public class RankedMotifPair extends java.lang.Object implements java.lang.Comparable<RankedMotifPair>, java.lang.Cloneable
Modifier and Type | Class and Description |
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static class |
RankedMotifPair.FoundMotifComparator
Compares two RankedMotifPairPair objects solely by the natural ordering of the motif instance variables.
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Modifier and Type | Field and Description |
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boolean |
found
Intended to be used to flag whether the rank is high enough, but can be any boolean.
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Motif |
knownMotif
Intended to be the known motif, but can be any motif.
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Motif |
motif
Intended to be the found motif, but can be any motif.
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int |
rank
Intended to be the rank of the found motif, but can be any int.
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Constructor and Description |
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RankedMotifPair()
This default constructor sets both motif and knownMotif to invalid motifs whose scores are -Infinity; also sets rank to -1 and found to
false.
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RankedMotifPair(Motif foundMotif,
Motif knownMotif,
int rank)
Specifies the found motif, known motif, and rank of the found motif; found is set to false.
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Modifier and Type | Method and Description |
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java.lang.Object |
clone()
Performs a deep copy of this object, cloning each of the motifs.
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int |
compareTo(RankedMotifPair obj)
Orders by rank.
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boolean |
equals(java.lang.Object obj)
Returns true if and only if
Comparable.compareTo(Object) returns 0. |
static java.lang.String |
getHeader()
A string that represents the order that things will be printed by the toString method.
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void |
setFound(boolean b) |
java.lang.String |
toString()
Prints in the following order: rank found, knownMotif.score motif.sequence knownMotif.sequence; each field is tab-delimited.
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public boolean found
public Motif knownMotif
public Motif motif
public int rank
public RankedMotifPair()
public static java.lang.String getHeader()
public java.lang.Object clone()
clone
in class java.lang.Object
public int compareTo(RankedMotifPair obj)
compareTo
in interface java.lang.Comparable<RankedMotifPair>
public boolean equals(java.lang.Object obj)
Comparable.compareTo(Object)
returns 0.equals
in class java.lang.Object
public void setFound(boolean b)
public java.lang.String toString()
toString
in class java.lang.Object