Package de.unibi.techfak.jpredictor.sequences

Interface Summary

SequenceEnumeration

Classes which implement this interface intend to read streams (like a file) full of single sequences that are to be parted.

Class Summary

FastaReader	Class for adding filter functionality to the SequenceReader.
MappedCharSequence	Class for mapping a file or a stream to a characters sequence.
MultiFileReader	A MultiFileReader represents the logical concatenation of other Readers.
RawReader	Class for adding filter functionality to the SequenceReader and, if wished, discarding of new line characters, too.
ResetableReader	This class is designed for only one purpose: to make sure, mark and reset function on a stream.
Sequence	This class represents a sequence of DNA or RNA.
SequenceEnumerator	Class which implements the SequenceEnumeration-interface.
SequenceFilter	This class holds filters to filter sequences with.
SequenceInformationBlock	Holds the data for sequence blocks in the file, that are characterized by name, description, start and length.
SequenceReader	This class is designed as a wrapper for other readers with two purposes.

Exception Summary

NewSequenceBlockException	Exception thrown when working with the SequenceReader class.
NoMoreSequencesAvailableException	Exception thrown when working with the SequenceEnumeration interface
ResetNotSupportedException	Exception thrown when working with Readers.