util.bio.annotation
Class GeneGroup

java.lang.Object
  util.bio.annotation.GeneGroup

All Implemented Interfaces:

java.lang.Comparable, java.io.Serializable

public class GeneGroup

extends java.lang.Object

implements java.lang.Comparable, java.io.Serializable

A GeneGroup is the top organizing level of a "Gene". It may contain multiple transGrps (one transcript, possibly a translation, each with one or more exons) and a composite/ summary GeneRep (a gene representation broken into coding and non-coding regions) . Thus GeneGroup -> one GeneRep + one or more TransGroups -> transcript, exon, introns....

See Also:

Serialized Form

Constructor Summary

GeneGroup(java.lang.String name, java.lang.String chromosome, int start, int end, java.lang.String type, TransGroup[] transGrps, int orientation, java.lang.String attributes)

Method Summary

static java.lang.String	ALToString(java.util.ArrayList al)
int	compareTo(java.lang.Object other)
static java.lang.String	convertNumOrientationToStrand(int orientation)
static int	convertPlusToNumOrientation(java.lang.String orientation)
static java.util.ArrayList	extractStartEnds(ExonIntron[] exons)
static int[][]	extractStartEndsInts(ExonIntron[] exons)
static java.util.ArrayList	fetchIntrons(java.util.ArrayList exons) Takes an ArrayList of exon startStop int[2]'s, returns an ArrayList of int[2]'s representing the start,stop for each intron
java.lang.String	fetchSumaryLine()
java.lang.String	getAttributes()
java.lang.String	getChromosome()
int	getEnd()
GeneRep	getGeneRep()
java.lang.String	getLabel()
java.lang.String	getName()
int	getOrientation()
int	getStart()
TransGroup[]	getTransGrps()
java.lang.String	getType()
static java.util.ArrayList	joinSegments(java.util.ArrayList segs) Takes an ArrayList of int[2]'s representing start stop coords kills the dups, and those cotained within another seg, will merge overlapping segments.
void	setOrientation(int orientation)
static java.util.ArrayList	sortSegments(java.util.ArrayList segs) Sorts an ArrayList of int[2]'s representing start, end
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneGroup

public GeneGroup(java.lang.String name,
                 java.lang.String chromosome,
                 int start,
                 int end,
                 java.lang.String type,
                 TransGroup[] transGrps,
                 int orientation,
                 java.lang.String attributes)

Method Detail

compareTo

public int compareTo(java.lang.Object other)

Specified by:

compareTo in interface java.lang.Comparable

fetchSumaryLine

public java.lang.String fetchSumaryLine()

toString

public java.lang.String toString()

getOrientation

public int getOrientation()

getGeneRep

public GeneRep getGeneRep()

getTransGrps

public TransGroup[] getTransGrps()

getLabel

public java.lang.String getLabel()

getChromosome

public java.lang.String getChromosome()

getAttributes

public java.lang.String getAttributes()

getName

public java.lang.String getName()

getEnd

public int getEnd()

getStart

public int getStart()

convertPlusToNumOrientation

public static int convertPlusToNumOrientation(java.lang.String orientation)

convertNumOrientationToStrand

public static java.lang.String convertNumOrientationToStrand(int orientation)

extractStartEndsInts

public static int[][] extractStartEndsInts(ExonIntron[] exons)

extractStartEnds

public static java.util.ArrayList extractStartEnds(ExonIntron[] exons)

fetchIntrons

public static java.util.ArrayList fetchIntrons(java.util.ArrayList exons)

Takes an ArrayList of exon startStop int[2]'s, returns an ArrayList of int[2]'s representing the start,stop for each intron

ALToString

public static java.lang.String ALToString(java.util.ArrayList al)

sortSegments

public static java.util.ArrayList sortSegments(java.util.ArrayList segs)

Sorts an ArrayList of int[2]'s representing start, end

joinSegments

public static java.util.ArrayList joinSegments(java.util.ArrayList segs)

Takes an ArrayList of int[2]'s representing start stop coords kills the dups, and those cotained within another seg, will merge overlapping segments.

getType

public java.lang.String getType()

setOrientation

public void setOrientation(int orientation)