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 4f82619..18e25cc 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -20,8 +20,13 @@
  */
 package jalview.ws;
 
-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;
@@ -44,52 +49,42 @@ public class SequenceFetcher extends ASequenceFetcher
    */
   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()]);