X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=34eace418f27ed7921c20679d6e73fbe995a35e7;hb=66993ec5b2bbc67ed10836d2288d938f6c368076;hp=7f5c6801865c9d076db0301bfc84841333491859;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 7f5c680..34eace4 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -1,23 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 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;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
 
 public class AMSAFile extends jalview.io.FastaFile
 {
@@ -32,14 +39,26 @@ public class AMSAFile extends jalview.io.FastaFile
     this.al = al;
   }
 
+  public AMSAFile(String inFile, DataSourceType sourceType)
+          throws IOException
+  {
+    super(inFile, sourceType);
+  }
+
+  public AMSAFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  public String print()
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
-    super.print(getSeqsAsArray());
+    super.print(sqs, jvsuffix);
 
     AlignmentAnnotation aa;
     if (al.getAlignmentAnnotation() != null)
@@ -60,7 +79,7 @@ public class AMSAFile extends jalview.io.FastaFile
           out.append(" " + aa.description);
         }
 
-        out.append("\n");
+        out.append(newline);
 
         int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
                 + 1;
@@ -93,7 +112,7 @@ public class AMSAFile extends jalview.io.FastaFile
             out.append(ch);
 
           }
-          out.append("\n");
+          out.append(newline);
         }
       }
     }