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

diff --git a/src/jalview/ws/SeqSearchWSThread.java b/src/jalview/ws/SeqSearchWSThread.java
index d96131d..2f28d64 100644 (file)
--- a/src/jalview/ws/SeqSearchWSThread.java
+++ b/src/jalview/ws/SeqSearchWSThread.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
@@ -63,9 +62,9 @@ class SeqSearchWSThread extends WSThread implements WSClientI
      * MsaWSJob\r
      * \r
      * @param jobNum\r
-     *                int\r
+     *          int\r
      * @param jobId\r
-     *                String\r
+     *          String\r
      */\r
     public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)\r
     {\r
@@ -89,9 +88,9 @@ class SeqSearchWSThread extends WSThread implements WSClientI
      * prepare input sequences for 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
@@ -110,11 +109,11 @@ class SeqSearchWSThread extends WSThread implements WSClientI
         }\r
       }\r
       boolean valid = nseqs >= 1; // need at least one sequence for valid input\r
-                                  // TODO: generalise\r
+      // TODO: generalise\r
       vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
               : null;\r
       boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted\r
-                                                        // with gaps\r
+      // with gaps\r
       for (int i = 0, n = 0; i < seqs.length; i++)\r
       {\r
 \r
@@ -318,9 +317,9 @@ class SeqSearchWSThread 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
   SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
@@ -335,15 +334,15 @@ class SeqSearchWSThread 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
   SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
@@ -648,8 +647,8 @@ class SeqSearchWSThread extends WSThread implements WSClientI
        * like this: 1. Merge each domain hit back onto the visible segments in\r
        * the same way as a Jnet prediction is mapped back\r
        * \r
-       * Object[] newview = input.getUpdatedView(results, orders, getGapChar()); //\r
-       * trash references to original result data for (int j = 0; j <\r
+       * Object[] newview = input.getUpdatedView(results, orders, getGapChar());\r
+       * // trash references to original result data for (int j = 0; j <\r
        * jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]\r
        * alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =\r
        * (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);\r