JAL-3446 from JAL-3253-applet SequenceFetcher.getInstance()

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index c54357e..b70e9f7 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -31,6 +31,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
+import jalview.ws.SequenceFetcher;
 import jalview.ws.SequenceFetcherFactory;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
@@ -402,7 +403,6 @@ public class CrossRef
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
           List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
-    ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
     SequenceI[] retrieved = null;
     SequenceI dss = seq.getDatasetSequence() == null ? seq
             : seq.getDatasetSequence();
@@ -418,7 +418,7 @@ public class CrossRef
     }
     try
     {
-      retrieved = sftch.getSequences(sourceRefs, !fromDna);
+      retrieved = SequenceFetcher.getInstance().getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
       System.err.println(

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index a480176..5c94faf 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws;
 
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.ext.ensembl.EnsemblGene;
 import jalview.ws.dbsources.EmblCdsSource;
 import jalview.ws.dbsources.EmblSource;
@@ -39,8 +41,39 @@ 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

diff --git a/src/jalview/ws/SequenceFetcherFactory.java b/src/jalview/ws/SequenceFetcherFactory.java
index 9cc4960..25144fc 100644 (file)
--- a/src/jalview/ws/SequenceFetcherFactory.java
+++ b/src/jalview/ws/SequenceFetcherFactory.java
@@ -24,29 +24,33 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 
 public class SequenceFetcherFactory
 {
-
-  private static SequenceFetcher instance;
-
-  /**
-   * Returns a new SequenceFetcher object, or a mock object if one has been set
-   * 
-   * @return
-   */
-  public static ASequenceFetcher getSequenceFetcher()
-  {
-    return instance == null ? new SequenceFetcher() : instance;
-  }
-
-  /**
-   * 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 setSequenceFetcher(SequenceFetcher sf)
-  {
-    instance = sf;
-  }
+  // BH the two methods in this class merged into SequenceFetcher
 }
+//public class SequenceFetcherFactory
+//{
+//
+//  private static SequenceFetcher instance;
+//
+//  /**
+//   * Returns a new SequenceFetcher object, or a mock object if one has been set
+//   * 
+//   * @return
+//   */
+//  public static ASequenceFetcher getSequenceFetcher()
+//  {
+//    return instance == null ? new SequenceFetcher() : instance;
+//  }
+//
+//  /**
+//   * 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 setSequenceFetcher(SequenceFetcher sf)
+//  {
+//    instance = sf;
+//  }
+//}

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 2ca112f..0123551 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -443,7 +443,7 @@ public class CrossRefTest
         return new SequenceI[] { pep1, pep2 };
       }
     };
-    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+    SequenceFetcher.setMockFetcher(mockFetcher);
 
     /*
      * find UNIPROT xrefs for nucleotide sequence
@@ -459,7 +459,7 @@ public class CrossRefTest
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
-    SequenceFetcherFactory.setSequenceFetcher(null);
+    SequenceFetcher.setMockFetcher(null);
   }
 
   /**
@@ -521,7 +521,7 @@ public class CrossRefTest
         return new SequenceI[] { pep1, pep2 };
       }
     };
-    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+    SequenceFetcher.setMockFetcher(mockFetcher);
 
     /*
      * find UNIPROT xrefs for gene and transcripts
@@ -681,7 +681,7 @@ public class CrossRefTest
         }
       }
     };
-    SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+    SequenceFetcher.setMockFetcher(mockFetcher);
 
     /*
      * find EMBL xrefs for Uniprot seqs and verify that