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public interface Mutable
This interface allows to modify a motif model.
Method Summary | |
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int[] |
determineNotSignificantPositions(double samples,
double[] weightsLeft,
double[] weightsRight,
double[][][][] contrastLeft,
double[][][][] contrastRight,
double sign)
This method determines the number of not significant positions from each side of the motif using the the significance level sign
and the contrast distributions of the left or right side,
contrastLeft and contrastRight ,
respectively. |
boolean |
modify(double[] weightsLeft,
double[] weightsRight,
double[][][][] replacementLeft,
double[][][][] replacementRight,
int offsetLeft,
int offsetRight)
Manually modifies the model. |
Method Detail |
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int[] determineNotSignificantPositions(double samples, double[] weightsLeft, double[] weightsRight, double[][][][] contrastLeft, double[][][][] contrastRight, double sign)
sign
and the contrast distributions of the left or right side,
contrastLeft
and contrastRight
,
respectively. The contrast array have four dimensions.
DNAAlphabet
,
the contrast array has the dimension new double[1][1][1][4]
. For the same example but with order 1, the contrast array has the dimension
new double[1][1][4][4]
. Left and right contrast can have different dimensions.
samples
- the summed weights of Sequence
containing this motifweightsLeft
- the weights for the left contrast distributionsweightsRight
- the weights for the right contrast distributionscontrastLeft
- the left contrast distributionscontrastRight
- the right contrast distributionssign
- the significance level
contrastLeft
and at position 1 the number of not
significant positions from the right side using
contrastRight
modify(double[], double[], double[][][][], double[][][][], int, int)
boolean modify(double[] weightsLeft, double[] weightsRight, double[][][][] replacementLeft, double[][][][] replacementRight, int offsetLeft, int offsetRight)
offsetLeft
and offsetRight
define how many positions the left or
right border positions shall be moved. Negative numbers indicate moves to
the left while positive numbers correspond to moves to the right.
weightsLeft
- the weights for the left replacement distributionsweightsRight
- the weights for the left replacement distributionsreplacementLeft
- the replacement distribution for the left sidereplacementRight
- the replacement distribution for the right sideoffsetLeft
- the offset on the left sideoffsetRight
- the offset on the right side
true
if the motif model was modified otherwise
false
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