X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=8ffcaf74f69993fc59f82dadc2a6a966d04b4aee;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=993737b38cefcf8d311fe1a4aaa4cde80b42582a;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 993737b..8ffcaf7 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,20 +1,20 @@
 /*
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -33,17 +33,17 @@ public class JnetAnnotationMaker
    * adds the annotation parsed by prediction to al.
    * 
    * @param prediction
-   *                JPredFile
+   *          JPredFile
    * @param al
-   *                AlignmentI
+   *          AlignmentI
    * @param firstSeq
-   *                int the index of the sequence to attach the annotation to
-   *                (usually zero)
+   *          int the index of the sequence to attach the annotation to (usually
+   *          zero)
    * @param noMsa
-   *                boolean
+   *          boolean
    * @param delMap
-   *                mapping from columns in JPredFile prediction to residue
-   *                number in al.getSequence(firstSeq)
+   *          mapping from columns in JPredFile prediction to residue number in
+   *          al.getSequence(firstSeq)
    */
   public static void add_annotation(JPredFile prediction, AlignmentI al,
           int firstSeq, boolean noMsa, int[] delMap) throws Exception
@@ -96,8 +96,8 @@ public class JnetAnnotationMaker
           {
             for (int j = 0; j < width; j++)
             {
-              annotations[gapmap[j]] = new Annotation("", "", preds[i]
-                      .getCharAt(j), 0);
+              annotations[gapmap[j]] = new Annotation("", "",
+                      preds[i].getCharAt(j), 0);
             }
           }
           else
@@ -127,9 +127,9 @@ public class JnetAnnotationMaker
             {
               float value = new Float(preds[i].getCharAt(j) + "")
                       .floatValue();
-              annotations[gapmap[delMap[j]]] = new Annotation(preds[i]
-                      .getCharAt(j)
-                      + "", "", preds[i].getCharAt(j), value);
+              annotations[gapmap[delMap[j]]] = new Annotation(
+                      preds[i].getCharAt(j) + "", "",
+                      preds[i].getCharAt(j), value);
             }
           }
         }
@@ -147,9 +147,8 @@ public class JnetAnnotationMaker
           {
             for (int j = 0; j < width; j++)
             {
-              annotations[gapmap[delMap[j]]] = new Annotation(preds[i]
-                      .getCharAt(j)
-                      + "", "", ' ', 0);
+              annotations[gapmap[delMap[j]]] = new Annotation(
+                      preds[i].getCharAt(j) + "", "", ' ', 0);
             }
           }
         }