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

  1. $seqbuilder new SeqFactory()
  2.  $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

Documentation generated on Sun, 28 Sep 2008 11:09:38 +0200 by phpDocumentor 1.4.2