Loading data: Difference between revisions
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<source lang="java5"> | <source lang="java5"> | ||
//defining the ids, we want to obtain from NCBI Genbank: | //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 | //conversion to Jstacs Sample | ||
Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null ); | Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null ); | ||
</source> | </source> |
Revision as of 09:29, 29 October 2008
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
Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100 ) );
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
Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100, StringExtractor.FASTA ) );
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 );