X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=80206c09a64a1c6b02694e70da891d7fb6c2932c;hb=2f8f2ea4f2bde392c2618df6a682f42082c9528c;hp=61f2d8b4ba9ce316718923d1a91df6f9f16eea57;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 61f2d8b..80206c0 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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
+ * 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.dbsources;
 
@@ -45,8 +44,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * retrieve and parse an emblxml file
    * 
    * @param emprefx
-   *                either EMBL or EMBLCDS strings are allowed - anything else
-   *                will not retrieve emblxml
+   *          either EMBL or EMBLCDS strings are allowed - anything else will
+   *          not retrieve emblxml
    * @param query
    * @return
    * @throws Exception
@@ -59,8 +58,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     File reply;
     try
     {
-      reply = dbFetch.fetchDataAsFile(emprefx.toLowerCase() + ":"
-              + query.trim(), "emblxml", null);
+      reply = dbFetch.fetchDataAsFile(
+              emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
     } catch (Exception e)
     {
       stopQuery();
@@ -74,11 +73,11 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * parse an emblxml file stored locally
    * 
    * @param emprefx
-   *                either EMBL or EMBLCDS strings are allowed - anything else
-   *                will not retrieve emblxml
+   *          either EMBL or EMBLCDS strings are allowed - anything else will
+   *          not retrieve emblxml
    * @param query
    * @param file
-   *                the EMBL XML file containing the results of a query
+   *          the EMBL XML file containing the results of a query
    * @return
    * @throws Exception
    */
@@ -107,15 +106,15 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       {
         EmblEntry entry = (EmblEntry) i.next();
         SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
-                                                                          // use
-                                                                          // !fetchNa,!fetchPeptide
-                                                                          // here
-                                                                          // instead
-                                                                          // -
-                                                                          // see
-                                                                          // todo
-                                                                          // in
-                                                                          // emblEntry
+        // use
+        // !fetchNa,!fetchPeptide
+        // here
+        // instead
+        // -
+        // see
+        // todo
+        // in
+        // emblEntry
         if (seqparts != null)
         {
           SequenceI[] newseqs = null;
@@ -137,7 +136,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
           for (int j = 0; j < seqparts.length; si++, j++)
           {
             newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
-                                                        // dataset and refer
+            // dataset and refer
           }
           seqs = newseqs;