JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / ws / seqfetcher / ASequenceFetcher.java

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 9e438d3..31168b4 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.seqfetcher;
 
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -54,7 +55,7 @@ public class ASequenceFetcher
   /**
    * Constructor
    */
-  public ASequenceFetcher()
+  protected ASequenceFetcher()
   {
     super();
 
@@ -111,8 +112,7 @@ public class ASequenceFetcher
         return true;
       }
     }
-    Cache.log.warn("isFetchable doesn't know about '" + source
-            + "'");
+    Cache.log.warn("isFetchable doesn't know about '" + source + "'");
     return false;
   }
 
@@ -124,20 +124,20 @@ public class ASequenceFetcher
    *          if true, only fetch from nucleotide data sources, else peptide
    * @return
    */
-  public SequenceI[] getSequences(DBRefEntry[] refs, boolean dna)
+  public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
   {
     Vector<SequenceI> rseqs = new Vector<SequenceI>();
     Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
-    for (int r = 0; r < refs.length; r++)
+    for (DBRefEntry ref : refs)
     {
-      if (!queries.containsKey(refs[r].getSource()))
+      if (!queries.containsKey(ref.getSource()))
       {
-        queries.put(refs[r].getSource(), new ArrayList<String>());
+        queries.put(ref.getSource(), new ArrayList<String>());
       }
-      List<String> qset = queries.get(refs[r].getSource());
-      if (!qset.contains(refs[r].getAccessionId()))
+      List<String> qset = queries.get(ref.getSource());
+      if (!qset.contains(ref.getAccessionId()))
       {
-        qset.add(refs[r].getAccessionId());
+        qset.add(ref.getAccessionId());
       }
     }
     Enumeration<String> e = queries.keys();
@@ -157,7 +157,8 @@ public class ASequenceFetcher
       Stack<String> queriesLeft = new Stack<String>();
       queriesLeft.addAll(query);
 
-      for (DbSourceProxy fetcher : getSourceProxy(db))
+      List<DbSourceProxy> proxies = getSourceProxy(db);
+      for (DbSourceProxy fetcher : proxies)
       {
         List<String> queriesMade = new ArrayList<String>();
         HashSet<String> queriesFound = new HashSet<String>();
@@ -167,8 +168,7 @@ public class ASequenceFetcher
           {
             continue; // wrong sort of data
           }
-          boolean doMultiple = fetcher.getAccessionSeparator() != null;
-          // No separator - no Multiple Queries
+          boolean doMultiple = fetcher.getMaximumQueryCount() > 1;
           while (!queriesLeft.isEmpty())
           {
             StringBuffer qsb = new StringBuffer();
@@ -187,8 +187,7 @@ public class ASequenceFetcher
             try
             {
               // create a fetcher and go to it
-              seqset = fetcher.getSequenceRecords(qsb.toString()); // ,
-              // queriesFailed);
+              seqset = fetcher.getSequenceRecords(qsb.toString());
             } catch (Exception ex)
             {
               System.err.println("Failed to retrieve the following from "
@@ -205,15 +204,12 @@ public class ASequenceFetcher
                 for (int is = 0; is < seqs.length; is++)
                 {
                   rseqs.addElement(seqs[is]);
-                  DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]
-                          .getDBRef(), new DBRefEntry(db, null, null));
-                  if (frefs != null)
+                  List<DBRefEntry> frefs = DBRefUtils.searchRefs(seqs[is]
+                          .getDBRefs(), new DBRefEntry(db, null, null));
+                  for (DBRefEntry dbr : frefs)
                   {
-                    for (DBRefEntry dbr : frefs)
-                    {
-                      queriesFound.add(dbr.getAccessionId());
-                      queriesMade.remove(dbr.getAccessionId());
-                    }
+                    queriesFound.add(dbr.getAccessionId());
+                    queriesMade.remove(dbr.getAccessionId());
                   }
                   seqs[is] = null;
                 }
@@ -255,7 +251,7 @@ public class ASequenceFetcher
         {
           System.out.println("# Adding " + queriesMade.size()
                   + " ids back to queries list for searching again (" + db
-                  + ".");
+                  + ")");
           queriesLeft.addAll(queriesMade);
         }
       }
@@ -436,4 +432,28 @@ public class ASequenceFetcher
     return prlist.toArray(new DbSourceProxy[0]);
   }
 
+  /**
+   * Returns a preferred feature colouring scheme for the given source, or null
+   * if none is defined.
+   * 
+   * @param source
+   * @return
+   */
+  public FeatureSettingsModelI getFeatureColourScheme(String source)
+  {
+    /*
+     * return the first non-null colour scheme for any proxy for
+     * this database source
+     */
+    for (DbSourceProxy proxy : getSourceProxy(source))
+    {
+      FeatureSettingsModelI preferredColours = proxy
+              .getFeatureColourScheme();
+      if (preferredColours != null)
+      {
+        return preferredColours;
+      }
+    }
+    return null;
+  }
 }