From 91416b3038a6f3fc655791512770da07cb6cb251 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 8 Jun 2006 18:17:35 +0000
Subject: [PATCH] Introduced DbRefEntry to DasSourceCoordinateSystem check to
 only call sources for sequences with a particular
 DBRefEntry id (PDB or Uniprot currently)

---
 src/jalview/gui/SequenceFetcher.java          |    2 +-
 src/jalview/io/DasSequenceFeatureFetcher.java |   25 +++++++++++++----
 src/jalview/io/ModellerDescription.java       |    2 +-
 src/jalview/io/SequenceFeatureFetcher.java    |    3 +-
 src/jalview/io/WSWUBlastClient.java           |    2 +-
 src/jalview/util/DBRefUtils.java              |   37 +++++++++++++++++++++++--
 6 files changed, 59 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 6bdba4a..e2b5730 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -437,7 +437,7 @@ public class SequenceFetcher
 
               // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
               // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
-              DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);
+              DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);
               sequences[i].getDatasetSequence().addDBRef(dbentry);
             }
             else
diff --git a/src/jalview/io/DasSequenceFeatureFetcher.java b/src/jalview/io/DasSequenceFeatureFetcher.java
index 99a2b70..8f104c5 100755
--- a/src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/src/jalview/io/DasSequenceFeatureFetcher.java
@@ -251,7 +251,10 @@ public class DasSequenceFeatureFetcher implements Runnable
       while (seqIndex < sequences.size())
       {
           Sequence sequence = (Sequence) sequences.get(seqIndex);
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[]  {"DBREF"});
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),
+              new String[]  {
+              jalview.datamodel.DBRefSource.PDB,
+              jalview.datamodel.DBRefSource.UNIPROT});
 
           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)
           {
@@ -262,11 +265,21 @@ public class DasSequenceFeatureFetcher implements Runnable
               // we know the id for this entry, so don't note its ID in the unknownSequences list
               for (int j = 0, k = uprefs.size(); j < k; j++)
               {
-
-                createFeatureFetcher(sequence,
-                                     dasSource.getUrl(),
-                                     ( (DBRefEntry) uprefs.get(j)).getAccessionId(),
-                                     dasSource.getNickname());
+                // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end
+                org.biojava.services.das.registry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();
+                for (int l=0; l<cs.length; l++) {
+                  if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)
+                      uprefs.get(j)))
+                  {
+                    Cache.log.debug("Launched fetcher for coordinate system " +
+                                    cs[l].getName());
+                    createFeatureFetcher(sequence,
+                                         dasSource.getUrl(),
+                                         ( (DBRefEntry) uprefs.get(j)).
+                                         getAccessionId(),
+                                         dasSource.getNickname());
+                  }
+                }
               }
             }
             else
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 62e1fbe..1e4f905 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -234,7 +234,7 @@ public class ModellerDescription
           {
             // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
             // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
-            if (dref.getSource().equals("PDB"))
+            if (dref.getSource().equals(jalview.datamodel.DBRefSource.PDB))
             {
               fields.put(Fields[LOCALID], dref.getAccessionId());
               t = 2;
diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 9bc214f..edbf862 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -116,7 +116,8 @@ public class SequenceFeatureFetcher implements Runnable
              seqIndex++, i++)
         {
           Sequence sequence = (Sequence) sequences.get(seqIndex);
-          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] { "Uniprot"});
+          Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {
+              jalview.datamodel.DBRefSource.UNIPROT});
           if (uprefs!=null)
           {
             // we know the id for this entry, so don't note its ID in the unknownSequences list
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 0906d12..391c9a8 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -168,7 +168,7 @@ public class WSWUBlastClient
           {
             DBRefEntry entry = (DBRefEntry) entries.elementAt(0);
             oldseq.addDBRef(new jalview.datamodel.
-                                                 DBRefEntry("UNIPROT",
+                                                 DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
                 "0",
                 entry.getAccessionId()));
           }
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 86ab201..2f844da 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,13 +1,20 @@
 package jalview.util;
 
-import java.util.Vector;
-import java.util.Hashtable;
+import java.util.*;
+
+import jalview.datamodel.*;
 
 public class DBRefUtils
 {
     /**
      * Utilities for handling DBRef objects and their collections.
      */
+    /**
+     *
+     * @param dbrefs Vector of DBRef objects to search
+     * @param sources String[] array of source DBRef IDs to retrieve
+     * @return Vector
+     */
     public static Vector selectRefs(java.util.Vector dbrefs, String[] sources) {
       if (dbrefs==null)
         return null;
@@ -29,4 +36,30 @@ public class DBRefUtils
       // there are probable  memory leaks in the hashtable!
       return null;
     }
+
+  /**
+   * isDasCoordinateSystem
+   *
+   * @param string String
+   * @param dBRefEntry DBRefEntry
+   * @return boolean true if Source DBRefEntry is compatible with DAS CoordinateSystem name
+   */
+  public static Hashtable DasCoordinateSystemsLookup = null;
+  public static boolean isDasCoordinateSystem(String string,
+                                              DBRefEntry dBRefEntry)
+  {
+    if (DasCoordinateSystemsLookup==null)
+    { // Initialise
+      DasCoordinateSystemsLookup = new Hashtable();
+      DasCoordinateSystemsLookup.put("pdbresnum",
+                                     jalview.datamodel.DBRefSource.PDB);
+      DasCoordinateSystemsLookup.put("uniprot",
+                                     jalview.datamodel.DBRefSource.UNIPROT);
+    }
+
+    String coordsys = (String) DasCoordinateSystemsLookup.get(string.toLowerCase());
+    if (coordsys!=null)
+      return coordsys.equals(dBRefEntry.getSource());
+    return false;
   }
+}
-- 
1.7.10.2