| addColumn(double[] site) | broad.core.motif.PositionWeightMatrix | |
| addPseudoCounts() | broad.core.motif.PositionWeightMatrix | |
| addToCentroid(Matrix m, PositionWeightMatrix pwm) | broad.core.motif.PositionWeightMatrix | protected |
| centroidOf(Collection< PositionWeightMatrix > pwmSet) | broad.core.motif.PositionWeightMatrix | |
| computeScoreDistribution(float backgroundA, float backgroundC, float backgroundG, float backgroundT, int sampleSize) | broad.core.motif.PositionWeightMatrix | |
| copy() | broad.core.motif.PositionWeightMatrix | |
| createIsoPWM(double[] column, String name) | broad.core.motif.PositionWeightMatrix | |
| distanceFrom(PositionWeightMatrix other) | broad.core.motif.PositionWeightMatrix | |
| flatWeightMatrix(double infoTh) | broad.core.motif.PositionWeightMatrix | |
| getAlignDir() | broad.core.motif.PositionWeightMatrix | |
| getConsensus() | broad.core.motif.PositionWeightMatrix | |
| getLeftHighInfoStart() | broad.core.motif.PositionWeightMatrix | |
| getLogLikelihood(char[] s) | broad.core.motif.PositionWeightMatrix | |
| getLogLikelihood(int[] s) | broad.core.motif.PositionWeightMatrix | |
| getLogLikelihood(short[] encodedSequence, int i) | broad.core.motif.PositionWeightMatrix | |
| getName() | broad.core.motif.PositionWeightMatrix | |
| getNextKmer(int[] kmer) | broad.core.motif.PositionWeightMatrix | static |
| getNumCol() | broad.core.motif.PositionWeightMatrix | |
| getNumEndPosToErase(double infoThreshold) | broad.core.motif.PositionWeightMatrix | |
| getNumStartPosToErase(double infoThreshold) | broad.core.motif.PositionWeightMatrix | |
| getRightHighInfoStart() | broad.core.motif.PositionWeightMatrix | |
| ic() | broad.core.motif.PositionWeightMatrix | |
| isEmpty() | broad.core.motif.PositionWeightMatrix | |
| kullbackLeiber(PositionWeightMatrix other) | broad.core.motif.PositionWeightMatrix | |
| match(SequenceRegion region, double[] background, float minScore) | broad.core.motif.PositionWeightMatrix | |
| permuteColumns(boolean preserveGCDinucleotides) | broad.core.motif.PositionWeightMatrix | |
| PositionWeightMatrix(String name) | broad.core.motif.PositionWeightMatrix | |
| printKmer(int[] kmer) | broad.core.motif.PositionWeightMatrix | |
| printRefinedWeightMatrix(double infoThreshold) | broad.core.motif.PositionWeightMatrix | |
| reverseComplement() | broad.core.motif.PositionWeightMatrix | |
| setAlignPos(int minAlignNum) | broad.core.motif.PositionWeightMatrix | |
| setMatrix(List< double[]> sites) | broad.core.motif.PositionWeightMatrix | |
| setMatrixFromRawData(List< String[]> unparsedRows) | broad.core.motif.PositionWeightMatrix | |
| setName(String name) | broad.core.motif.PositionWeightMatrix | |
| setUnparsedRow(int colNum, String[] unparsedRow) | broad.core.motif.PositionWeightMatrix | |
| trimByInformationContent(double ic) | broad.core.motif.PositionWeightMatrix | |
| write(BufferedWriter bw, NumberFormat formatter) | broad.core.motif.PositionWeightMatrix | |
| writeUNIPROBE(BufferedWriter bw, NumberFormat formatter) | broad.core.motif.PositionWeightMatrix | |
1.8.7
