mRNAModel Class Reference
#include <RNAModel.h>
Public Member Functions | |
| mRNAModel (const Noschain &seg, const string &chrom, const string &gs) | |
| mRNAModel (const string &exstarts, const string &exends, char strand, int gcb, int gce, const string &gi, const string &genomic) | |
| Noschain | FivePrimeUTR () const |
| Noschain | ThreePrimeUTR () const |
| int | num5NoncodingExons () const |
| int | num3NoncodingExons () const |
| Noschain | CDSChain () const throw (PointOutChain) |
| Range | CDSRange () const |
| int | CDSLength () const |
| string | CDSSeq () const |
| string | CDSSequence () const |
| char | CDSDirection () const |
| double | CDSFraction () const |
| int | FivePrimeUTRLength () const |
| int | ThreePrimeUTRLength () const |
| int | UTRLength () const |
| bool | hasStart () const |
| bool | hasStop () const |
| bool | operator== (const mRNAModel &md) const |
| int | numberOfInternalStops () const |
| const string & | getProtein () const |
| string | JGIModelRow (const char sep='\t') const |
| string | JGITranscriptRow (const char sep='\t') const |
| string | JGIProteinRow (char sep='\t') const |
| string | sfCDSGenomic () const |
| Noschain | CDSOnewayChain () const |
| void | CDSOnewayChain (Noschain &ch) const |
| string | sfCDSTranscript () const |
| string | sfExonsProtein () const |
Static Public Member Functions | |
| static int | currentId () |
| static int | nextId () |
| static void | advanceId () |
Protected Attributes | |
| int | cdsb |
| int | cdse |
| int | gcdsb |
| int | gcdse |
| string | pep |
Static Protected Attributes | |
| static int | serialid = 1 |
| mRNAModel Class ///// | |
| static int | shortestpep = 30 |
| static int | shortestmodel = 90 |
Detailed Description
for mRNA models on the Genomic Sequence The class added cds information in addition to RNAModel. If the CDS informationis provided it will use it, otherwise it will compute it from the spliced mRNA product. Partial mRNA models are possible.Constructor & Destructor Documentation
| mRNAModel::mRNAModel | ( | const Noschain & | seg, | |
| const string & | chrom, | |||
| const string & | gs | |||
| ) | [explicit] |
guess the CDS range as the longest ORF More or less EST model. Done more of the work of ESTModel
References cdsb, cdse, gcdsb, gcdse, RNAModel::genomicIndex(), bioseq::getSequence(), DNA::longestORFForward(), Noschain::numberOfRanges(), pep, DNA::revcomp(), Noschain::reverse(), RNAModel::rna, and shortestpep.
| mRNAModel::mRNAModel | ( | const string & | exstarts, | |
| const string & | exends, | |||
| char | strand, | |||
| int | gcb, | |||
| int | gce, | |||
| const string & | gi, | |||
| const string & | genomic | |||
| ) |
this is the JGI input format, where strand indicate the direction, all numbers are from small to large
References cdsb, cdse, gcdsb, gcdse, pep, RNAModel::rna, RNAModel::RNAIndex(), and translate().
Member Function Documentation
| Noschain mRNAModel::FivePrimeUTR | ( | ) | const [inline] |
| Noschain mRNAModel::ThreePrimeUTR | ( | ) | const [inline] |
| int mRNAModel::num5NoncodingExons | ( | ) | const [inline] |
References FivePrimeUTR(), and Noschain::numberOfRanges().
| int mRNAModel::num3NoncodingExons | ( | ) | const [inline] |
References Noschain::numberOfRanges(), and ThreePrimeUTR().
| Noschain mRNAModel::CDSChain | ( | ) | const throw (PointOutChain) [inline] |
CDS exons in genomic coordinates
References gcdsb, gcdse, and Noschain::subchain().
Referenced by CDSOnewayChain(), sfCDSGenomic(), and sfExonsProtein().
| Range mRNAModel::CDSRange | ( | ) | const [inline] |
the genomic Range of the CDS
References gcdsb, gcdse, and Range::Range().
Referenced by JGIModel::valid().
| int mRNAModel::CDSLength | ( | ) | const [inline] |
| string mRNAModel::CDSSeq | ( | ) | const [inline] |
shorter name for CDSSequence()
References cdsb, cdse, and RNAModel::rna.
Referenced by JGIModel::valid().
| string mRNAModel::CDSSequence | ( | ) | const [inline] |
return the underlying CDS ORF
References cdsb, cdse, and RNAModel::rna.
Referenced by JGITranscriptRow().
| char mRNAModel::CDSDirection | ( | ) | const [inline] |
| double mRNAModel::CDSFraction | ( | ) | const [inline] |
References CDSLength(), and Range::length().
| int mRNAModel::FivePrimeUTRLength | ( | ) | const [inline] |
| int mRNAModel::ThreePrimeUTRLength | ( | ) | const [inline] |
| int mRNAModel::UTRLength | ( | ) | const [inline] |
References FivePrimeUTRLength(), and ThreePrimeUTRLength().
| bool mRNAModel::hasStart | ( | ) | const [inline] |
| bool mRNAModel::hasStop | ( | ) | const [inline] |
| bool mRNAModel::operator== | ( | const mRNAModel & | md | ) | const [inline] |
compare the translated product which is 3x faster than comparing RNA sequences
References pep.
| int mRNAModel::numberOfInternalStops | ( | ) | const |
| const string& mRNAModel::getProtein | ( | ) | const [inline] |
| string mRNAModel::JGIModelRow | ( | const char | sep = '\t' |
) | const |
output one row of JGI Model Schema data dump excep the useless columns id, chrom, strand, start, end, cdsStart, cdsEnd, sfCount, sfStarts, sfEnds Note name column will be produced by the derived class
References Range::begin(), currentId(), Range::direction(), Range::end(), gcdsb, gcdse, RNAModel::gid, Noschain::numberOfRanges(), and Noschain::startEnd().
Referenced by ESTAssembly::writetab().
| string mRNAModel::JGITranscriptRow | ( | const char | sep = '\t' |
) | const |
NP= not produced transcriptId, locusId (NP), name (NP), description (NP), status (NP), type (NP) lengthGenomic, lengthTranscript, lengthCDS, sfExonsGenomic, sfCDSGenomic, sfExonsTranscript, sfCDSTranscript, seqGenomic, seqTranscript, seqCDS, annotatorId (NP), annotatable (NP), creationDate (NP) transcriptId will be the same as modelid. This is the worst creation (crime) by any programmer!
name, and description will be delayed by derived classes.
References CDSLength(), CDSSequence(), currentId(), Range::length(), RNAModel::rna, RNAModel::RNASequence(), RNAModel::seqGenomic(), sfCDSGenomic(), sfCDSTranscript(), Noschain::sfExonsGenomic(), and Noschain::sfExonsTranscript().
Referenced by ESTAssembly::writetab().
| string mRNAModel::JGIProteinRow | ( | char | sep = '\t' |
) | const |
proteinId, transcriptId, name (NP), description (NP), length, sfExons, seq, annotatable (NP)
References currentId(), pep, and sfExonsProtein().
Referenced by ESTAssembly::writetab().
| string mRNAModel::sfCDSGenomic | ( | ) | const |
helper function used by JGITranscriptRow()
References Noschain::asDelimitedString(), Range::begin(), CDSChain(), Range::direction(), and Noschain::numberOfRanges().
Referenced by JGITranscriptRow().
| Noschain mRNAModel::CDSOnewayChain | ( | ) | const |
one way chain in transcript coordinate system
References Range::begin(), CDSChain(), and Range::direction().
Referenced by sfCDSTranscript().
| void mRNAModel::CDSOnewayChain | ( | Noschain & | ch | ) | const |
References Range::begin(), CDSChain(), and Range::direction().
| string mRNAModel::sfCDSTranscript | ( | ) | const |
| string mRNAModel::sfExonsProtein | ( | ) | const |
References Noschain::asDelimitedString(), Range::begin(), CDSChain(), Range::end(), Noschain::exonOnlyChain(), n2p(), Noschain::numberOfRanges(), Noschain::onewayChain(), and Range::Range().
Referenced by JGIProteinRow().
| static int mRNAModel::currentId | ( | ) | [inline, static] |
does not increment serialid
References serialid.
Referenced by ESTAssembly::ESTAssembly(), JGIModelRow(), JGIProteinRow(), JGITranscriptRow(), ESTAssembly::write(), and ESTAssembly::writetab().
| static int mRNAModel::nextId | ( | ) | [inline, static] |
return current id then increment it
References serialid.
| static void mRNAModel::advanceId | ( | ) | [inline, static] |
Member Data Documentation
int mRNAModel::cdsb [protected] |
this are index inside the spliced RNA product for Genomic Position you need to use the parent class's genomicIndex() method 1-based index! [cdsb, cdse]
Referenced by CDSLength(), CDSSeq(), CDSSequence(), ESTAssembly::ESTAssembly(), FivePrimeUTRLength(), mRNAModel(), ESTAssembly::write(), and ESTAssembly::writetab().
int mRNAModel::cdse [protected] |
int mRNAModel::gcdsb [protected] |
for performance we store computed result there are the genomic indx of the CDS location This represent the range of the CDS. On - strand gcdsb > gcdse
Referenced by CDSChain(), CDSDirection(), CDSRange(), FivePrimeUTR(), JGIModel::JGIModel(), JGIModelRow(), mRNAModel(), JGIModel::show(), JGIModel::toJGIString(), JGIModel::toSQLString(), JGIModel::toString(), JGIModel::valid(), ESTAssembly::write(), and ESTAssembly::writetab().
int mRNAModel::gcdse [protected] |
Referenced by CDSChain(), CDSDirection(), CDSRange(), JGIModel::growEnd(), JGIModel::JGIModel(), JGIModelRow(), mRNAModel(), JGIModel::show(), ThreePrimeUTR(), JGIModel::toJGIString(), JGIModel::toSQLString(), JGIModel::toString(), JGIModel::valid(), ESTAssembly::write(), and ESTAssembly::writetab().
string mRNAModel::pep [protected] |
int mRNAModel::serialid = 1 [static, protected] |
mRNAModel Class /////
for making unique identifier of objects in this class
Referenced by advanceId(), currentId(), and nextId().
int mRNAModel::shortestpep = 30 [static, protected] |
Referenced by mRNAModel(), and JGIModel::valid().
int mRNAModel::shortestmodel = 90 [static, protected] |
Referenced by JGIModel::JGIModel(), and JGIModel::valid().
The documentation for this class was generated from the following files:
- range/RNAModel.h
- range/RNAModel.cpp
