X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=d4bcfe8277af119a8f7715cec9274fba1041f932;hb=98af16ccc5890b980f0c4f3acfb72d7128e3a6f0;hp=7b455bf7f2dbfac92a48012525e003b89a634e99;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 7b455bf..d4bcfe8 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.AlignmentI;
@@ -86,10 +103,10 @@ public class ASequenceFetcher
                   "Don't know how to fetch from this database :" + db);
         DbSourceProxy fetcher = getSourceProxy(db);
         boolean doMultiple = fetcher.getAccessionSeparator() != null; // No
-                                                                      // separator
-                                                                      // - no
-                                                                      // Multiple
-                                                                      // Queries
+        // separator
+        // - no
+        // Multiple
+        // Queries
         Enumeration qs = query.elements();
         while (qs.hasMoreElements())
         {
@@ -98,20 +115,22 @@ public class ASequenceFetcher
           {
             qsb.append((String) qs.nextElement());
             if (qs.hasMoreElements() && doMultiple) // and not reached limit for
-                                                    // multiple queries at one
-                                                    // time for this source
+            // multiple queries at one
+            // time for this source
             {
               qsb.append(fetcher.getAccessionSeparator());
             }
           } while (doMultiple && qs.hasMoreElements());
-          
-          AlignmentI seqset=null;
-          try {
+
+          AlignmentI seqset = null;
+          try
+          {
             // create a fetcher and go to it
             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);
           }
@@ -176,7 +195,7 @@ public class ASequenceFetcher
     {
       ret = new SequenceI[rseqs.size()];
       Enumeration sqs = rseqs.elements();
-      int si=0;
+      int si = 0;
       while (sqs.hasMoreElements())
       {
         SequenceI s = (SequenceI) sqs.nextElement();
@@ -201,4 +220,115 @@ public class ASequenceFetcher
     return dbs;
   }
 
-}
\ No newline at end of file
+  /**
+   * constructs and instance of the proxy and registers it as a valid
+   * dbrefsource
+   * 
+   * @param dbSourceProxy
+   *          reference for class implementing
+   *          jalview.ws.seqfetcher.DbSourceProxy
+   * @throws java.lang.IllegalArgumentException
+   *           if class does not implement jalview.ws.seqfetcher.DbSourceProxy
+   */
+  protected void addDBRefSourceImpl(Class dbSourceProxy)
+          throws java.lang.IllegalArgumentException
+  {
+    DbSourceProxy proxy = null;
+    try
+    {
+      Object proxyObj = dbSourceProxy.getConstructor(null)
+              .newInstance(null);
+      if (!DbSourceProxy.class.isInstance(proxyObj))
+      {
+        throw new IllegalArgumentException(
+                dbSourceProxy.toString()
+                        + " does not implement the jalview.ws.seqfetcher.DbSourceProxy");
+      }
+      proxy = (DbSourceProxy) proxyObj;
+    } catch (IllegalArgumentException e)
+    {
+      throw e;
+    } catch (Exception e)
+    {
+      // Serious problems if this happens.
+      throw new Error("DBRefSource Implementation Exception", e);
+    }
+    addDbRefSourceImpl(proxy);
+  }
+
+  /**
+   * add the properly initialised DbSourceProxy object 'proxy' to the list of
+   * sequence fetchers
+   * 
+   * @param proxy
+   */
+  protected void addDbRefSourceImpl(DbSourceProxy proxy)
+  {
+    if (proxy != null)
+    {
+      if (FETCHABLEDBS == null)
+      {
+        FETCHABLEDBS = new Hashtable();
+      }
+      FETCHABLEDBS.put(proxy.getDbSource(), proxy);
+    }
+  }
+
+  /**
+   * test if the database handler for dbName contains the given dbProperty
+   * 
+   * @param dbName
+   * @param dbProperty
+   * @return true if proxy has the given property
+   */
+  public boolean hasDbSourceProperty(String dbName, String dbProperty)
+  {
+    // TODO: decide if invalidDbName exception is thrown here.
+    DbSourceProxy proxy = getSourceProxy(dbName);
+    if (proxy != null)
+    {
+      if (proxy.getDbSourceProperties() != null)
+      {
+        return proxy.getDbSourceProperties().containsKey(dbProperty);
+      }
+    }
+    return false;
+  }
+
+  /**
+   * select sources which are implemented by instances of the given class
+   * 
+   * @param class that implements DbSourceProxy
+   * @return null or vector of source names for fetchers
+   */
+  public String[] getDbInstances(Class class1)
+  {
+    if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
+    {
+      throw new Error(
+              "Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given '"
+                      + class1 + "')");
+    }
+    if (FETCHABLEDBS == null)
+    {
+      return null;
+    }
+    String[] sources = null;
+    Vector src = new Vector();
+    Enumeration dbs = FETCHABLEDBS.keys();
+    while (dbs.hasMoreElements())
+    {
+      String dbn = (String) dbs.nextElement();
+      DbSourceProxy dbp = (DbSourceProxy) FETCHABLEDBS.get(dbn);
+      if (class1.isAssignableFrom(dbp.getClass()))
+      {
+        src.addElement(dbn);
+      }
+    }
+    if (src.size() > 0)
+    {
+      src.copyInto(sources = new String[src.size()]);
+    }
+    return sources;
+  }
+}