fetch database references for all EBI db + selected das sequence sources or a specifi...

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

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