JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / ws / SequenceFetcher.java

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 18e25cc..10a2b28 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,13 +20,10 @@
  */
 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.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.Uniprot;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
@@ -36,55 +33,101 @@ 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);
+  }
+
   /**
-   * 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.
+   * 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;
+  }
+
+  /**
+   * 
+   * This public constructor is only is for use by testng to anonymously
+   * subclass SequenceFetcher.
+   * 
    * 
    */
   public SequenceFetcher()
   {
-    addDBRefSourceImpl(EnsemblGene.class);
-    // addDBRefSourceImpl(EnsemblGenomes.class);
-    addDBRefSourceImpl(EmblSource.class);
-    addDBRefSourceImpl(EmblCdsSource.class);
-    addDBRefSourceImpl(Uniprot.class);
-    addDBRefSourceImpl(Pdb.class);
-    addDBRefSourceImpl(PfamFull.class);
-    addDBRefSourceImpl(PfamSeed.class);
-    addDBRefSourceImpl(RfamSeed.class);
+    addAllDatabases();
+  }
+
+  public void addAllDatabases()
+  {
+    addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
+    addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class
+    // addDBRefSourceImpl(EmblSource.class);
+    // addDBRefSourceImpl(EmblCdsSource.class);
+    // addDBRefSourceImpl(Pdb.class);
+    // addDBRefSourceImpl(PfamFull.class);
+    // addDBRefSourceImpl(PfamSeed.class);
+    // addDBRefSourceImpl(RfamSeed.class);
+    addDBRefSourceImpl(DBRefSource.EMBL,
+            "jalview.ws.dbsources.EmblSource");
+    addDBRefSourceImpl(DBRefSource.EMBLCDS,
+            "jalview.ws.dbsources.EmblCdsSource");
+    addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb");
+    addDBRefSourceImpl(DBRefSource.PFAM_FULL,
+            "jalview.ws.dbsources.PfamFull");
+    addDBRefSourceImpl(DBRefSource.PFAM_SEED,
+            "jalview.ws.dbsources.PfamSeed");
+    addDBRefSourceImpl(DBRefSource.RFAM_SEED,
+            "jalview.ws.dbsources.RfamSeed");
   }
 
   /**
-   * 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()]);