X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=35a237e97d8147ffd6de5a90eee4fb578be04b82;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=4526b26ddde4f885ae64463d5d06895f4135d9df;hpb=81667097b92ba72f5eb4d824646b31e7ff5383a0;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 4526b26d..35a237e 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,14 +20,16 @@
  */
 package jalview.ws;
 
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.ext.ensembl.EnsemblGene;
-import jalview.ext.ensembl.EnsemblGenomes;
 import jalview.ws.dbsources.EmblCdsSource;
 import jalview.ws.dbsources.EmblSource;
 import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.PfamFull;
 import jalview.ws.dbsources.PfamSeed;
 import jalview.ws.dbsources.RfamSeed;
+import jalview.ws.dbsources.TDBeacons;
 import jalview.ws.dbsources.Uniprot;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
@@ -40,8 +42,39 @@ import java.util.List;
  * This implements the run-time discovery of sequence database clients.
  * 
  */
-public class SequenceFetcher extends ASequenceFetcher
+public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
 {
+  /*
+   * set a mock fetcher here for testing only - reset to null afterwards
+   */
+  private static SequenceFetcher mockFetcher;
+
+  /**
+   * Set the instance object to use (intended for unit testing with mock
+   * objects).
+   * 
+   * Be sure to reset to null in the tearDown method of any tests!
+   * 
+   * @param sf
+   */
+  public static void setMockFetcher(SequenceFetcher sf)
+  {
+    mockFetcher = sf;
+  }
+  
+  /**
+   * Returns a new SequenceFetcher singleton, or a mock object if one has been
+   * set.
+   * 
+   * @return
+   */
+  public static SequenceFetcher getInstance()
+  {
+    return mockFetcher != null ? mockFetcher
+            : (SequenceFetcher) ApplicationSingletonProvider
+                    .getInstance(SequenceFetcher.class);
+  }
+
   /**
    * Thread safe construction of database proxies TODO: extend to a configurable
    * database plugin mechanism where classes are instantiated by reflection and
@@ -51,10 +84,12 @@ public class SequenceFetcher extends ASequenceFetcher
   public SequenceFetcher()
   {
     addDBRefSourceImpl(EnsemblGene.class);
-    addDBRefSourceImpl(EnsemblGenomes.class);
+    // addDBRefSourceImpl(EnsemblGenomes.class);
     addDBRefSourceImpl(EmblSource.class);
     addDBRefSourceImpl(EmblCdsSource.class);
     addDBRefSourceImpl(Uniprot.class);
+    // not a sequence source yet
+    // addDBRefSourceImpl(TDBeacons.class);
     addDBRefSourceImpl(Pdb.class);
     addDBRefSourceImpl(PfamFull.class);
     addDBRefSourceImpl(PfamSeed.class);
@@ -62,7 +97,8 @@ public class SequenceFetcher extends ASequenceFetcher
   }
 
   /**
-   * return an ordered list of database sources excluding alignment only databases
+   * return an ordered list of database sources excluding alignment only
+   * databases
    */
   public String[] getNonAlignmentSources()
   {
@@ -87,6 +123,7 @@ public class SequenceFetcher extends ASequenceFetcher
         src.add(srcs[i]);
       }
     }
+
     Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
     return src.toArray(new String[src.size()]);
   }