X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=10a2b282ddaefeefa447880c2f494ede691cf325;hb=6f2c3b8cb30d8ccf7ff9ab949a7b244f0c415bc1;hp=0d9a92676e2a7d557a00c2de08f9681275f74180;hpb=5721b73c6d5de84b21a989a8734e4c161f5dc630;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 0d9a926..10a2b28 100644
--- 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.datamodel.DBRefSource;
 import jalview.ext.ensembl.EnsemblGene;
 import jalview.ws.dbsources.Uniprot;
@@ -31,15 +33,51 @@ import java.util.Collections;
 import java.util.List;
 
 /**
- * This implements the run-time discovery of sequence database clients.
+ * Thread safe construction of database proxies. This implements the run-time
+ * discovery of sequence database clients.
  * 
+ * TODO: extend to a configurable database plugin mechanism where classes are
+ * instantiated by reflection and queried for their DbRefSource and version
+ * association.
  */
-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;
+
+  /**
+   * 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);
+  }
+
+  /**
+   * 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)
+  {
+    mockFetcher = sf;
+  }
+
   /**
-   * Thread safe construction of database proxies TODO: extend to a configurable
-   * database plugin mechanism where classes are instantiated by reflection and
-   * queried for their DbRefSource and version association.
+   * 
+   * This public constructor is only is for use by testng to anonymously
+   * subclass SequenceFetcher.
+   * 
    * 
    */
   public SequenceFetcher()
@@ -71,30 +109,25 @@ 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()
   {
     String[] srcs = this.getSupportedDb();
     List<String> src = new ArrayList<>();
-
-    for (int i = 0; i < srcs.length; i++)
+    outer: for (int i = 0; i < srcs.length; i++)
     {
-      boolean accept = true;
       for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
       {
         // Skip the alignment databases for the moment - they're not useful for
         // verifying a single sequence against its reference source
         if (dbs.isAlignmentSource())
         {
-          accept = false;
-          break;
+          continue outer;
         }
       }
-      if (accept)
-      {
-        src.add(srcs[i]);
-      }
+      src.add(srcs[i]);
     }
     Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
     return src.toArray(new String[src.size()]);