Download

    biojava-seqxml-1.0.tar.gz

Usage

   

  Reading with the standard BioJava IOTools:

1. Class.forName("org.biojavax.bio.seq.io.SeqXMLFormat");
   

2. Namespace ns = RichObjectFactory.getDefaultNamespace();
   

3. RichSequenceIterator seqs = RichSequence.IOTools.readFile(seqXMLFile,ns);
   

  Writing individual sequences:

1. import org.biojavax.bio.seq.io.SeqXMLFormat;
   

2. 
   

3. RichSequenceFormat seqXMLWrite = new SeqXMLFormat();
   

4. seqXMLWrite.setPrintStream(System.out);
   

5. seqXMLWrite.beginWriting();
   

6. while(seqs.hasNext())
   

7.     seqXMLWrite.writeSequence(seqs.nextRichSequence() ,ns);
   

8. seqXMLWrite.finishWriting();
   

    Stream writing:

1. 
   

2. import org.biojavax.bio.seq.io.SeqXMLFormat;
   

3. 
   

4. RichSequenceFormat seqXMLWrite = new SeqXMLFormat();
   

5. RichStreamWriter seqsOut = new RichStreamWriter(System.out, seqXMLWrite);
   

6. seqsOut.writeStream(seqs, ns);