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public interface MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.
Nested Class Summary | |
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static class |
MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile
should be returned. |
Method Summary | |
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MotifDiscoverer |
clone()
This method returns a deep clone of the instance. |
int |
getGlobalIndexOfMotifInComponent(int component,
int motif)
Returns the global index of the motif used in
component . |
int |
getIndexOfMaximalComponentFor(Sequence sequence)
Returns the index of the component with the maximal score for the sequence sequence . |
int |
getMotifLength(int motif)
This method returns the length of the motif with index motif
. |
int |
getNumberOfComponents()
Returns the number of components in this MotifDiscoverer . |
int |
getNumberOfMotifs()
Returns the number of motifs for this MotifDiscoverer . |
int |
getNumberOfMotifsInComponent(int component)
Returns the number of motifs that are used in the component component of this MotifDiscoverer . |
double[] |
getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
Returns the profile of the scores for component component
and motif motif at all possible start positions of the motif
in the sequence sequence beginning at startpos . |
double[] |
getStrandProbabilitiesFor(int component,
int motif,
Sequence sequence,
int startpos)
This method returns the probabilities of the strand orientations for a given subsequence if it is considered as site of the motif model in a specific component. |
Methods inherited from interface de.jstacs.Storable |
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toXML |
Method Detail |
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MotifDiscoverer clone() throws CloneNotSupportedException
CloneNotSupportedException
- if the instance could not be clonedCloneable
int getMotifLength(int motif)
motif
.
motif
- the index of the motif
motif
int getNumberOfComponents()
MotifDiscoverer
.
int getNumberOfMotifs()
MotifDiscoverer
.
int getNumberOfMotifsInComponent(int component)
component
of this MotifDiscoverer
.
component
- the component of the MotifDiscoverer
int getIndexOfMaximalComponentFor(Sequence sequence) throws Exception
sequence
.
sequence
- the given sequence
Exception
- if the index could not be computed for any reasonsint getGlobalIndexOfMotifInComponent(int component, int motif)
motif
used in
component
. The index returned must be at least 0 and less
than getNumberOfMotifs()
.
component
- the component indexmotif
- the motif index in the component
motif in component
getProfileOfScoresFor
double[] getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
throws Exception
- Returns the profile of the scores for component
component
and motif motif
at all possible start positions of the motif
in the sequence sequence
beginning at startpos
.
This array should be of length
sequence.length() - startpos - motifs[motif].length() + 1
.
A high score should encode for a probable start position.
- Parameters:
component
- the component indexmotif
- the index of the motif in the componentsequence
- the given sequencestartpos
- the start position in the sequencekind
- indicates the kind of profile
- Returns:
- the profile of scores
- Throws:
Exception
- if the score could not be computed for any reasons
getStrandProbabilitiesFor
double[] getStrandProbabilitiesFor(int component,
int motif,
Sequence sequence,
int startpos)
throws Exception
- This method returns the probabilities of the strand orientations for a given subsequence if it is
considered as site of the motif model in a specific component.
- Parameters:
component
- the component indexmotif
- the index of the motif in the componentsequence
- the given sequencestartpos
- the start position in the sequence
- Returns:
- the probabilities of the strand orientations
- Throws:
Exception
- if the strand could not be computed for any reasons
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