jalview 2.5 release banner

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index db95c71..65e84d1 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.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.datamodel;\r
 \r
@@ -107,7 +106,7 @@ public class AlignmentView
    * regions\r
    * \r
    * @param gapCharacter\r
-   *                char\r
+   *          char\r
    * @return Object[] { SequenceI[], ColumnSelection}\r
    */\r
   public Object[] getAlignmentAndColumnSelection(char gapCharacter)\r
@@ -124,7 +123,7 @@ public class AlignmentView
    * getSequenceStrings\r
    * \r
    * @param c\r
-   *                char\r
+   *          char\r
    * @return String[]\r
    */\r
   public String[] getSequenceStrings(char c)\r
@@ -170,7 +169,7 @@ public class AlignmentView
    * get the contiguous subalignments in an alignment view.\r
    * \r
    * @param gapCharacter\r
-   *                char\r
+   *          char\r
    * @return SequenceI[][]\r
    */\r
   public SequenceI[][] getVisibleContigs(char gapCharacter)\r
@@ -193,7 +192,7 @@ public class AlignmentView
           njobs++;\r
         }\r
         fwidth += contigs[contig + 2]; // end up with full region width\r
-                                        // (including hidden regions)\r
+        // (including hidden regions)\r
         start = contigs[contig + 1] + contigs[contig + 2];\r
       }\r
       if (start < fwidth)\r
@@ -247,9 +246,9 @@ public class AlignmentView
    * sub alignments\r
    * \r
    * @param nvismsa\r
-   *                SequenceI[][]\r
+   *          SequenceI[][]\r
    * @param orders\r
-   *                AlignmentOrder[] corresponding to each SequenceI[] block.\r
+   *          AlignmentOrder[] corresponding to each SequenceI[] block.\r
    * @return Object[]\r
    */\r
   public Object[] getUpdatedView(SequenceI[][] nvismsa,\r
@@ -294,7 +293,7 @@ public class AlignmentView
                                 + sequences.length + ")");\r
               }\r
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded\r
-                                            // here.\r
+              // here.\r
               for (int s = 0; s < mseq.length; s++)\r
               {\r
                 if (alignment[s] == null)\r
@@ -495,7 +494,7 @@ public class AlignmentView
           nvis++;\r
         }\r
         fwidth += contigs[contig + 2]; // end up with full region width\r
-                                        // (including hidden regions)\r
+        // (including hidden regions)\r
         start = contigs[contig + 1] + contigs[contig + 2];\r
       }\r
       if (start < fwidth)\r