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[jalview.git] / src / jalview / ws / dbsources / EmblXmlSource.java

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 01f502b..7a1ed17 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
  * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
  * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.ws.dbsources;\r
 \r
@@ -45,8 +44,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * retrieve and parse an emblxml file\r
    * \r
    * @param emprefx\r
-   *                either EMBL or EMBLCDS strings are allowed - anything else\r
-   *                will not retrieve emblxml\r
+   *          either EMBL or EMBLCDS strings are allowed - anything else will\r
+   *          not retrieve emblxml\r
    * @param query\r
    * @return\r
    * @throws Exception\r
@@ -74,11 +73,11 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
    * parse an emblxml file stored locally\r
    * \r
    * @param emprefx\r
-   *                either EMBL or EMBLCDS strings are allowed - anything else\r
-   *                will not retrieve emblxml\r
+   *          either EMBL or EMBLCDS strings are allowed - anything else will\r
+   *          not retrieve emblxml\r
    * @param query\r
    * @param file\r
-   *                the EMBL XML file containing the results of a query\r
+   *          the EMBL XML file containing the results of a query\r
    * @return\r
    * @throws Exception\r
    */\r
@@ -107,15 +106,15 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       {\r
         EmblEntry entry = (EmblEntry) i.next();\r
         SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:\r
-                                                                          // use\r
-                                                                          // !fetchNa,!fetchPeptide\r
-                                                                          // here\r
-                                                                          // instead\r
-                                                                          // -\r
-                                                                          // see\r
-                                                                          // todo\r
-                                                                          // in\r
-                                                                          // emblEntry\r
+        // use\r
+        // !fetchNa,!fetchPeptide\r
+        // here\r
+        // instead\r
+        // -\r
+        // see\r
+        // todo\r
+        // in\r
+        // emblEntry\r
         if (seqparts != null)\r
         {\r
           SequenceI[] newseqs = null;\r
@@ -137,7 +136,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
           for (int j = 0; j < seqparts.length; si++, j++)\r
           {\r
             newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on\r
-                                                        // dataset and refer\r
+            // dataset and refer\r
           }\r
           seqs = newseqs;\r
 \r