Package de.unibi.techfak.jpredictor.motifs

Interface Summary

MotifSearcher	This interface should be implemented by classes that wants to define methods for searching motifs.
MotifSearchWithError	The Interface MotifSearchWithError should be implemented by classes that wants to define methods for searching motifs on sequences, where errors in the match are allowed.
MotifSearchWithThreshold	The Interface MotifSearchWithThreshold should be implemented by classes that wants to define methods for searching motifs on sequences, where every position is scored and the threshold is used to distinguish between a hit and none.
SequenceWindowScorer	The Interface SequenceWindowScorer should be implemented by classes that wants to support scoring in any kind.

Class Summary

DoubleMotif	Class for defining a special MultiMotif - only two motifs are comprised within this motif, furthermore the distances between them and a score.
FoundMotifStruct	Class for holding the results when searching through the operator.
Motif	Abstract superclass of all classes representing a motif.
MotifFilter	This class holds some filters used for filtering strings to become a sequence or regular expression motif.
MotifList	Stores motifs in a Vector.
MotifSearchAdapter	An abstract adapter class for searching motifs on a sequence.
MultiMotif	Superclass of all classes representing a pattern made of more then one motif.
PSPMotif	Contains a motif represented by probabilities for every base in every position (PSPM = position specific probability matrix).
PSSMotif	Contains a motif represented by scores for every base in every position (PSSM = position specific score matrix).
RegularExpressionMotif	Contains a regular expression sequence as motif, that is given as a string e.g.
SequenceMotif	Specialization of a RegularExpressionMotif.

Exception Summary

CycleInMultiMotifExeption	This exception is thrown, if a motif is inserted or added to a MultiMotif which would lead to a cycle in the MultiMotif
MissingCharSequenceException	Exception thrown if a motif wants to search itself but no sequence to search on was set previously.
MissingMotifException	This exception is thrown, if a motif is worked with but no appropriate representation of the motif was set.
MotifNotCompleteException	Thrown if a MultiMotif was not designed completely.