Docs For Class Seq

Class Seq

Description

Seq

Mutable sequence class

author: Mark Brooks <markabrooks@users.sourceforge.net>
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>
link: http://plasmidb.sf.net/
abstract:
access: public
license: GPL

Located in /Seq/Seq.php (line 53)

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

Direct descendents

Class	Description
Protein	Protein
NucAcid	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.

Method Summary

static void MolWt_ ([ $sSeqStr = ""], string $sSeq)

static void PrettyView_ (string $sSeq, [integer $iLineLength = 50], [ $iBlockLength = ""], [string $sMethod = 'web'])

static bool ValidateSeqVersusLetters_ (string $sStr, string $sLetters)

static string WriteRuler_ (int $iLen)

object __construct ([string $sSeq = ""], [string $sAlphabetName = "SingleLetterAlphabet"], [string $sName = ""], [boolean $bIsRev = 0])

object A alphabetFactory (string $sType)

void cat (object Seq $other)

string catStr (string $sOther)

object getAlphabet ()

string getAlphabetLetters ()

string getAlphabetType ()

string getAlphabetWeights (none 0)

float getMolWt ()

void getName (string $sName)

string getPrettyView ([ $iLineLength = 50], [ $iBlockLength = 10], [string $sMethod = 'web'])

float molWt ()

void setAlphabet (object $oAlphabet)

void setAlphabetByName (string $sAlphabetName)

void setMolWt (float $fMolWt)

void setName (string $sName)

boolean stripIMet ()

boolean stripStop ()

void __call (string $sMethod, array $aArguments)

string __toString (none 0)

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

static method MolWt_ (line 350)

function MolWt_

Calculates the molecular weight of a protein sequence override this with your function of choice in child classes

access: public

static void MolWt_ ([ $sSeqStr = ""], string $sSeq)

string $sSeq
$sSeqStr

Redefined in descendants as:

Protein::MolWt_() : function MolWt_
Dna::MolWt_() : function MolWt_
Rna::MolWt_() : function MolWt_

static method PrettyView_ (line 510)

function PrettyView_

Makes a pretty display of the input sequence string Adds a space between every block, a new line or
between every line

author: Nico Stuurman

static void PrettyView_ (string $sSeq, [integer $iLineLength = 50], [ $iBlockLength = ""], [string $sMethod = 'web'])

string $sSeq
integer $iLineLength
string $sMethod: can be 'web' (use '
'), 'txt' (use "\n")
$iBlockLength

static method ValidateSeqVersusLetters_ (line 475)

function validateSeqVersusLetters_

Checks the sequence to see whether or not it matches its alphabet Case insensitive

return: is OK.
access: public

static bool ValidateSeqVersusLetters_ (string $sStr, string $sLetters)

string $sStr
string $sLetters

static method WriteRuler_ (line 560)

function WriteRuler_

static string WriteRuler_ (int $iLen)

int $iLen: Length of ruler to make

Constructor __construct (line 100)

function __construct

return: Sequence Instance

object __construct ([string $sSeq = ""], [string $sAlphabetName = "SingleLetterAlphabet"], [string $sName = ""], [boolean $bIsRev = 0])

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

Redefinition of:

Str::__construct(): function __construct

Redefined in descendants as:

Protein::__construct() : function __construct
NucAcid::__construct() : __construct
Dna::__construct() : function __construct
Rna::__construct() : function __construct

alphabetFactory (line 429)

function alphabetFactory

Create a new alphabet object for the specified IUPAC type

return: new IUPAC object. A DB_Error object on failure.
author: Partly Stolen from PEAR DB
access: public

object A alphabetFactory (string $sType)

string $sType: The data type (eg "IUPACProtein")

cat (line 612)

function cat

concats Seq objects $other with $this

void cat (object Seq $other)

object Seq $other

Redefinition of:

Str::cat(): function cat

catStr (line 592)

function catStr

Workalike for MutableSeq::append in BioPython

access: public

string catStr (string $sOther)

string $sOther

Redefinition of:

Str::catStr(): function catStr

getAlphabet (line 250)

function getAlphabet

accessor for alphabet

access: public

object getAlphabet ()

getAlphabetLetters (line 307)

function getAlphabetLetters

returns the letters of Alpahbet the Seq contains

string getAlphabetLetters ()

getAlphabetType (line 285)

function getAlphabetType

Returns the type of Alpahbet the Seq contains

string getAlphabetType ()

getAlphabetWeights (line 326)

function getAlphabetWeights

returns the weights of Alpahbet the Seq contains

string getAlphabetWeights (none 0)

none 0

getMolWt (line 216)

function getMolWt()

access: public

float getMolWt ()

getName (line 166)

function getName

access: public

void getName (string $sName)

string $sName: sName of the molecule

getPrettyView (line 543)

function getPrettyView

Makes a getPrettyView display of the Seq object Adds a space between every block, a new line or
between every line

author: Nico Stuurman

string getPrettyView ([ $iLineLength = 50], [ $iBlockLength = 10], [string $sMethod = 'web'])

string $sMethod: can be 'web' (use '
'), 'txt' (use "\n")
$iLineLength
$iBlockLength

molWt (line 408)

function molWt

Calculates the molecular weight of this Seq

access: public

float molWt ()

setAlphabet (line 233)

function setAlphabet

accessor for alphabet

access: public

void setAlphabet (object $oAlphabet)

object $oAlphabet

setAlphabetByName (line 268)

function setAlphabetByName

accessor for alphabet

access: public

void setAlphabetByName (string $sAlphabetName)

string $sAlphabetName

setMolWt (line 199)

function setMolWt

access: public

void setMolWt (float $fMolWt)

float $fMolWt: Molecular weight

setName (line 182)

function setName

access: public

void setName (string $sName)

string $sName: Name

stripIMet (line 365)

stripIMet

access: public

boolean stripIMet ()

stripStop (line 386)

stripStop

access: public

boolean stripStop ()

__call (line 143)

function __call

void __call (string $sMethod, array $aArguments)

string $sMethod
array $aArguments

__toString (line 126)

function __toString

Returns a sequence as a string representation

string __toString (none 0)

none 0

Redefinition of:

Str::__toString(): function __toString

Inherited Methods

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

Documentation generated on Sun, 28 Sep 2008 11:09:36 +0200 by phpDocumentor 1.4.2