JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 10a2b28..18e25cc 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,10 +20,13 @@
  */
 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;
@@ -33,101 +36,55 @@ import java.util.Collections;
 import java.util.List;
 
 /**
- * Thread safe construction of database proxies. This implements the run-time
- * discovery of sequence database clients.
+ * 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 implements ApplicationSingletonI
+public class SequenceFetcher extends ASequenceFetcher
 {
-  /*
-   * 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;
-  }
-
-  /**
-   * 
-   * This public constructor is only is for use by testng to anonymously
-   * subclass SequenceFetcher.
-   * 
+   * 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.
    * 
    */
   public SequenceFetcher()
   {
-    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");
+    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);
   }
 
   /**
-   * 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<>();
-    outer: for (int i = 0; i < srcs.length; i++)
+
+    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())
         {
-          continue outer;
+          accept = false;
+          break;
         }
       }
-      src.add(srcs[i]);
+      if (accept)
+      {
+        src.add(srcs[i]);
+      }
     }
     Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
     return src.toArray(new String[src.size()]);