trans.roc
Class ControlGene

java.lang.Object
  trans.roc.ControlGene

public class ControlGene

extends java.lang.Object

Constructor Summary

ControlGene(java.lang.String line)

Method Summary

boolean	containsPoint(int bp) Looks to see if point is contained in any of the exons, ends are inclusive.
java.lang.String	getChromosome()
int[]	getExonEnds()
int[]	getExonStarts()
float[]	getIntensities()
java.lang.String	getName()
java.lang.String	getNotes()
java.lang.String	getStrand()
static void	makeExons(ControlGene[] cgs, int endOffSet) Fires makeExons on each CG within the ControlGene[].
void	makeExons(int endOffSet) Subtracts the endOffSet from the end and only creates an exon if 1+ end-start > 0
static ControlGene[]	parseControlGeneFile(java.io.File file) parses a control gene file ex: #name chrom strand exonStarts exonEnds notes ex: NM_001035267 chr12 + 54796640,54797239,54797532, 54796850,54797262,54797882, Z12962_Homologue to yeast ribosomal protein L41_H
void	setIntensities(float[] intensities)
void	setNotes(java.lang.String notes)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ControlGene

public ControlGene(java.lang.String line)

Method Detail

containsPoint

public boolean containsPoint(int bp)

Looks to see if point is contained in any of the exons, ends are inclusive.

makeExons

public void makeExons(int endOffSet)

Subtracts the endOffSet from the end and only creates an exon if 1+ end-start > 0

makeExons

public static void makeExons(ControlGene[] cgs,
                             int endOffSet)

Fires makeExons on each CG within the ControlGene[].

parseControlGeneFile

public static ControlGene[] parseControlGeneFile(java.io.File file)

parses a control gene file ex: #name chrom strand exonStarts exonEnds notes ex: NM_001035267 chr12 + 54796640,54797239,54797532, 54796850,54797262,54797882, Z12962_Homologue to yeast ribosomal protein L41_H

getIntensities

public float[] getIntensities()

setIntensities

public void setIntensities(float[] intensities)

getNotes

public java.lang.String getNotes()

setNotes

public void setNotes(java.lang.String notes)

getChromosome

public java.lang.String getChromosome()

getExonEnds

public int[] getExonEnds()

getExonStarts

public int[] getExonStarts()

getName

public java.lang.String getName()

getStrand

public java.lang.String getStrand()