apollo.datamodel
Class GenomicRange

java.lang.Object
  apollo.datamodel.Range
      apollo.datamodel.GenomicRange

All Implemented Interfaces:

RangeI, java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

CurationSet

public class GenomicRange
extends Range

See Also:

Serialized Form

Field Summary

protected java.lang.String

chromosome

Fields inherited from class apollo.datamodel.Range

high, logger, low, name, refSeq, strand, type

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Constructor Summary

GenomicRange()

GenomicRange(java.lang.String chr, int start, int end)

Method Summary

java.lang.String	getChromosome()
java.lang.String	getOrganism()
void	setChromosome(java.lang.String chr) Im thinking this should be changed to setTopLevelName to generalize beyond chromosome (chrom_arm, contigs, super contigs...)
void	setOrganism(java.lang.String org)

Methods inherited from class apollo.datamodel.Range

canHaveChildren, contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getEnd, getEndAsString, getFeatureType, getHigh, getLeftOverlap, getLow, getName, getRangeClone, getRefSequence, getResidues, getRightOverlap, getStart, getStartAsString, getStrand, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, rangeIsUnassigned, sameRange, setEnd, setFeatureType, setHigh, setLow, setName, setRefSequence, setStart, setStrand, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

chromosome

protected java.lang.String chromosome

Constructor Detail

GenomicRange

public GenomicRange()

GenomicRange

public GenomicRange(java.lang.String chr,
                    int start,
                    int end)

Method Detail

getChromosome

public java.lang.String getChromosome()

setChromosome

public void setChromosome(java.lang.String chr)

Im thinking this should be changed to setTopLevelName to generalize beyond chromosome (chrom_arm, contigs, super contigs...)

getOrganism

public java.lang.String getOrganism()

setOrganism

public void setOrganism(java.lang.String org)