringBuffer();\r
+ do\r
{\r
- for (int is = 0; is < seqs.length; is++)\r
+ if (qsb.length() > 0)\r
{\r
- rseqs.addElement(seqs[is]);\r
- seqs[is] = null;\r
+ qsb.append(fetcher.getAccessionSeparator());\r
}\r
+ String q = queriesLeft.pop();\r
+ queriesMade.add(q);\r
+ qsb.append(q);\r
+ } while (doMultiple && !queriesLeft.isEmpty());\r
+\r
+ AlignmentI seqset = null;\r
+ try\r
+ {\r
+ // create a fetcher and go to it\r
+ seqset = fetcher.getSequenceRecords(qsb.toString()); // ,\r
+ // queriesFailed);\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Failed to retrieve the following from "\r
+ + db);\r
+ System.err.println(qsb);\r
+ ex.printStackTrace(System.err);\r
}\r
- else\r
+ // TODO: Merge alignment together - perhaps\r
+ if (seqset != null)\r
{\r
- if (fetcher.getRawRecords() != null)\r
+ SequenceI seqs[] = seqset.getSequencesArray();\r
+ if (seqs != null)\r
{\r
- System.out.println("# Retrieved from " + db + ":"\r
- + qs.toString());\r
- StringBuffer rrb = fetcher.getRawRecords();\r
- /*\r
- * for (int rr = 0; rr<rrb.length; rr++) {\r
- */\r
- String hdr;\r
- // if (rr<qs.length)\r
- // {\r
- hdr = "# " + db + ":" + qsb.toString();\r
- /*\r
- * } else { hdr = "# part "+rr; }\r
- */\r
- System.out.println(hdr);\r
- if (rrb != null)\r
- System.out.println(rrb);\r
- System.out.println("# end of " + hdr);\r
+ for (int is = 0; is < seqs.length; is++)\r
+ {\r
+ rseqs.addElement(seqs[is]);\r
+ DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]\r
+ .getDBRef(), new DBRefEntry(db, null, null));\r
+ if (frefs != null)\r
+ {\r
+ for (DBRefEntry dbr : frefs)\r
+ {\r
+ queriesFound.add(dbr.getAccessionId());\r
+ queriesMade.remove(dbr.getAccessionId());\r
+ }\r
+ }\r
+ seqs[is] = null;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (fetcher.getRawRecords() != null)\r
+ {\r
+ System.out.println("# Retrieved from " + db + ":"\r
+ + qsb.toString());\r
+ StringBuffer rrb = fetcher.getRawRecords();\r
+ /*\r
+ * for (int rr = 0; rr<rrb.length; rr++) {\r
+ */\r
+ String hdr;\r
+ // if (rr<qs.length)\r
+ // {\r
+ hdr = "# " + db + ":" + qsb.toString();\r
+ /*\r
+ * } else { hdr = "# part "+rr; }\r
+ */\r
+ System.out.println(hdr);\r
+ if (rrb != null)\r
+ System.out.println(rrb);\r
+ System.out.println("# end of " + hdr);\r
+ }\r
+\r
}\r
}\r
+\r
}\r
+ } catch (Exception ex)\r
+ {\r
+ reportStdError(db, queriesMade, ex);\r
}\r
- } catch (Exception ex)\r
- {\r
- System.err\r
- .println("Failed to retrieve the following references from "\r
- + db);\r
- Enumeration qv = query.elements();\r
- int n = 0;\r
- while (qv.hasMoreElements())\r
+ if (queriesMade.size() > 0)\r
{\r
- System.err.print(" " + qv.nextElement() + ";");\r
- if (n++ > 10)\r
- {\r
- System.err.println();\r
- n = 0;\r
- }\r
+ System.out.println("# Adding " + queriesMade.size()\r
+ + " ids back to queries list for searching again (" + db\r
+ + ".");\r
+ queriesLeft.addAll(queriesMade);\r
}\r
- System.err.println();\r
- ex.printStackTrace();\r
}\r
}\r
if (rseqs.size() > 0)\r
return ret;\r
}\r
\r
+ public void reportStdError(String db, List<String> queriesMade,\r
+ Exception ex)\r
+ {\r
+\r
+ System.err.println("Failed to retrieve the following references from "\r
+ + db);\r
+ int n = 0;\r
+ for (String qv : queriesMade)\r
+ {\r
+ System.err.print(" " + qv + ";");\r
+ if (n++ > 10)\r
+ {\r
+ System.err.println();\r
+ n = 0;\r
+ }\r
+ }\r
+ System.err.println();\r
+ ex.printStackTrace();\r
+ }\r
+\r
/**\r
* Retrieve an instance of the proxy for the given source\r
* \r
* retrieval of specific DB source/version combinations.\r
* @return an instance of DbSourceProxy for that db.\r
*/\r
- public DbSourceProxy getSourceProxy(String db)\r
+ public List<DbSourceProxy> getSourceProxy(String db)\r
{\r
- DbSourceProxy dbs = (DbSourceProxy) FETCHABLEDBS.get(db);\r
+ List<DbSourceProxy> dbs = FETCHABLEDBS.get(db);\r
return dbs;\r
}\r
\r
{\r
if (FETCHABLEDBS == null)\r
{\r
- FETCHABLEDBS = new Hashtable();\r
+ FETCHABLEDBS = new Hashtable<String, List<DbSourceProxy>>();\r
}\r
- FETCHABLEDBS.put(proxy.getDbSource(), proxy);\r
+ List<DbSourceProxy> slist = FETCHABLEDBS.get(proxy.getDbSource());\r
+ if (slist == null)\r
+ {\r
+ FETCHABLEDBS.put(proxy.getDbSource(),\r
+ slist = new ArrayList<DbSourceProxy>());\r
+ }\r
+ slist.add(proxy);\r
}\r
}\r
\r
/**\r
* test if the database handler for dbName contains the given dbProperty\r
- * \r
+ * when a dbName resolves to a set of proxies - this method will return the result of the test for the first instance.\r
+ * TODO implement additional method to query all sources for a db to find one with a particular property\r
* @param dbName\r
* @param dbProperty\r
* @return true if proxy has the given property\r
public boolean hasDbSourceProperty(String dbName, String dbProperty)\r
{\r
// TODO: decide if invalidDbName exception is thrown here.\r
- DbSourceProxy proxy = getSourceProxy(dbName);\r
- if (proxy != null)\r
+\r
+ List<DbSourceProxy> proxies = getSourceProxy(dbName);\r
+ if (proxies != null)\r
{\r
- if (proxy.getDbSourceProperties() != null)\r
+ for (DbSourceProxy proxy : proxies)\r
{\r
- return proxy.getDbSourceProperties().containsKey(dbProperty);\r
+ if (proxy.getDbSourceProperties() != null)\r
+ {\r
+ return proxy.getDbSourceProperties().containsKey(dbProperty);\r
+ }\r
}\r
}\r
return false;\r
while (dbs.hasMoreElements())\r
{\r
String dbn = (String) dbs.nextElement();\r
- DbSourceProxy dbp = (DbSourceProxy) FETCHABLEDBS.get(dbn);\r
- if (class1.isAssignableFrom(dbp.getClass()))\r
+ for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn))\r
{\r
- src.addElement(dbn);\r
+ if (class1.isAssignableFrom(dbp.getClass()))\r
+ {\r
+ src.addElement(dbn);\r
+ }\r
}\r
}\r
if (src.size() > 0)\r
git://source.jalview.org / jalview.git / commitdiff