/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 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
*/\r
package jalview.ws;\r
\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import org.exolab.castor.mapping.*;\r
-import org.exolab.castor.xml.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
+import jalview.analysis.AlignSeq;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.datamodel.DBRefSource;\r
import jalview.datamodel.Mapping;\r
-import jalview.gui.*;\r
-import jalview.ws.dbsources.Uniprot;\r
-import jalview.ws.ebi.EBIFetchClient;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.gui.AlignFrame;\r
+import jalview.gui.CutAndPasteTransfer;\r
+import jalview.gui.Desktop;\r
+import jalview.gui.IProgressIndicator;\r
+import jalview.gui.OOMWarning;\r
+\r
+import java.util.Enumeration;\r
+import java.util.Hashtable;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
+import org.biojava.dasobert.dasregistry.DasSource;\r
+\r
+import uk.ac.ebi.picr.model.UPEntry;\r
\r
/**\r
* Implements a runnable for validating a sequence against external databases\r
StringBuffer sbuffer = new StringBuffer();\r
\r
boolean running = false;\r
+ /**\r
+ * picr client instance\r
+ */\r
+ uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;\r
\r
// /This will be a collection of Vectors of sequenceI refs.\r
// The key will be the seq name or accession id of the seq\r
}\r
\r
/**\r
- * Creates a new SequenceFeatureFetcher object.\r
+ * Creates a new SequenceFeatureFetcher object and fetches from the\r
+ * currently selected set of databases.\r
* \r
* @param seqs\r
* fetch references for these sequences\r
*/\r
public DBRefFetcher(SequenceI[] seqs, AlignFrame af)\r
{\r
+ this(seqs, af, null);\r
+ }\r
+ /**\r
+ * Creates a new SequenceFeatureFetcher object and fetches from the\r
+ * currently selected set of databases.\r
+ * \r
+ * @param seqs\r
+ * fetch references for these sequences\r
+ * @param af\r
+ * the parent alignframe for progress bar monitoring.\r
+ * @param sources array of database source strings to query references from\r
+ */\r
+ public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)\r
+ {\r
this.af = af;\r
SequenceI[] ds = new SequenceI[seqs.length];\r
for (int i = 0; i < seqs.length; i++)\r
this.dataset = ds;\r
// TODO Jalview 2.5 lots of this code should be in the gui package!\r
sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);\r
- // select appropriate databases based on alignFrame context.\r
- if (af.getViewport().getAlignment().isNucleotide())\r
+ if (sources==null)\r
{\r
- dbSources = DBRefSource.DNACODINGDBS;\r
+ // af.featureSettings_actionPerformed(null);\r
+ String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()\r
+ : new jalview.gui.DasSourceBrowser().getSelectedSources();\r
+ Enumeration en = dasselsrc.elements();\r
+ while (en.hasMoreElements())\r
+ {\r
+ DasSource src = (DasSource) en.nextElement();\r
+ selsources.addElement(src.getNickname());\r
+ }\r
+ int osel = 0;\r
+ for (int o=0;otherdb!=null && o<otherdb.length;o++)\r
+ {\r
+ if (!selsources.contains(otherdb[o]))\r
+ {\r
+ otherdb[o] = null;\r
+ } else {\r
+ osel++;\r
+ }\r
+ }\r
+ // select appropriate databases based on alignFrame context.\r
+ if (af.getViewport().getAlignment().isNucleotide())\r
+ {\r
+ defdb = DBRefSource.DNACODINGDBS;\r
+ }\r
+ else\r
+ {\r
+ defdb = DBRefSource.PROTEINDBS;\r
+ }\r
+ // append the selected sequence sources to the default dbs \r
+ dbSources = new String[defdb.length+osel];\r
+ System.arraycopy(defdb, 0, dbSources, 0, defdb.length);\r
+ for (int o=0,op=defdb.length; otherdb!=null && o<otherdb.length; o++)\r
+ {\r
+ if (otherdb[o]!=null)\r
+ {\r
+ dbSources[op++] = otherdb[o];\r
+ }\r
+ }\r
+ } else {\r
+ // we assume the caller knows what they're doing and ensured that all the db source names are valid\r
+ dbSources = sources;\r
}\r
- else\r
+ }\r
+ /**\r
+ * retrieve all the das sequence sources and add them to the list of db sources to retrieve from \r
+ */\r
+ public void appendAllDasSources()\r
+ {\r
+ if (dbSources == null)\r
{\r
- dbSources = DBRefSource.PROTEINDBS;\r
+ dbSources = new String[] {};\r
+ }\r
+ // append additional sources\r
+ String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ if (otherdb!=null && otherdb.length>0)\r
+ {\r
+ String[] newsrc = new String[dbSources.length+otherdb.length];\r
+ System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);\r
+ System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);\r
+ dbSources = newsrc;\r
}\r
}\r
-\r
/**\r
* start the fetcher thread\r
* \r
{\r
throw new Error("Implementation error. Must initialise dbSources");\r
}\r
+ running = true;\r
long startTime = System.currentTimeMillis();\r
af.setProgressBar("Fetching db refs", startTime);\r
- running = true;\r
+ try {\r
+ picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); \r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Couldn't locate PICR service instance.\n");\r
+ e.printStackTrace();\r
+ }\r
int db = 0;\r
Vector sdataset = new Vector();\r
for (int s = 0; s < dataset.length; s++)\r
{\r
// Still queries to make for current seqIndex\r
StringBuffer queryString = new StringBuffer("");\r
- int nqSize = (maxqlen > queries.size()) ? queries.size()\r
+ int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()\r
: maxqlen;\r
- for (int nq = 0, numq = 0; nq < nqSize; nq++)\r
+ \r
+ while (queries.size()>0 && numq < nqSize)\r
{\r
- String query = (String) queries.elementAt(nq);\r
+ String query = (String) queries.elementAt(0);\r
if (dbsource.isValidReference(query))\r
{\r
- queryString.append((nq == 0) ? "" : dbsource\r
+ queryString.append((numq == 0) ? "" : dbsource\r
.getAccessionSeparator());\r
queryString.append(query);\r
numq++;\r
}\r
- }\r
- for (int nq = 0; nq < nqSize; nq++)\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
+ {\r
+ jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");\r
+ }\r
retrieved = dbsource.getSequenceRecords(queryString.toString());\r
} catch (Exception ex)\r
{\r
{ dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
// });\r
// check for existing dbrefs to use\r
- if (uprefs != null)\r
+ if (uprefs != null && uprefs.length>0)\r
{\r
for (int j = 0; j < uprefs.length; j++)\r
{\r
while (st.hasMoreTokens())\r
{\r
String token = st.nextToken();\r
- addSeqId(sequence, token);\r
- queries.addElement(token.toUpperCase());\r
+ UPEntry[] presp = null;\r
+ try {\r
+ presp=picrClient.getUPIForAccession(token, null, picrClient.getMappedDatabaseNames(), null, true);\r
+ } catch (Exception e) {\r
+ System.err.println("Exception with Picr for '"+token+"'\n");\r
+ e.printStackTrace();\r
+ }\r
+ if (presp!=null && presp.length>0)\r
+ {\r
+ for (int id=0;id<presp.length; id++)\r
+ {\r
+ // construct sequences from response if sequences are present, and do a transferReferences\r
+ // otherwise transfer non sequence x-references directly.\r
+ }\r
+ addSeqId(sequence, token);\r
+ queries.addElement(token.toUpperCase());\r
+ } else {\r
+ System.out.println("Not querying source with token="+token+"\n");\r
+ //addSeqId(sequence, token);\r
+ //queries.addElement(token.toUpperCase());\r
+ }\r
}\r
}\r
}\r
// and remove it from the rest\r
// TODO: decide if we should remove annotated sequence from set\r
sdataset.remove(sequence);\r
+ // TODO: should we make a note of sequences that have received new DB ids, so we can query all enabled DAS servers for them ?\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff