jalview 2.5 release banner

[jalview.git] / src / jalview / ws / MsaWSThread.java

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 5189b91..7142e5c 100644 (file)
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.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;\r
 \r
@@ -66,9 +65,9 @@ class MsaWSThread extends WSThread implements WSClientI
      * MsaWSJob\r
      * \r
      * @param jobNum\r
-     *                int\r
+     *          int\r
      * @param jobId\r
-     *                String\r
+     *          String\r
      */\r
     public MsaWSJob(int jobNum, SequenceI[] inSeqs)\r
     {\r
@@ -92,9 +91,9 @@ class MsaWSThread extends WSThread implements WSClientI
      * prepare input sequences for MsaWS service\r
      * \r
      * @param seqs\r
-     *                jalview sequences to be prepared\r
+     *          jalview sequences to be prepared\r
      * @param minlen\r
-     *                minimum number of residues required for this MsaWS service\r
+     *          minimum number of residues required for this MsaWS service\r
      * @return true if seqs contains sequences to be submitted to service.\r
      */\r
     private boolean prepareInput(SequenceI[] seqs, int minlen)\r
@@ -303,9 +302,9 @@ class MsaWSThread extends WSThread implements WSClientI
    * set basic options for this (group) of Msa jobs\r
    * \r
    * @param subgaps\r
-   *                boolean\r
+   *          boolean\r
    * @param presorder\r
-   *                boolean\r
+   *          boolean\r
    */\r
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
@@ -322,15 +321,15 @@ class MsaWSThread extends WSThread implements WSClientI
    * create one or more Msa jobs to align visible seuqences in _msa\r
    * \r
    * @param title\r
-   *                String\r
+   *          String\r
    * @param _msa\r
-   *                AlignmentView\r
+   *          AlignmentView\r
    * @param subgaps\r
-   *                boolean\r
+   *          boolean\r
    * @param presorder\r
-   *                boolean\r
+   *          boolean\r
    * @param seqset\r
-   *                Alignment\r
+   *          Alignment\r
    */\r
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r