CDSExon Class Reference

#include <TranscriptExon.h>

Inheritance diagram for CDSExon:

List of all members.

Public Member Functions
	CDSExon ()
	CDSExon (const string &exstr)
vector< pair< int, int > >	intronloc () const
vector< int >	intronlocCDS () const

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Detailed Description

Derived class essentially the same as TranscriptExon but added method to return intron location in the coordinates of CDS

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Constructor & Destructor Documentation

CDSExon::CDSExon

(

)

[inline]

CDSExon::CDSExon

(

const string &

exstr

)

[inline]

Input is 56,122:123,135:136,188:189,236:237,322:323,830:831,1013 This used the transcript coordinate system 56 is the location of ATG if it is a complete ORF.

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Member Function Documentation

vector< pair< int, int > > CDSExon::intronloc

(

)

const

simple formating function Intron located after the number indicated with 1-based index.

References TranscriptExon::exons.

vector< int > CDSExon::intronlocCDS

(

)

const

intron location in CDS coordinate, starting from 1 to stop codon, user needs to translate into amino acid coordinate by N/3 and phase N3.

References TranscriptExon::exons.

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

• range/TranscriptExon.h
• range/TranscriptExon.cpp