X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFastaFile.java;h=b867ba4982adff7976c142b1602f79c5ef55d39d;hb=refs%2Fheads%2Fj2s%2Fdevelop-bh;hp=3a7197fb92560bae173cf32b76cada7753998b61;hpb=474a52c5afda08ff9edbb6dda7a37c87be83f0d3;p=jalview.git
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 3a7197f..b867ba4 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,26 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
@@ -76,7 +82,7 @@ public class FastaFile extends AlignFile
StringBuffer sb = new StringBuffer();
boolean firstLine = true;
- String line,uline;
+ String line, uline;
Sequence seq = null;
boolean annotation = false;
@@ -138,23 +144,24 @@ public class FastaFile extends AlignFile
seqs.addElement(seq);
}
}
+
private AlignmentAnnotation makeAnnotation(SequenceI seq, StringBuffer sb)
{
Annotation[] anots = new Annotation[sb.length()];
char cb;
- for (int i=0;i