jalview 2.5 release banner

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 2735fb3..dc0526d 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * 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.
  * 
- * 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
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.io;
 
@@ -62,16 +61,15 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   /**
-   * Format a vector of sequences as a flat alignment file.
-   * TODO: allow caller to detect errors and warnings encountered when generating output
-   *
+   * Format a vector of sequences as a flat alignment file. TODO: allow caller
+   * to detect errors and warnings encountered when generating output
+   * 
    * 
    * @param format
-   *                Format string as givien in the AppletFormatAdaptor list
-   *                (exact match to name of class implementing file io for that
-   *                format)
+   *          Format string as givien in the AppletFormatAdaptor list (exact
+   *          match to name of class implementing file io for that format)
    * @param seqs
-   *                vector of sequences to write
+   *          vector of sequences to write
    * 
    * @return String containing sequences in desired format
    */
@@ -126,8 +124,8 @@ public class FormatAdapter extends AppletFormatAdapter
       }
       /*
        * amsa is not supported by this function - it requires an alignment
-       * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA")) {
-       * afile = new AMSAFile(); afile.addJVSuffix(
+       * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA"))
+       * { afile = new AMSAFile(); afile.addJVSuffix(
        * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
        */
 
@@ -135,7 +133,8 @@ public class FormatAdapter extends AppletFormatAdapter
       String afileresp = afile.print();
       if (afile.hasWarningMessage())
       {
-        System.err.println("Warning raised when writing as "+format+" : "+afile.getWarningMessage());
+        System.err.println("Warning raised when writing as " + format
+                + " : " + afile.getWarningMessage());
       }
       return afileresp;
     } catch (Exception e)
@@ -177,10 +176,9 @@ public class FormatAdapter extends AppletFormatAdapter
    * @param format
    * @param alignment
    * @param omitHidden
-   *                sequence strings to write out in order of sequences in
-   *                alignment
+   *          sequence strings to write out in order of sequences in alignment
    * @param colSel
-   *                defines hidden columns that are edited out of annotation
+   *          defines hidden columns that are edited out of annotation
    * @return string representation of the alignment formatted as format
    */
   public String formatSequences(String format, AlignmentI alignment,
@@ -225,10 +223,10 @@ public class FormatAdapter extends AppletFormatAdapter
    * Application only formats like 'Jalview'.
    * 
    * @param format
-   *                a format string to be compared with list of readable or writable formats (READABLE_FORMATS
-   *                or WRITABLE_FORMATS)
+   *          a format string to be compared with list of readable or writable
+   *          formats (READABLE_FORMATS or WRITABLE_FORMATS)
    * @param forwriting
-   *                when true, format is checked against list of writable formats.
+   *          when true, format is checked against list of writable formats.
    * @return true if format is valid
    */
   public static final boolean isValidIOFormat(String format,