X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FAMSAFile.java;h=34eace418f27ed7921c20679d6e73fbe995a35e7;hb=efb5cfa00ee832a62dfdf59f5fb847a0e16424d9;hp=0a4624b3802440c1e3ad80bd0d22f91107190e0f;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 0a4624b..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 2.6)
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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);
}
}
}