X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=8a8cf445571aba433882a710202331bc03c8cf63;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=0785ea2c044be3aeff136c4930d611cd8a6db9d9;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 0785ea2..8a8cf44 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.AlignmentI;
@@ -86,10 +104,10 @@ 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 +116,22 @@ 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 +196,7 @@ 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();
@@ -191,8 +211,8 @@ public class ASequenceFetcher
    * Retrieve an instance of the proxy for the given source
    * 
    * @param db
-   *          database source string TODO: add version string/wildcard for
-   *          retrieval of specific DB source/version combinations.
+   *                database source string TODO: add version string/wildcard for
+   *                retrieval of specific DB source/version combinations.
    * @return an instance of DbSourceProxy for that db.
    */
   public DbSourceProxy getSourceProxy(String db)
@@ -215,11 +235,11 @@ public class ASequenceFetcher
   protected void addDBRefSourceImpl(Class dbSourceProxy)
           throws java.lang.IllegalArgumentException
   {
-    DbSourceProxy proxy = null; 
+    DbSourceProxy proxy = null;
     try
     {
-      Object proxyObj = dbSourceProxy.getConstructor(
-              null).newInstance(null);
+      Object proxyObj = dbSourceProxy.getConstructor(null)
+              .newInstance(null);
       if (!DbSourceProxy.class.isInstance(proxyObj))
       {
         throw new IllegalArgumentException(
@@ -227,20 +247,21 @@ public class ASequenceFetcher
                         + " does not implement the jalview.ws.seqfetcher.DbSourceProxy");
       }
       proxy = (DbSourceProxy) proxyObj;
-    } 
-    catch (IllegalArgumentException e)
+    } catch (IllegalArgumentException e)
     {
       throw e;
-    }
-    catch (Exception 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
+   * add the properly initialised DbSourceProxy object 'proxy' to the list of
+   * sequence fetchers
+   * 
    * @param proxy
    */
   protected void addDbRefSourceImpl(DbSourceProxy proxy)
@@ -257,6 +278,7 @@ public class ASequenceFetcher
 
   /**
    * test if the database handler for dbName contains the given dbProperty
+   * 
    * @param dbName
    * @param dbProperty
    * @return true if proxy has the given property
@@ -265,9 +287,9 @@ public class ASequenceFetcher
   {
     // TODO: decide if invalidDbName exception is thrown here.
     DbSourceProxy proxy = getSourceProxy(dbName);
-    if (proxy!=null)
+    if (proxy != null)
     {
-      if (proxy.getDbSourceProperties()!=null)
+      if (proxy.getDbSourceProperties() != null)
       {
         return proxy.getDbSourceProperties().containsKey(dbProperty);
       }
@@ -275,4 +297,4 @@ public class ASequenceFetcher
     return false;
   }
 
-}
\ No newline at end of file
+}