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
Linear Supertypes
Iterator[(String, String)], TraversableOnce[(String, String)], GenTraversableOnce[(String, String)], AnyRef, Any
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Instance Constructors
newPamlReader(filename: String)
Type Members
classGroupedIterator[B >: A] extends AbstractIterator[Seq[B]] with Iterator[Seq[B]]
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