From faf6281b4ee692a989d0d625b1bb0d581cc0269c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 8 Jun 2009 11:20:50 +0000
Subject: [PATCH] *experimental use of picr* apply gpl development license

---
 src/jalview/ws/DBRefFetcher.java |   69 +++++++++++++++++++++++++++++---------
 1 file changed, 54 insertions(+), 15 deletions(-)

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 825b0f9..5400d4e 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,18 +18,27 @@
  */
 package jalview.ws;
 
-import java.io.*;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 import org.biojava.dasobert.dasregistry.DasSource;
-import org.exolab.castor.mapping.*;
-import org.exolab.castor.xml.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.datamodel.Mapping;
-import jalview.gui.*;
-import jalview.ws.dbsources.Uniprot;
-import jalview.ws.ebi.EBIFetchClient;
+
+import uk.ac.ebi.picr.model.UPEntry;
 
 /**
  * Implements a runnable for validating a sequence against external databases
@@ -49,6 +58,10 @@ public class DBRefFetcher implements Runnable
   StringBuffer sbuffer = new StringBuffer();
 
   boolean running = false;
+  /**
+   * picr client instance
+   */
+  uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
 
   // /This will be a collection of Vectors of sequenceI refs.
   // The key will be the seq name or accession id of the seq
@@ -237,9 +250,16 @@ public class DBRefFetcher implements Runnable
     {
       throw new Error("Implementation error. Must initialise dbSources");
     }
+    running = true;
     long startTime = System.currentTimeMillis();
     af.setProgressBar("Fetching db refs", startTime);
-    running = true;
+    try {
+      picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); 
+    } catch (Exception e)
+    {
+      System.err.println("Couldn't locate PICR service instance.\n");
+      e.printStackTrace();
+    }
     int db = 0;
     Vector sdataset = new Vector();
     for (int s = 0; s < dataset.length; s++)
@@ -350,8 +370,27 @@ public class DBRefFetcher implements Runnable
               while (st.hasMoreTokens())
               {
                 String token = st.nextToken();
-                addSeqId(sequence, token);
-                queries.addElement(token.toUpperCase());
+                UPEntry[] presp = null;
+                try {
+                  presp=picrClient.getUPIForAccession(token, null, picrClient.getMappedDatabaseNames(), null, true);
+                } catch (Exception e) {
+                  System.err.println("Exception with Picr for '"+token+"'\n");
+                  e.printStackTrace();
+                }
+                if (presp!=null && presp.length>0)
+                {
+                  for (int id=0;id<presp.length; id++)
+                  {
+                    // construct sequences from response if sequences are present, and do a transferReferences
+                    // otherwise transfer non sequence x-references directly.
+                  }
+                  addSeqId(sequence, token);
+                  queries.addElement(token.toUpperCase());
+                } else {
+                  System.out.println("Not querying source with token="+token+"\n");
+                  //addSeqId(sequence, token);
+                  //queries.addElement(token.toUpperCase());
+                }
               }
             }
           }
-- 
1.7.10.2