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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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void |
adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters. |
void |
initializeMotif(int motifIndex,
DataSet data,
double[] weights)
This method allows to initialize the model of a motif manually using a weighted sample. |
void |
initializeMotifRandomly(int motif)
This method initializes the motif with index motif randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean) . |
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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clone, getGlobalIndexOfMotifInComponent, getIndexOfMaximalComponentFor, getMotifLength, getNumberOfComponents, getNumberOfMotifs, getNumberOfMotifsInComponent, getProfileOfScoresFor, getStrandProbabilitiesFor |
Methods inherited from interface de.jstacs.Storable |
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toXML |
Method Detail |
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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
- if some unexpected error occurred during the modificationmodifyMotif(int, int, int)
,
Mutable.modify(int, int)
void initializeMotif(int motifIndex, DataSet 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 possiblevoid initializeMotifRandomly(int motif) throws Exception
motif
randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean)
.
Furthermore, if available, it also initializes the positional distribution.
motif
- the index of the motif
Exception
- either if the index is wrong or if it is thrown by the method DifferentiableSequenceScore.initializeFunctionRandomly(boolean)
void adjustHiddenParameters(int index, DataSet[] data, double[][] weights) throws Exception
index
- the index of the class of this MutableMotifDiscoverer
data
- the array of data for all classesweights
- the weights for all sequences in data
Exception
- thrown if the hidden parameters could not be adjusted
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