From: jprocter <Jim Procter>
Date: Fri, 12 Jun 2009 15:46:22 +0000 (+0000)
Subject: reinstated blind querying of datasources. Transfer references to alignment from Map... 
X-Git-Tag: Release_2_5~272
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=37c97b109c3a03f4640bce3855069f8ad8e17123;p=jalview.git

reinstated blind querying of datasources. Transfer references to alignment from Map.To sequences on retrieved entries (e.g. protein product from EMBLCDS record)
---

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 5400d4e..4b7c07e 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -31,6 +31,7 @@ import jalview.gui.Desktop;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
 
+import java.lang.reflect.Array;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
@@ -384,12 +385,14 @@ public class DBRefFetcher implements Runnable
                     // construct sequences from response if sequences are present, and do a transferReferences
                     // otherwise transfer non sequence x-references directly.
                   }
+                  System.out.println("Validated ID against PICR... (for what its worth):"+token);
                   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());
+                  //if ()
+                  //System.out.println("Not querying source with token="+token+"\n");
+                  addSeqId(sequence, token);
+                  queries.addElement(token.toUpperCase());
                 }
               }
             }
@@ -433,7 +436,7 @@ public class DBRefFetcher implements Runnable
     {
       return;
     }
-    SequenceI[] retrieved = retrievedAl.getSequencesArray();
+    SequenceI[] retrieved = recoverDbSequences(retrievedAl.getSequencesArray());
     SequenceI sequence = null;
 
     // Vector entries = new Uniprot().getUniprotEntries(file);
@@ -600,4 +603,34 @@ public class DBRefFetcher implements Runnable
       }
     }
   }
+
+  /**
+   * loop thru and collect additional sequences in Map.
+   * @param sequencesArray
+   * @return
+   */
+  private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
+  {
+    Vector nseq = new Vector();
+    for (int i=0;sequencesArray!=null && i<sequencesArray.length;i++)
+    {
+      nseq.addElement(sequencesArray[i]);
+      DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+      jalview.datamodel.Mapping map = null;
+      for (int r=0;(dbr!=null) && r<dbr.length; r++) {
+        if ((map=dbr[r].getMap())!=null)
+        {
+          if (!nseq.contains(map.getTo()))
+          {
+            nseq.addElement(map.getTo());
+          }
+        }
+      }
+    }
+    if (nseq.size()>0) {
+      sequencesArray = new SequenceI[nseq.size()];
+      nseq.toArray(sequencesArray);
+    }
+    return sequencesArray;
+  }
 }