Docs For Class Rna

Description

Rna

RNA sequence class

author: Mark Brooks <markabrooks@users.sourceforge.net>
version: 0.8.2
1. $oRna = new Rna("GAGATGGATGTAGATTATTAGTATATG", NULL, "sequence name");
2. $oRna->printvars();
3. $sSeq = $oRna->getData();
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>

Located in /Seq/Rna.php (line 43)

PEAR
   |
   --Bio
      |
      --Str
         |
         --Seq
            |
            --NucAcid
               |
               --Rna

Method Summary

static void MolWt_ ( $sSeq)

object __construct ([string $sSeq = ""], [string $sAlphabetName = "RnaAlphabet"], [string $sName = ""], [boolean $bIsRev = false], [boolean $bIsComp = false])

string addFivePrimeHH ( $fivePrimeHH, $fivePrimeStemlen, string $sSeq)

string addFivePrimeHHStr (string $sSeq, $fivePrimeHH, $fivePrimeStemlen)

string addThreePrimeHH ( $threePrimeHH, $threePrimeStemlen, string $sSeq)

string addThreePrimeHHStr (string $sSeq, $hammerhead, $iStemLen)

void filterSeq ( $sSeq, string $sStr)

void getTm ()

void setTm ( $fTm)

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

static method MolWt_ (line 208)

function MolWt_

Calculates the molecular weight of a protein sequence without an instance required

author: Serge Gregorio
access: public

static void MolWt_ ( $sSeq)

$sSeq

Redefinition of:

Seq::MolWt_(): function MolWt_

Constructor __construct (line 58)

function __construct

Instantiate nucleic acid sequence

object __construct ([string $sSeq = ""], [string $sAlphabetName = "RnaAlphabet"], [string $sName = ""], [boolean $bIsRev = false], [boolean $bIsComp = false])

string $sSeq: String representation of sequence
string $sAlphabetName: Alphabet used by sequence
string $sName: Name of sequence
boolean $bIsRev: Is the sequence reversed?
boolean $bIsComp: Is the sequence complementary?

Redefinition of:

NucAcid::__construct(): __construct

addFivePrimeHH (line 187)

function addFivePrimeHH

Adds a 5prime HH ribozyme to a sequence

string addFivePrimeHH ( $fivePrimeHH, $fivePrimeStemlen, string $sSeq)

string $sSeq
$fivePrimeHH
$fivePrimeStemlen

addFivePrimeHHStr (line 155)

function addFivePrimeHHStr

Adds a 5prime HH ribozyme to a sequence

string addFivePrimeHHStr (string $sSeq, $fivePrimeHH, $fivePrimeStemlen)

string $sSeq
$fivePrimeHH
$fivePrimeStemlen

addThreePrimeHH (line 135)

function addThreePrimeHH

Adds a 3prime HH ribozyme to a sequence

string addThreePrimeHH ( $threePrimeHH, $threePrimeStemlen, string $sSeq)

string $sSeq
$threePrimeHH
$threePrimeStemlen

addThreePrimeHHStr (line 105)

function addThreePrimeHHStr

Adds a three prime HH ribozyme to a sequence

string addThreePrimeHHStr (string $sSeq, $hammerhead, $iStemLen)

string $sSeq
$hammerhead
$iStemLen

filterSeq (line 317)

function setData

access: public

void filterSeq ( $sSeq, string $sStr)

string $sStr: String represented
$sSeq

getTm (line 88)

function getTm

void getTm ()

Redefinition of:

NucAcid::getTm(): function getTm

setTm (line 74)

function setTm

void setTm ( $fTm)

$fTm

Redefinition of:

NucAcid::setTm(): function setTm

Inherited Methods

Inherited From NucAcid

NucAcid::__construct()
NucAcid::calcBaseContent()
NucAcid::comp()
NucAcid::CompBase_()
NucAcid::Comp_()
NucAcid::DoubleStrandedView_()
NucAcid::getAtuBaseContent()
NucAcid::getComp()
NucAcid::getDoubleStrandedView()
NucAcid::getGcBaseContent()
NucAcid::getGcBasePct()
NucAcid::getIsComp()
NucAcid::getRevComp()
NucAcid::getTm()
NucAcid::InTrim_()
NucAcid::revComp()
NucAcid::RevComp_()
NucAcid::setAtuBaseContent()
NucAcid::setGcBaseContent()
NucAcid::setGcBasePct()
NucAcid::setIsComp()
NucAcid::setTm()
NucAcid::showVars()
NucAcid::toggleIsComp()

Inherited From Seq

Seq::__construct()
Seq::alphabetFactory()
Seq::cat()
Seq::catStr()
Seq::getAlphabet()
Seq::getAlphabetLetters()
Seq::getAlphabetType()
Seq::getAlphabetWeights()
Seq::getMolWt()
Seq::getName()
Seq::getPrettyView()
Seq::molWt()
Seq::MolWt_()
Seq::PrettyView_()
Seq::setAlphabet()
Seq::setAlphabetByName()
Seq::setMolWt()
Seq::setName()
Seq::stripIMet()
Seq::stripStop()
Seq::ValidateSeqVersusLetters_()
Seq::WriteRuler_()
Seq::__call()
Seq::__toString()

Inherited From Str

Str::__construct()
Str::cat()
Str::catStr()
Str::CatStr_()
Str::errorCallBack()
Str::getData()
Str::getIsRev()
Str::getRev()
Str::inTrim()
Str::InTrim_()
Str::left()
Str::Left_()
Str::len()
Str::Len_()
Str::reMatch()
Str::ReMatch_()
Str::ReReplace_()
Str::ReSplit_()
Str::rev()
Str::Rev_()
Str::right()
Str::Right_()
Str::setData()
Str::setIsRev()
Str::sub()
Str::Sub_()
Str::symFreq()
Str::SymFreq_()
Str::toggleIsRev()
Str::trim()
Str::Trim_()
Str::__toString()

Inherited From Bio

Bio::__construct()
Bio::printWithNl()

Class Constants

Inherited Constants

Inherited from Bio

Bio::NEWLINE