X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=be0a8b0b67aead74f34ea35e26fa40c5e00d6f4d;hb=1145380bdd6555637794c9db36624fa42a8818c8;hp=96ac7e8e84c7cc8940bcd901fbe128260986289e;hpb=5d55702b40b8a0b198a0a22b4fbb8458fa2bc7f4;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 96ac7e8..be0a8b0 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -21,6 +21,7 @@ package jalview.ws;
 import java.io.*;
 import java.util.*;
 
+import org.biojava.dasobert.dasregistry.DasSource;
 import org.exolab.castor.mapping.*;
 import org.exolab.castor.xml.*;
 import jalview.analysis.*;
@@ -62,7 +63,8 @@ public class DBRefFetcher implements Runnable
   }
 
   /**
-   * Creates a new SequenceFeatureFetcher object.
+   * Creates a new SequenceFeatureFetcher object and fetches from the
+   * currently selected set of databases.
    * 
    * @param seqs
    *                fetch references for these sequences
@@ -71,6 +73,20 @@ public class DBRefFetcher implements Runnable
    */
   public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
   {
+    this(seqs, af, null);
+  }
+  /**
+   * Creates a new SequenceFeatureFetcher object and fetches from the
+   * currently selected set of databases.
+   * 
+   * @param seqs
+   *                fetch references for these sequences
+   * @param af
+   *                the parent alignframe for progress bar monitoring.
+   * @param sources array of database source strings to query references from
+   */
+  public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)
+  {
     this.af = af;
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
@@ -83,17 +99,71 @@ public class DBRefFetcher implements Runnable
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
     sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
-    // select appropriate databases based on alignFrame context.
-    if (af.getViewport().getAlignment().isNucleotide())
+    if (sources==null)
     {
-      dbSources = DBRefSource.DNACODINGDBS;
+      // af.featureSettings_actionPerformed(null);
+      String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+      Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()
+              : new jalview.gui.DasSourceBrowser().getSelectedSources();
+      Enumeration en = dasselsrc.elements();
+      while (en.hasMoreElements())
+      {
+        DasSource src = (DasSource) en.nextElement();
+        selsources.addElement(src.getNickname());
+      }
+      int osel = 0;
+      for (int o=0;otherdb!=null && o<otherdb.length;o++)
+      {
+        if (!selsources.contains(otherdb[o]))
+        {
+          otherdb[o] = null;
+        } else {
+          osel++;
+        }
+      }
+      // select appropriate databases based on alignFrame context.
+      if (af.getViewport().getAlignment().isNucleotide())
+      {
+        defdb = DBRefSource.DNACODINGDBS;
+      }
+      else
+      {
+        defdb = DBRefSource.PROTEINDBS;
+      }
+      // append the selected sequence sources to the default dbs 
+      dbSources = new String[defdb.length+osel];
+      System.arraycopy(defdb, 0, dbSources, 0, defdb.length);
+      for (int o=0,op=defdb.length; otherdb!=null && o<otherdb.length; o++)
+      {
+        if (otherdb[o]!=null)
+        {
+          dbSources[op++] = otherdb[o];
+        }
+      }
+    } else {
+      // we assume the caller knows what they're doing and ensured that all the db source names are valid
+      dbSources = sources;
     }
-    else
+  }
+  /**
+   * retrieve all the das sequence sources and add them to the list of db sources to retrieve from 
+   */
+  public void appendAllDasSources()
+  {
+    if (dbSources == null)
+    {
+      dbSources = new String[] {};
+    }
+    // append additional sources
+    String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+    if (otherdb!=null && otherdb.length>0)
     {
-      dbSources = DBRefSource.PROTEINDBS;
+      String[] newsrc = new String[dbSources.length+otherdb.length];
+      System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);
+      System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);
+      dbSources = newsrc;
     }
   }
-
   /**
    * start the fetcher thread
    *