Docs For Class SeqFactory

Description

SeqFactory.php

Factory Class to produce sequences

author: Mark Brooks
version: 0.8.2
1. $oSeqBuilder = new SeqFactory()
2. $oChromosomeVI = $oSeqBuilder->create('CAGT', "DnaAlphabet", "Chromosome VI");
access: public

Located in /Seq/SeqFactory.php (line 62)

PEAR
   |
   --Bio
      |
      --Factory
         |
         --SeqFactory

Method Summary

object __construct ([string $sSeqType = "Dna"], string $sSeq, boolean $bSeqIsRev)

object create (string $sSeq, [string $sAlphabetName = "DnaAlphabet"], [string $sName = "Unnamed DNA"], [string $bIsRev = false])

string getType ()

boolean setType (string $sSeqType)

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

Constructor __construct (line 75)

function __construct

return: SeqFactory Instance
access: public

object __construct ([string $sSeqType = "Dna"], string $sSeq, boolean $bSeqIsRev)

string $sSeq: String representation of sequence
string $sSeqType: Alphabet used by sequence
boolean $bSeqIsRev: Is the sequence reversed?

Redefinition of:

Bio::__construct(): function Bio ()

create (line 101)

function create

$seqbuilder = new SeqFactory()
$seq = $seqbuilder->create('CAGT', -id => 'name');

return: Fresh sequence object
access: public

object create (string $sSeq, [string $sAlphabetName = "DnaAlphabet"], [string $sName = "Unnamed DNA"], [string $bIsRev = false])

string $sSeq: Sequence as a string
string $sAlphabetName: Sequece as a string
string $sName: Name of the sequence as a string
string $bIsRev: Is the sequence reversed?

Redefinition of:

Factory::create(): function create

getType (line 150)

function getType

access: public

string getType ()

Redefinition of:

Factory::getType(): function getType

setType (line 125)

function setType

return: TRUE on success
access: public

boolean setType (string $sSeqType)

string $sSeqType: Type of sequnce

Redefinition of:

Factory::setType(): function setType

Inherited Methods

Inherited From Factory

Factory::create()
Factory::getType()
Factory::setType()

Inherited From Bio

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

Class Constants

Inherited Constants

Inherited from Bio

Bio::NEWLINE