JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 65179a2..48aafca 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -21,21 +21,19 @@
 package jalview.ws;
 
 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.RfamFull;
 import jalview.ws.dbsources.RfamSeed;
+import jalview.ws.dbsources.TDBeacons;
 import jalview.ws.dbsources.Uniprot;
-import jalview.ws.dbsources.UniprotName;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 /**
@@ -52,126 +50,48 @@ public class SequenceFetcher extends ASequenceFetcher
    */
   public SequenceFetcher()
   {
-    this(true);
-  }
-
-  public SequenceFetcher(boolean addDas)
-  {
     addDBRefSourceImpl(EnsemblGene.class);
-    addDBRefSourceImpl(EnsemblGenomes.class);
+    // addDBRefSourceImpl(EnsemblGenomes.class);
     addDBRefSourceImpl(EmblSource.class);
     addDBRefSourceImpl(EmblCdsSource.class);
     addDBRefSourceImpl(Uniprot.class);
-    addDBRefSourceImpl(UniprotName.class);
+    // not a sequence source yet
+    // addDBRefSourceImpl(TDBeacons.class);
     addDBRefSourceImpl(Pdb.class);
     addDBRefSourceImpl(PfamFull.class);
     addDBRefSourceImpl(PfamSeed.class);
     addDBRefSourceImpl(RfamSeed.class);
-    if (addDas)
-    {
-      registerDasSequenceSources();
-    }
   }
 
   /**
-   * return an ordered list of database sources where non-das database classes
-   * appear before das database classes
+   * return an ordered list of database sources excluding alignment only
+   * databases
    */
-  public String[] getOrderedSupportedSources()
+  public String[] getNonAlignmentSources()
   {
     String[] srcs = this.getSupportedDb();
-    ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+    List<String> src = new ArrayList<>();
+
     for (int i = 0; i < srcs.length; i++)
     {
-      boolean das = false, skip = false;
-      String nm;
+      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;
-        }
-        else
-        {
-          nm = dbs.getDbName();
-          if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
-          {
-            if (nm.startsWith("das:"))
-            {
-              nm = nm.substring(4);
-              das = true;
-            }
-            break;
-          }
+          accept = false;
+          break;
         }
       }
-      if (skip)
+      if (accept)
       {
-        continue;
+        src.add(srcs[i]);
       }
-      if (das)
-      {
-        dassrc.add(srcs[i]);
-      }
-      else
-      {
-        nondas.add(srcs[i]);
-      }
-    }
-    String[] tosort = nondas.toArray(new String[0]), sorted = nondas
-            .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
-
-    srcs = new String[sorted.length + dassrc.size()];
-    int i = 0;
-    for (int j = sorted.length - 1; j >= 0; j--, i++)
-    {
-      srcs[i] = sorted[j];
-      sorted[j] = null;
     }
 
-    sorted = dassrc.toArray(new String[0]);
-    tosort = dassrc.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);
-    for (int j = sorted.length - 1; j >= 0; j--, i++)
-    {
-      srcs[i] = sorted[j];
-    }
-    return srcs;
-  }
-
-  /**
-   * query the currently defined DAS source registry for sequence sources and
-   * add a DasSequenceSource instance for each source to the SequenceFetcher
-   * source list.
-   */
-  public void registerDasSequenceSources()
-  {
-    // TODO: define a context as a registry provider (either desktop,
-    // jalview.bin.cache, or something else).
-    for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
-            .getSources())
-    {
-      if (source.isSequenceSource())
-      {
-        List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
-        for (DbSourceProxy seqsrc : dassources)
-        {
-          addDbRefSourceImpl(seqsrc);
-        }
-      }
-    }
+    Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+    return src.toArray(new String[src.size()]);
   }
-
 }