X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=10a2b282ddaefeefa447880c2f494ede691cf325;hb=28e9024f09a78a9625ed4defa2012bf342bec51e;hp=a28be2ca054fa14813ec78a8ca30f907c0cf3e94;hpb=e6002f475183c8b54afaf24ae16aca3b6c794b56;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index a28be2c..10a2b28 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,85 +20,116 @@
  */
 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;
 
 import java.util.ArrayList;
+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;
+
   /**
-   * 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.
+   * 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;
+  }
+
+  /**
+   * 
+   * 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[] getOrderedSupportedSources()
+  public String[] getNonAlignmentSources()
   {
     String[] srcs = this.getSupportedDb();
-    ArrayList<String> src = new ArrayList<>();
-
-    for (int i = 0; i < srcs.length; i++)
+    List<String> src = new ArrayList<>();
+    outer: for (int i = 0; i < srcs.length; i++)
     {
-      boolean skip = false;
       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())
         {
-          skip = true;
+          continue outer;
         }
       }
-      if (skip)
-      {
-        continue;
-      }
-      {
-        src.add(srcs[i]);
-      }
-    }
-    String[] tosort = src.toArray(new String[0]),
-            sorted = src.toArray(new String[0]);
-    for (int j = 0, jSize = sorted.length; j < jSize; j++)
-    {
-      tosort[j] = tosort[j].toLowerCase();
-    }
-    jalview.util.QuickSort.sort(tosort, sorted);
-    // construct array with all sources listed
-    int i = 0;
-    for (int j = sorted.length - 1; j >= 0; j--, i++)
-    {
-      srcs[i] = sorted[j];
+      src.add(srcs[i]);
     }
-    return srcs;
+    Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+    return src.toArray(new String[src.size()]);
   }
 }