import java.io.Writer;
import java.util.List;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.ForesterUtil;
public class SequenceWriter {
FASTA;
}
- public static StringBuilder toFasta( final Sequence seq, final int width ) {
+ public static StringBuilder toFasta( final MolecularSequence seq, final int width ) {
return toFasta( seq.getIdentifier(), seq.getMolecularSequenceAsString(), width );
}
return sb;
}
- public static void toFasta( final Sequence seq, final Writer w, final int width ) throws IOException {
+ public static void toFasta( final MolecularSequence seq, final Writer w, final int width ) throws IOException {
w.write( ">" );
- w.write( seq.getIdentifier().toString() );
+ w.write( seq.getIdentifier() );
w.write( ForesterUtil.LINE_SEPARATOR );
if ( ( width < 1 ) || ( width >= seq.getLength() ) ) {
w.write( seq.getMolecularSequence() );
}
}
- public static void writeSeqs( final List<Sequence> seqs, final File file, final SEQ_FORMAT format, final int width )
- throws IOException {
+ public static void writeSeqs( final List<MolecularSequence> seqs,
+ final File file,
+ final SEQ_FORMAT format,
+ final int width ) throws IOException {
final Writer w = ForesterUtil.createBufferedWriter( file );
SequenceWriter.writeSeqs( seqs, w, format, width );
w.close();
}
- public static void writeSeqs( final List<Sequence> seqs,
+ public static void writeSeqs( final List<MolecularSequence> seqs,
final Writer writer,
final SEQ_FORMAT format,
final int width ) throws IOException {
switch ( format ) {
case FASTA:
- for( final Sequence s : seqs ) {
+ for( final MolecularSequence s : seqs ) {
toFasta( s, writer, width );
writer.write( ForesterUtil.LINE_SEPARATOR );
}