Docs For Class NucAcid

Description

NucAcid Sequence class specific to nucleic acid sequences Performs operations common to RNA and DNA Do not instantiate this class; is subclassed by DNA and RNA classes.

author: Mark Brooks <markabrooks@users.sourceforge.net>
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>
abstract:

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

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

Direct descendents

Class	Description
Dna	Dna
Rna	Rna

Method Summary

static string CompBase_ (string $cBase)

static string DoubleStrandedView_ (string $sSeq, [integer $iLineLen = 60])

static string InTrim_ (string $sStr)

static string RevComp_ ([string $sSeq = ""])

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

void calcBaseContent ()

string comp ()

string Comp_ ([string $sSeq = ""])

integer getAtuBaseContent ()

string getComp ()

string getDoubleStrandedView ([integer $iLineLen = 60])

integer getGcBaseContent ()

float getGcBasePct ()

boolean getIsComp ()

string getRevComp ()

void getTm ()

string revComp ()

void setAtuBaseContent (integer $iAtuBaseContent)

void setGcBaseContent (integer $iGcBaseContent)

void setGcBasePct (float $fGcPct)

void setIsComp (boolean $bIsComp)

void setTm ( $fTm)

void showVars ()

boolean toggleIsComp ()

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

static method CompBase_ (line 340)

CompBase_

Complement the given base

return: the base complemented
access: public

static string CompBase_ (string $cBase)

string $cBase: the base to complement

static method DoubleStrandedView_ (line 606)

DoubleStrandedView_

A sequence object returns a double-stranded view

author: Joseba Bikandi
access: public

static string DoubleStrandedView_ (string $sSeq, [integer $iLineLen = 60])

string $sSeq: Sequence to output
integer $iLineLen

static method InTrim_ (line 136)

InTrim_

Strips internal whitespace from a sequence

static string InTrim_ (string $sStr)

string $sStr

Redefinition of:

Str::InTrim_(): function InTrim_

static method RevComp_ (line 500)

RevComp_

Reverse & complement the given string

return: The sequence reverse-complemented
access: public

static string RevComp_ ([string $sSeq = ""])

string $sSeq: The sequence to reverse & complement

Constructor __construct (line 97)

__construct

Instantiate nucleic acid sequence

return: NucAcid Sequence object

object __construct ([string $sSeq = ""], [string $sAlphabetName = "NucleotideAlphabet"], [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:

Seq::__construct(): function __construct

Redefined in descendants as:

Dna::__construct() : function __construct
Rna::__construct() : function __construct

calcBaseContent (line 522)

calcBaseContent

Calculates and sets Base content for $this

access: public

void calcBaseContent ()

comp (line 390)

comp

Complement the sequence string of the Sequence object Modifies the instance in place

return: The sequence string complemented
access: public

string comp ()

Comp_ (line 431)

Comp_

Complement the given string

return: the sequence complemented
access: public

string Comp_ ([string $sSeq = ""])

string $sSeq: the sequence to complement

getAtuBaseContent (line 220)

getAtuBaseContent

Accessor for AtuBaseContent

access: public

integer getAtuBaseContent ()

getComp (line 411)

getComp

Complement the sequence string of the Sequence object Does not alter the instance in place

return: the sequence string complemented
access: public

string getComp ()

getDoubleStrandedView (line 585)

getDoubleStrandedView

A sequence object returns a double-stranded view Does not modify the sequence in place

author: Joseba Bikandi
access: public

string getDoubleStrandedView ([integer $iLineLen = 60])

integer $iLineLen

getGcBaseContent (line 183)

getGcBaseContent

Accessor for iGcBaseContent

access: public

integer getGcBaseContent ()

getGcBasePct (line 257)

getGcPct

Accessor for GC percent

access: public

float getGcBasePct ()

getIsComp (line 284)

getIsComp

Accesssor for bIsComp

access: public

boolean getIsComp ()

getRevComp (line 480)

getRevComp

Reverse & complement the Seq object, which is not modified in place

return: The sequence reverse-complemented
access: public

string getRevComp ()

getTm (line 123)

function getTm

abstract:

void getTm ()

Redefined in descendants as:

Dna::getTm() : function getTm
Rna::getTm() : function getTm

revComp (line 459)

revComp

Reverse & complement this sequence object & return a string

return: the sequence reverse-complemented
access: public

string revComp ()

setAtuBaseContent (line 203)

setAtuBaseContent

Accessor for iAtuBaseContent

access: public

void setAtuBaseContent (integer $iAtuBaseContent)

integer $iAtuBaseContent

setGcBaseContent (line 166)

setGcBaseContent

Accessor for iGcBaseContent

access: public

void setGcBaseContent (integer $iGcBaseContent)

integer $iGcBaseContent

setGcBasePct (line 239)

setGcBasePct

Accessor for fGcPct

access: public

void setGcBasePct (float $fGcPct)

float $fGcPct: Percentage GC to set

setIsComp (line 301)

setIsComp

access: public

void setIsComp (boolean $bIsComp)

boolean $bIsComp: Is the sequence complementary?

setTm (line 113)

function setTm

abstract:

void setTm ( $fTm)

$fTm

Redefined in descendants as:

Dna::setTm() : function setTm
Rna::setTm() : function setTm

showVars (line 564)

printvars()

access: public

void showVars ()

toggleIsComp (line 317)

function toggleIsComp()

access: public

boolean toggleIsComp ()

Inherited Methods

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