Docs For Class Dna

Description

Dna

author: Mark Brooks <markabrooks@users.sourceforge.net> Sequence library nucleic acid sequences.
version: 0.8.2
1. $oDna = new Dna("GAGATGGATGTAGATTATTAGTATATG", "Test Sequence");
2. $oDna->revComp(); // Modifies the sequence in place.
3. $oDna->getRevComp(); // Does not modify the sequence in place.
4. $sSeq = $oDna->getData();

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

PEAR
   |
   --Bio
      |
      --Str
         |
         --Seq
            |
            --NucAcid
               |
               --Dna

Method Summary

static void MolWt_ ( $sSeq, [ $bIsStringent = FALSE])

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

float calcTm (none 0)

void getTm ()

void setTm (float $fTm)

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

static method MolWt_ (line 264)

function MolWt_

Calculates the molecular weight of a protein sequence

author: Serge Gregorio
access: public

static void MolWt_ ( $sSeq, [ $bIsStringent = FALSE])

$sSeq
$bIsStringent

Redefinition of:

Seq::MolWt_(): function MolWt_

Constructor __construct (line 61)

function __construct

Instantiate Dna sequence

Dna __construct ([string $sSeq = ""], [string $sAlphabetName = "DnaAlphabet"], [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 seq Comp?

Redefinition of:

NucAcid::__construct(): __construct

calcTm (line 131)

function calcTm

return: Tm
access: public

float calcTm (none 0)

none 0

getTm (line 97)

function getTm

access: public
uses: accessor - for Tm

void getTm ()

Redefinition of:

NucAcid::getTm(): function getTm

setTm (line 80)

function setTm

Accessor for Tm (melting temperature)

access: public

void setTm (float $fTm)

float $fTm: Melting temperature

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