X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=35a237e97d8147ffd6de5a90eee4fb578be04b82;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=29d4ec790de4508477b4d0325d7dd2d5b5c1e98c;hpb=26501f76ef450657c530de489b8404356a98aca3;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 29d4ec7..35a237e 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,26 +20,61 @@
  */
 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;
 
 import java.util.ArrayList;
+import java.util.Collections;
+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
@@ -49,10 +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);
@@ -60,46 +97,34 @@ 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[] getOrderedSupportedSources()
+  public String[] getNonAlignmentSources()
   {
     String[] srcs = this.getSupportedDb();
-    ArrayList<String> src = new ArrayList<>();
+    List<String> src = new ArrayList<>();
 
     for (int i = 0; i < srcs.length; i++)
     {
-      boolean skip = false;
+      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())
         {
-          skip = true;
+          accept = false;
+          break;
         }
       }
-      if (skip)
-      {
-        continue;
-      }
+      if (accept)
       {
         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];
-    }
-    return srcs;
+
+    Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+    return src.toArray(new String[src.size()]);
   }
 }