public interface CREModel
Modifier and Type | Field and Description |
---|---|
static boolean |
DEFAULT_RC |
Modifier and Type | Method and Description |
---|---|
MotifList |
expandAsMotifList()
Returns a MotifList containing the unambiguous Motifs that this cre represents.
|
java.lang.String[] |
expandAsStrings()
Returns an array of the strings of primary bases that this cre represents.
|
boolean |
generatesString(java.lang.String s)
Returns true if this model generates the given string at the current stringency, which can be specified by
setStringency(double) . |
java.util.Comparator<Motif> |
getComparator()
Returns a comparator that sorts arrays from greatest to least.
|
MotifList |
getHits(java.lang.String sequence)
Returns those sequences in sequence that match this pwm according to
generatesString(String) as a MotifList. |
java.lang.String |
getName()
Return a name that will be uniq to this type of model.
|
CREModel |
newInstanceOf(MotifList ml)
Must generate a new instance of the given CREModel based of the given MotifList.
|
Motif.ScoreData |
scoreString(java.lang.String sequence)
Returns the score that a given model would give to a sequence.
|
void |
setStringency(double d)
Sets the stringency of this model.
|
java.lang.String |
toString()
Just make it pretty and informative.
|
static final boolean DEFAULT_RC
MotifList expandAsMotifList() throws ExpansionTooLargeException
ExpansionTooLargeException
java.lang.String[] expandAsStrings() throws ExpansionTooLargeException
ExpansionTooLargeException
boolean generatesString(java.lang.String s)
setStringency(double)
.java.util.Comparator<Motif> getComparator()
MotifList getHits(java.lang.String sequence)
generatesString(String)
as a MotifList. The returned
MotifList is a set, meaning there are guarenteed to be no duplicates. The list is sorted, with the "best" motifs first down to the
"worst" motifs, however the implementing class decides to define it. The score of each Motif in the MotifList is the score assigned to
the corresponding string by the model. Note that depending on the nature of the score, some implementing classes with return a list in
ascending order by score, others in decending order, and still others may have no notion of a score. In general, you should trust the
order. Each class must guarantee that the list is sorted from "good" to "bad" by whatever scale makes sense for that model.
Specified by the CREModel interface.
java.lang.String getName()
CREModel newInstanceOf(MotifList ml)
Motif.ScoreData scoreString(java.lang.String sequence)
void setStringency(double d)
java.lang.String toString()
toString
in class java.lang.Object