broad.core.siphy.ConservedPWMScanner Member List

This is the complete list of members for broad.core.siphy.ConservedPWMScanner, including all inherited members.

ConservedPWMScanner(String pwmFile)	broad.core.siphy.ConservedPWMScanner
ConservedPWMScanner(List< PositionWeightMatrix > matrices)	broad.core.siphy.ConservedPWMScanner
getAlignmentChunkSize()	broad.core.siphy.ConservedPWMScanner
getPWMiterator()	broad.core.siphy.ConservedPWMScanner
scan(MAFIO chrMafIO, List< BED > annotations, int shuffles, float seedMinScore)	broad.core.siphy.ConservedPWMScanner
setAlignmentChunkSize(int alignmentChunkSize)	broad.core.siphy.ConservedPWMScanner
setBackgroundModel(AnnotationReader<?extends GenomicAnnotation > reader, Map< String, Sequence > org)	broad.core.siphy.ConservedPWMScanner
setIgnoreList(List< String > ignoreList)	broad.core.siphy.ConservedPWMScanner
setModel(EvolutionaryModel model)	broad.core.siphy.ConservedPWMScanner
slidePWM(PositionWeightMatrix pwm, double minSeedScore, short[] encodedRef, List< int[]> ungappedChunks, int numPermutations)	broad.core.siphy.ConservedPWMScanner	protected