trans.roc
Class ControlGene

java.lang.Object
  extended bytrans.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()