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public interface MutableMotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand. These operations are possible if the motif is mutable.
Mutable
Nested Class Summary |
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Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer |
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MotifDiscoverer.KindOfProfile |
Method Summary | |
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int[] |
determineNotSignificantPositionsFor(int motif,
Sample[] data,
double[][] weights,
int classIdx)
This method determines the number of not significant positions from each side of the motif with index motif . |
void |
initializeMotif(int motifIndex,
Sample data,
double[] weights)
This method allows to initialize the model of a motif manually using a weighted sample. |
boolean |
modifyMotif(int motifIndex,
double[] weightsLeft,
double[] weightsRight,
double[][][][] replacementLeft,
double[][][][] replacementRight,
int offsetLeft,
int offsetRight)
Manually modifies the motif model with index motifIndex . |
boolean |
modifyMotif(int motifIndex,
int offsetLeft,
int offsetRight)
Manually modifies the motif model with index motifIndex . |
Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer |
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getGlobalIndexOfMotifInComponent, getIndexOfMaximalComponentFor, getMotifLength, getNumberOfComponents, getNumberOfMotifs, getNumberOfMotifsInComponent, getProfileOfScoresFor, getStrandFor |
Methods inherited from interface de.jstacs.Storable |
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toXML |
Method Detail |
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int[] determineNotSignificantPositionsFor(int motif, Sample[] data, double[][] weights, int classIdx)
motif
.
motif
- the index of the motif in the motif discovererdata
- an array Sample
s, each array-entry represents on classweights
- the weights of each Sequence
for each classclassIdx
- the index of the current class in classCounts
Mutable.determineNotSignificantPositions(double, double[], double[], double[][][][], double[][][][], double)
,
modifyMotif(int, int, int)
,
modifyMotif(int, double[], double[], double[][][][], double[][][][], int, int)
boolean modifyMotif(int motifIndex, double[] weightsLeft, double[] weightsRight, double[][][][] replacementLeft, double[][][][] replacementRight, int offsetLeft, int offsetRight) throws Exception
motifIndex
. The two offsets 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.
motifIndex
- the index of the motif in the motif discovererweightsLeft
- the weights for the left contrast distributionsweightsRight
- the weights for the right contrast 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
Exception
boolean modifyMotif(int motifIndex, int offsetLeft, int offsetRight) throws Exception
motifIndex
. The two offsets 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. The distribution for sequences to the left and right side of the motif shall be computed internally.
motifIndex
- the index of the motif in the motif discovereroffsetLeft
- the offset on the left sideoffsetRight
- the offset on the right side
true
if the motif model was modified otherwise false
Exception
modifyMotif(int, double[], double[], double[][][][], double[][][][], int, int)
void initializeMotif(int motifIndex, Sample data, double[] weights) throws Exception
motifIndex
- the index of the motif in the motif discovererdata
- the sample of sequencesweights
- either null
or an array of length data.getNumberofElements()
with non-negative weights.
Exception
- if initialize was not possible
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