X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=f4569dc3d6439655336be72db6cb325e9c5fa3ed;hb=2026a420963f094072607c0495b6369ba96e60c0;hp=ad291db0258ffb4bf835b6f3c799e9319dfd01d7;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index ad291db..f4569dc 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.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.io;
 
@@ -49,21 +48,20 @@ public class WSWUBlastClient
    * Creates a new WSWUBlastClient object.
    * 
    * @param al
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param ids
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
   {
     this.ap = ap;
     this.al = al;
-    output
-            .setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
-                    + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
-                    + "\n\nRunning WSWUBlast at EBI."
-                    + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
-                    + "\nSOAP-based services provided by the European Bioinformatics Institute."
-                    + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+    output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
+            + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
+            + "\n\nRunning WSWUBlast at EBI."
+            + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
+            + "\nSOAP-based services provided by the European Bioinformatics Institute."
+            + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
 
     Desktop.addInternalFrame(output,
             "BLASTing for unidentified sequences ", 800, 300);
@@ -86,9 +84,9 @@ public class WSWUBlastClient
    * DOCUMENT ME!
    * 
    * @param id1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param res
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void parseResult(Sequence seq, String res)
   {
@@ -287,8 +285,8 @@ public class WSWUBlastClient
         Data inputs[] = new Data[1];
         Data input = new Data();
         input.setType("sequence");
-        input.setContent(AlignSeq.extractGaps("-. ", sequence
-                .getSequenceAsString()));
+        input.setContent(AlignSeq.extractGaps("-. ",
+                sequence.getSequenceAsString()));
         inputs[0] = input;
 
         WSWUBlastService service = new WSWUBlastServiceLocator();