Loading data

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Most simple way for loading DNA-sequences from a FastA file:

Sample data = new DNASample( home+"myfile.fa" );

Loading DNA-sequences from a FastA file:

//create a DNA-alphabet
AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );
 
//create a Sample using the alphabet from above in FastA-format
data = new Sample( container, new SparseStringExtractor( home+"myfile.fa", StringExtractor.FASTA ));

Loading DNA-sequences from a plain text file:

//create a DNA-alphabet
AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );
 
//create a Sample using the alphabet from above
data = new Sample( container, new SparseStringExtractor( home+"myfile.txt" ));


Creating a Sample from a BioJava SequenceIterator:

//defining the ids, we want to obtain from NCBI Genbank:
GenbankRichSequenceDB db = new GenbankRichSequenceDB();
 
SimpleSequenceIterator it = new SimpleSequenceIterator(
		db.getRichSequence( "NC_001284.2" ),
		db.getRichSequence( "NC_000932.1" )
	);
 
//conversion to Jstacs Sample
Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null );
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