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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f5a1494..8f1aa46 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3642,30 +3642,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   private void resetWebServiceMenu()
   {
     webService.removeAll();
-    // Temporary hack - DBRef Fetcher always top level ws entry.
-    JMenuItem rfetch = new JMenuItem("Fetch DB References");
-    rfetch
-            .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
-    webService.add(rfetch);
-    rfetch.addActionListener(new ActionListener()
-    {
-
-      public void actionPerformed(ActionEvent e)
-      {
-        new Thread(new Runnable()
-        {
-
-          public void run()
-          {
-            new jalview.ws.DBRefFetcher(alignPanel.av
-                    .getSequenceSelection(), alignPanel.alignFrame)
-                    .fetchDBRefs(false);
-          }
-        }).start();
-
-      }
-
-    });
+    build_fetchdbmenu(webService);
   }
 
   /*
@@ -4184,6 +4161,86 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return false;
   }
+  protected void build_fetchdbmenu(JMenu webService) {
+    // Temporary hack - DBRef Fetcher always top level ws entry.
+    // TODO We probably want to store a sequence database checklist in preferences and have checkboxes.. rather than individual sources selected here
+    JMenu rfetch = new JMenu("Fetch DB References");
+    rfetch
+            .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+    webService.add(rfetch);
+
+    JMenuItem fetchr = new JMenuItem("Standard Databases");
+    fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+    fetchr.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        new Thread(new Runnable()
+        {
+
+          public void run()
+          {
+            new jalview.ws.DBRefFetcher(alignPanel.av
+                    .getSequenceSelection(), alignPanel.alignFrame)
+                    .fetchDBRefs(false);
+          }
+        }).start();
+
+      }
+
+    });
+    rfetch.add(fetchr);
+    JMenu dfetch = new JMenu();
+    rfetch.add(dfetch);
+    jalview.ws.SequenceFetcher sf = SequenceFetcher.getSequenceFetcherSingleton(this);
+    String[] otherdb = sf.getOrderedSupportedSources(); 
+    // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+    // jalview.util.QuickSort.sort(otherdb, otherdb);
+    int comp=0,mcomp=15;
+    String mname=null;
+    if (otherdb!=null && otherdb.length>0)
+    {
+      for (int i=0; i<otherdb.length; i++)
+      {
+        String dbname =sf.getSourceProxy(otherdb[i]).getDbName();
+        if (mname == null)
+        {
+          mname = "from '"+dbname+"'";
+        }
+        fetchr = new JMenuItem(otherdb[i]);
+        final String[] dassource = new String[] { otherdb[i] };
+        fetchr.addActionListener(new ActionListener()
+        {
+
+          public void actionPerformed(ActionEvent e)
+          {
+            new Thread(new Runnable()
+            {
+
+              public void run()
+              {
+                new jalview.ws.DBRefFetcher(alignPanel.av
+                        .getSequenceSelection(), alignPanel.alignFrame, dassource)
+                        .fetchDBRefs(false);
+              }
+            }).start();
+          }
+          
+        });
+        fetchr.setToolTipText("Retrieve from "+dbname);
+        dfetch.add(fetchr);
+        if (comp++==mcomp || i==(otherdb.length-1))
+        {
+          dfetch.setText(mname+" to '"+dbname+"'");
+          rfetch.add(dfetch);
+          dfetch = new JMenu();
+          mname = null;
+          comp=0;
+        }
+      }
+    }
+  }
 }
 
 class PrintThread extends Thread

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