broad.pda.rnai.RNAiGeneAnnotation Class Reference

Collaboration diagram for broad.pda.rnai.RNAiGeneAnnotation:

Public Member Functions
	RNAiGeneAnnotation (Gene gene, Alignments linc, String geneName, int versionNumber, String seq, String species, String ncbiBuild)
	RNAiGeneAnnotation (String rnaiString)
String	toString ()
String	toRNAi ()
String	getTranscriptSequence ()
String	getTranscriptName ()
Alignments	getRegion ()
String	getGeneName ()
Sequence	getSequence ()
String	toNanostring ()

Static Public Attributes
static String	nanostringHeader ="GENE.SOURCEID\tGENE.TAXONID\tGENE.NCBI_BUILDID\tGENE.SOURCECHR\tGENE.SOURCESTART\tGENE.SOURCEEND\tGENE.SOURCESTRAND\tTRANS.SOURCEID\tTRANS.SEQ\tTRANS.LENGTH"

Constructor & Destructor Documentation

broad.pda.rnai.RNAiGeneAnnotation.RNAiGeneAnnotation	(	Gene	gene,
		Alignments	linc,
		String	geneName,
		int	versionNumber,
		String	seq,
		String	species,
		String	ncbiBuild
	)

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broad.pda.rnai.RNAiGeneAnnotation.RNAiGeneAnnotation

(

String

rnaiString

)

Member Function Documentation

String broad.pda.rnai.RNAiGeneAnnotation.getGeneName

(

)

Alignments broad.pda.rnai.RNAiGeneAnnotation.getRegion

(

)

Sequence broad.pda.rnai.RNAiGeneAnnotation.getSequence

(

)

String broad.pda.rnai.RNAiGeneAnnotation.getTranscriptName

(

)

String broad.pda.rnai.RNAiGeneAnnotation.getTranscriptSequence

(

)

String broad.pda.rnai.RNAiGeneAnnotation.toNanostring

(

)

String broad.pda.rnai.RNAiGeneAnnotation.toRNAi

(

)

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String broad.pda.rnai.RNAiGeneAnnotation.toString

(

)

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Member Data Documentation

String broad.pda.rnai.RNAiGeneAnnotation.nanostringHeader ="GENE.SOURCEID\tGENE.TAXONID\tGENE.NCBI_BUILDID\tGENE.SOURCECHR\tGENE.SOURCESTART\tGENE.SOURCEEND\tGENE.SOURCESTRAND\tTRANS.SOURCEID\tTRANS.SEQ\tTRANS.LENGTH"

static

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The documentation for this class was generated from the following file:

• java/broad/pda/rnai/RNAiGeneAnnotation.java