X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=8f3f3b83bd2b1369fbc56b88c152bfe71842cf1a;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=9e438d335dab9e1a79dcb16d46be501079d69427;hpb=d015dda1e582c4654acd7fb7761fb0c0a2dc3573;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 9e438d3..8f3f3b8 100644
--- 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();
 
@@ -97,8 +98,8 @@ public class ASequenceFetcher
     {
       return null;
     }
-    String[] sf = fetchableDbs.keySet().toArray(
-            new String[fetchableDbs.size()]);
+    String[] sf = fetchableDbs.keySet()
+            .toArray(new String[fetchableDbs.size()]);
     return sf;
   }
 
@@ -111,8 +112,7 @@ public class ASequenceFetcher
         return true;
       }
     }
-    Cache.log.warn("isFetchable doesn't know about '" + source
-            + "'");
+    Cache.warn("isFetchable doesn't know about '" + source + "'");
     return false;
   }
 
@@ -124,20 +124,21 @@ 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++)
+    Vector<SequenceI> rseqs = new Vector<>();
+    Hashtable<String, List<String>> queries = new Hashtable<>();
+    for (DBRefEntry ref : refs)
     {
-      if (!queries.containsKey(refs[r].getSource()))
+      String canonical = DBRefUtils.getCanonicalName(ref.getSource());
+      if (!queries.containsKey(canonical))
       {
-        queries.put(refs[r].getSource(), new ArrayList<String>());
+        queries.put(canonical, new ArrayList<String>());
       }
-      List<String> qset = queries.get(refs[r].getSource());
-      if (!qset.contains(refs[r].getAccessionId()))
+      List<String> qset = queries.get(canonical);
+      if (!qset.contains(ref.getAccessionId()))
       {
-        qset.add(refs[r].getAccessionId());
+        qset.add(ref.getAccessionId());
       }
     }
     Enumeration<String> e = queries.keys();
@@ -154,21 +155,21 @@ public class ASequenceFetcher
         continue;
       }
 
-      Stack<String> queriesLeft = new Stack<String>();
+      Stack<String> queriesLeft = new Stack<>();
       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>();
+        List<String> queriesMade = new ArrayList<>();
+        HashSet<String> queriesFound = new HashSet<>();
         try
         {
           if (fetcher.isDnaCoding() != dna)
           {
             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();
@@ -187,12 +188,11 @@ 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 "
-                      + db);
+              System.err.println(
+                      "Failed to retrieve the following from " + db);
               System.err.println(qsb);
               ex.printStackTrace(System.err);
             }
@@ -205,15 +205,14 @@ 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)
+                  // BH 2015.01.25 check about version/accessid being null here
+                  List<DBRefEntry> frefs = DBRefUtils.searchRefs(
+                          seqs[is].getDBRefs(),
+                          new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL);
+                  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;
                 }
@@ -222,8 +221,8 @@ public class ASequenceFetcher
               {
                 if (fetcher.getRawRecords() != null)
                 {
-                  System.out.println("# Retrieved from " + db + ":"
-                          + qsb.toString());
+                  System.out.println(
+                          "# Retrieved from " + db + ":" + qsb.toString());
                   StringBuffer rrb = fetcher.getRawRecords();
                   /*
                    * for (int rr = 0; rr<rrb.length; rr++) {
@@ -255,7 +254,7 @@ public class ASequenceFetcher
         {
           System.out.println("# Adding " + queriesMade.size()
                   + " ids back to queries list for searching again (" + db
-                  + ".");
+                  + ")");
           queriesLeft.addAll(queriesMade);
         }
       }
@@ -279,8 +278,8 @@ public class ASequenceFetcher
           Exception ex)
   {
 
-    System.err.println("Failed to retrieve the following references from "
-            + db);
+    System.err.println(
+            "Failed to retrieve the following references from " + db);
     int n = 0;
     for (String qv : queriesMade)
     {
@@ -309,13 +308,13 @@ public class ASequenceFetcher
     Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
     if (dblist == null)
     {
-      return new ArrayList<DbSourceProxy>();
+      return new ArrayList<>();
     }
 
     /*
      * sort so that primary sources precede secondary
      */
-    List<DbSourceProxy> dbs = new ArrayList<DbSourceProxy>(dblist.values());
+    List<DbSourceProxy> dbs = new ArrayList<>(dblist.values());
     Collections.sort(dbs, proxyComparator);
     return dbs;
   }
@@ -342,10 +341,8 @@ public class ASequenceFetcher
     } catch (Exception e)
     {
       // Serious problems if this happens.
-      throw new Error(
-              MessageManager
-                      .getString("error.dbrefsource_implementation_exception"),
-              e);
+      throw new Error(MessageManager
+              .getString("error.dbrefsource_implementation_exception"), e);
     }
     addDbRefSourceImpl(proxy);
   }
@@ -362,14 +359,14 @@ public class ASequenceFetcher
     {
       if (fetchableDbs == null)
       {
-        fetchableDbs = new Hashtable<String, Map<String, DbSourceProxy>>();
+        fetchableDbs = new Hashtable<>();
       }
-      Map<String, DbSourceProxy> slist = fetchableDbs.get(proxy
-              .getDbSource());
+      Map<String, DbSourceProxy> slist = fetchableDbs
+              .get(proxy.getDbSource());
       if (slist == null)
       {
         fetchableDbs.put(proxy.getDbSource(),
-                slist = new Hashtable<String, DbSourceProxy>());
+                slist = new Hashtable<>());
       }
       slist.put(proxy.getDbName(), proxy);
     }
@@ -378,25 +375,25 @@ public class ASequenceFetcher
   /**
    * select sources which are implemented by instances of the given class
    * 
-   * @param class that implements DbSourceProxy
+   * @param class
+   *          that implements DbSourceProxy
    * @return null or vector of source names for fetchers
    */
   public String[] getDbInstances(Class class1)
   {
     if (!DbSourceProxy.class.isAssignableFrom(class1))
     {
-      throw new Error(
-              MessageManager
-                      .formatMessage(
-                              "error.implementation_error_dbinstance_must_implement_interface",
-                              new String[] { class1.toString() }));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_dbinstance_must_implement_interface",
+              new String[]
+              { class1.toString() }));
     }
     if (fetchableDbs == null)
     {
       return null;
     }
     String[] sources = null;
-    Vector<String> src = new Vector<String>();
+    Vector<String> src = new Vector<>();
     Enumeration<String> dbs = fetchableDbs.keys();
     while (dbs.hasMoreElements())
     {
@@ -418,7 +415,7 @@ public class ASequenceFetcher
 
   public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
   {
-    List<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> prlist = new ArrayList<>();
     for (String fetchable : getSupportedDb())
     {
       for (DbSourceProxy pr : getSourceProxy(fetchable))
@@ -436,4 +433,28 @@ 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;
+  }
 }