bio

Type Members

1. abstract class AbstractSequence extends AnyRef

   

2. class Alignment[T] extends AnyRef

   

   An Alignment has an (immutable) list of GappedSequences.

   An Alignment has an (immutable) list of GappedSequences. A Sequence can consist of nucleotides, amino acids and/or gaps. Each of these can have attributes, sequences can have attributes and the Alignment can have attributes.

3. abstract class Attribute extends AnyRef

   

   Base class for all attributes

4. class FastaReader extends Iterator[(String, String, String)]

   

5. class FastaWriter extends AnyRef

   

6. class GappedConvert[T] extends StringConverter[T]

   

7. abstract class Message extends AnyRef

   

8. class PamlReader extends Iterator[(String, String)]

   

   PamlReader opens a file and parses the PAML Phylip CODON contents using an iterator.

   PamlReader opens a file and parses the PAML Phylip CODON contents using an iterator. Rather than using BioJava's PHYLIPReader, which only allows 9 char tags, we roll our own as PAML is more relaxed on the tag. PAML wants more than 2 spaces after the ID. Essentially it is a simple format, where you know the size of the sequences - just remove the spaces.

   Note: no support for interleaved files

9. class PamlWriter extends AnyRef

   

10. class PhylipReader extends Iterator[(String, String)]

    

    PhylipReader opens a file and parses the Phylip contents using an iterator.

    PhylipReader opens a file and parses the Phylip contents using an iterator. This implementation is not ready - it may use the BioJava PHYLIPFileListener as below, but one problem is that ID names are restricted to 9 characters.

    Note: this is a hack. I am trying to get to grips with the BioJava way of doing this - and it does not map easily to an iterator.

11. class SegmentizeGappedSequence[T] extends AnyRef

    

12. abstract class Sequence[T] extends AbstractSequence with AttributeAccess

    

13. class SequenceAlignment[Sequence] extends AnyRef

    

    Alignment container for Sequences.

    Alignment container for Sequences. Each sequence has an ID that can not be lost. The reason for this class are the functions that update columns. (NYI)

14. class SequenceTranslation[T] extends AnyRef

    

15. trait SparseAlignment[T] extends AnyRef

    

    Trait contains methods for modifying sparse alignments

16. abstract class StatusMessage extends AnyRef

    

17. abstract class StringConverter[T] extends AnyRef

    

18. abstract class Symbol extends AnyRef

    

    Base class for all (one letter) symbols used in BioScala.