/*\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
+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.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
-import org.exolab.castor.mapping.*;\r
-import org.exolab.castor.xml.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.datamodel.Mapping;\r
-import jalview.gui.*;\r
-import jalview.ws.dbsources.Uniprot;\r
-import jalview.ws.ebi.EBIFetchClient;\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
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
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