package org.forester.io.writers;
+import java.io.File;
import java.io.IOException;
import java.io.Writer;
import java.util.List;
-import org.forester.sequence.BasicSequence;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.ForesterUtil;
public class SequenceWriter {
FASTA;
}
- public static void main( final String[] args ) {
- final Sequence s = BasicSequence.createAaSequence( "name", "abcdefghiiklmnap" );
- System.out.println( s.toString() );
- System.out.println( SequenceWriter.toFasta( s, 0 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 5 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 8 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 4 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 3 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 2 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 1 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 100 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 15 ).toString() );
- System.out.println( SequenceWriter.toFasta( s, 16 ).toString() );
+ public static StringBuilder toFasta( final MolecularSequence seq, final int width ) {
+ return toFasta( seq.getIdentifier(), seq.getMolecularSequenceAsString(), width );
}
- public static StringBuilder toFasta( final Sequence seq, final int width ) {
+ public static StringBuilder toFasta( final String name, final String mol_seq, final int width ) {
final StringBuilder sb = new StringBuilder();
sb.append( ">" );
- sb.append( seq.getIdentifier().toString() );
+ sb.append( name );
sb.append( ForesterUtil.LINE_SEPARATOR );
- if ( ( width < 1 ) || ( width >= seq.getLength() ) ) {
- sb.append( seq.getMolecularSequence() );
+ if ( ( width < 1 ) || ( width >= mol_seq.length() ) ) {
+ sb.append( mol_seq );
}
else {
- final int lines = seq.getLength() / width;
- final int rest = seq.getLength() - ( lines * width );
+ final int lines = mol_seq.length() / width;
+ final int rest = mol_seq.length() - ( lines * width );
for( int i = 0; i < lines; ++i ) {
- sb.append( seq.getMolecularSequence(), i * width, width );
+ sb.append( mol_seq, i * width, ( i + 1 ) * width );
if ( i < ( lines - 1 ) ) {
sb.append( ForesterUtil.LINE_SEPARATOR );
}
}
if ( rest > 0 ) {
sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( seq.getMolecularSequence(), lines * width, rest );
+ sb.append( mol_seq, lines * width, mol_seq.length() );
}
}
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,
+ 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<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 );
}