de.jstacs.data.bioJava

Class BioJavaAdapter

java.lang.Object

de.jstacs.data.bioJava.BioJavaAdapter

public class BioJavaAdapter
extends Object

This class provides static methods to convert BioJava datatypes ( SequenceIterator, Sequence) to DataSets and vice versa.

Here are two small examples how to create a RichSequenceIterator that can be used to create a DataSet.

GenbankRichSequenceDB db = new GenbankRichSequenceDB();
org.biojava.bio.seq.Sequence seq = db.getSequence( id );
RichSequenceIterator iter = new RichSequence.IOTools.SingleRichSeqIterator(seq);

or

RichSequenceIterator iter = RichSequence.IOTools.readFile( new File( fName ), null );

Author:

Jens Keilwagen, Jan Grau

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOTATION_ID A generic annotation ID for new annotations

Constructor Summary

Constructors

Constructor and Description
BioJavaAdapter()

Method Summary

Methods

Modifier and Type	Method and Description
static SequenceIterator	dataSetToSequenceIterator(DataSet sample, boolean flat, boolean alwaysUseDNAAlphabet) Creates a SequenceIterator from the DataSet sample preserving as much annotation as possible.
static DataSet	sequenceIteratorToDataSet(SequenceIterator it, FeatureFilter filter, AlphabetContainer con) This method creates a new DataSet from a SequenceIterator.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ANNOTATION_ID

public static final String ANNOTATION_ID

A generic annotation ID for new annotations

See Also:

Constant Field Values

Constructor Detail

BioJavaAdapter

public BioJavaAdapter()

Method Detail

sequenceIteratorToDataSet

public static DataSet sequenceIteratorToDataSet(SequenceIterator it,
                                FeatureFilter filter,
                                AlphabetContainer con)
                                         throws Exception

This method creates a new DataSet from a SequenceIterator. In cases where BioJava does return Sequences instead of a SequenceIterator, you can use a SimpleSequenceIterator to wrap them up.

Parameters:

it - the sequence iterator

filter - null or an arbitrary feature filter that determines which features will be adopted

con - the AlphabetContainer to use for the returned DataSet

Returns:

the Sequences in it converted to a DataSet

Throws:

Exception - if something went wrong

dataSetToSequenceIterator

public static SequenceIterator dataSetToSequenceIterator(DataSet sample,
                                         boolean flat,
                                         boolean alwaysUseDNAAlphabet)
                                                  throws WrongAlphabetException,
                                                         BioException

Creates a SequenceIterator from the DataSet sample preserving as much annotation as possible. This method works only for discrete alphabets.

Parameters:

sample - the DataSet

flat - indicates if the features should be flattened, this may be necessary to preserve all features, because some data formats do not support hierarchical features

alwaysUseDNAAlphabet - if true, always use a DNA alphabet

Returns:

the corresponding SequenceIterator

Throws:

WrongAlphabetException - if the alphabet of the DataSet is not discrete

BioException - if forwarded from BioJava