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

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 272b147..98c9506 100644 (file)
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.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
@@ -38,7 +37,8 @@ class JPredThread extends WSThread implements WSClientI
     // TODO: make JPredJob deal only with what was sent to and received from a\r
     // JNet service\r
     int[] predMap = null; // mapping from sequence(i) to the original\r
-                          // sequence(predMap[i]) being predicted on\r
+\r
+    // sequence(predMap[i]) being predicted on\r
 \r
     vamsas.objects.simple.Sequence sequence;\r
 \r
@@ -47,8 +47,9 @@ class JPredThread extends WSThread implements WSClientI
     java.util.Hashtable SequenceInfo = null;\r
 \r
     int msaIndex = 0; // the position of the original sequence in the array of\r
-                      // Sequences in the input object that this job holds a\r
-                      // prediction for\r
+\r
+    // Sequences in the input object that this job holds a\r
+    // prediction for\r
 \r
     /**\r
      * \r
@@ -270,7 +271,7 @@ class JPredThread extends WSThread implements WSClientI
       nview.pruneDeletions(ShiftList\r
               .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])\r
                       .gapMap())); // recover original prediction sequence's\r
-                                    // mapping to view.\r
+      // mapping to view.\r
       int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());\r
       int spos = 0;\r
       int offset = 0;\r
@@ -438,7 +439,7 @@ class JPredThread extends WSThread implements WSClientI
       else if (job.sequence != null)\r
       {\r
         job.jobId = server.predict(job.sequence); // debug like : job.jobId =\r
-                                                  // "/jobs/www-jpred/jp_Yatat29";//\r
+        // "/jobs/www-jpred/jp_Yatat29";//\r
       }\r
 \r
       if (job.jobId != null)\r
@@ -614,8 +615,9 @@ class JPredThread extends WSThread implements WSClientI
           {\r
             /*\r
              * java.lang.Object[] alandcolsel =\r
-             * input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
-             * if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
+             * input.getAlignmentAndColumnSelection\r
+             * (alignFrame.getViewport().getGapCharacter()); if\r
+             * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
              * if (msa) { throw new Error("Implementation Error! ColumnSelection\r
              * from input alignment will not map to result alignment!"); } } if\r
              * (!msa) { // update hidden regions to account for loss of gaps in\r