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java.lang.Object nix.affy.anno.BindingRegion
For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval.
Constructor Summary | |
BindingRegion(int rank,
double score,
java.lang.String chromosome,
int start,
int end,
int sizeNeighborhood)
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Method Summary | |
void |
compare(GeneGroup geneGrp)
Compares a binding region to a gene grp looking for where it is in relation to the binding region, 5', 3', overlap, contained? Saves all that overlap or are contained as well as the closest 5' and the closest 3'. |
int |
compareTo(java.lang.Object obj)
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static java.lang.String |
extractGeneGrps(java.util.ArrayList geneGrps,
boolean returnSummaryLine)
Returns summary line or name for each GeneGrp in ArrayList |
java.lang.String |
getChromosome()
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BindingRegion |
getClosestBindingRegion()
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java.util.ArrayList |
getContainingGeneGrps()
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int |
getDistanceTo3PrimeGeneGrp()
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int |
getDistanceTo5PrimeGeneGrp()
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int |
getEnd()
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GeneGroup |
getGeneGrp3Prime()
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GeneGroup |
getGeneGrp5Prime()
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int |
getNeighborhood()
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java.util.ArrayList |
getNeighboringGeneGrps()
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java.util.ArrayList |
getOverlap3PrimeGeneGrps()
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java.util.ArrayList |
getOverlap5PrimeGeneGrps()
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int |
getRank()
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double |
getScore()
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int |
getStart()
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boolean |
intersects(BindingRegion other)
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int |
overlap(BindingRegion other)
Returns -1 for no overlap 0 for complete overlap or a positive int for the # bases of overlap. |
void |
setClosestBindingRegion(BindingRegion closestBindingRegion)
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void |
setNeighborhood(int neighborhood)
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java.lang.String |
simpleSummaryLine()
Returns a binding region line, tab delimited: chrom, start, end, score |
java.lang.String |
summaryLine()
Returns tab delimited line: rank, chrom, start, end, dist to closes gene, gene name(s), # neighbors |
java.lang.String |
toString()
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Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public BindingRegion(int rank, double score, java.lang.String chromosome, int start, int end, int sizeNeighborhood)
Method Detail |
public int compareTo(java.lang.Object obj)
compareTo
in interface java.lang.Comparable
public boolean intersects(BindingRegion other)
public int overlap(BindingRegion other)
public java.lang.String simpleSummaryLine()
public java.lang.String summaryLine()
public java.lang.String toString()
public static java.lang.String extractGeneGrps(java.util.ArrayList geneGrps, boolean returnSummaryLine)
public void compare(GeneGroup geneGrp)
public java.lang.String getChromosome()
public java.util.ArrayList getContainingGeneGrps()
public int getDistanceTo3PrimeGeneGrp()
public int getDistanceTo5PrimeGeneGrp()
public GeneGroup getGeneGrp3Prime()
public GeneGroup getGeneGrp5Prime()
public java.util.ArrayList getOverlap3PrimeGeneGrps()
public java.util.ArrayList getOverlap5PrimeGeneGrps()
public int getRank()
public int getStart()
public int getEnd()
public int getNeighborhood()
public void setNeighborhood(int neighborhood)
public java.util.ArrayList getNeighboringGeneGrps()
public double getScore()
public BindingRegion getClosestBindingRegion()
public void setClosestBindingRegion(BindingRegion closestBindingRegion)
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