pwiz::analysis::Pseudo2DGel::Config Struct Reference

Holds the configuration for an instance of Pseudo2DGel. More...

#include <Pseudo2DGel.hpp>

List of all members.

Public Member Functions
	Config ()
	Config (const std::string &args)
	Config (const std::string &args, boost::shared_ptr< pwiz::peptideid::PeptideID > peptide_id)
void	process (const std::string &args)
	parses a keyword/value string to set instance variables.

Public Attributes
std::string	label
	The filename label.
float	mzLow
	lower m/z cutoff.
float	mzHigh
	upper m/z cutoff.
float	timeScale
	scale of the time axis.
int	binCount
	histogram bin count.
float	zRadius
	intensity z-score function radius.
bool	bry
	flag for blue-red-yellow coloration.
bool	grey
	flag for grey scale coloration.
bool	binSum
	flag to sum intensity in bins.
bool	ms2
	flag to set marks for ms2 locations.
bool	positiveMs2Only
	flag to only draw ms2 locations that exist in the peptide_id object and have a score >= 0.
bool	binScan
	flag to render linearly with scan.
boost::shared_ptr < pwiz::peptideid::PeptideID >	peptide_id
	PeptideID object to retrieve peptide id's from.
MarkupShape	markupShape
	The shape used for pseudo2d gel markups.
int	output_width
	Optional user-specified bitmap width and height.
int	output_height

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Detailed Description

Holds the configuration for an instance of Pseudo2DGel.

Controls both the image generation as well as markups on the image from ms2 scans or peptide locations.

Definition at line 62 of file Pseudo2DGel.hpp.

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Constructor & Destructor Documentation

pwiz::analysis::Pseudo2DGel::Config::Config

(

)

pwiz::analysis::Pseudo2DGel::Config::Config

(

const std::string &

args

)

pwiz::analysis::Pseudo2DGel::Config::Config	(	const std::string &	args,
		boost::shared_ptr< pwiz::peptideid::PeptideID >	peptide_id
	)

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Member Function Documentation

void pwiz::analysis::Pseudo2DGel::Config::process

(

const std::string &

args

)

parses a keyword/value string to set instance variables.

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Member Data Documentation

std::string pwiz::analysis::Pseudo2DGel::Config::label

The filename label.

Definition at line 65 of file Pseudo2DGel.hpp.

float pwiz::analysis::Pseudo2DGel::Config::mzLow

lower m/z cutoff.

Definition at line 68 of file Pseudo2DGel.hpp.

float pwiz::analysis::Pseudo2DGel::Config::mzHigh

upper m/z cutoff.

Definition at line 71 of file Pseudo2DGel.hpp.

float pwiz::analysis::Pseudo2DGel::Config::timeScale

scale of the time axis.

Definition at line 74 of file Pseudo2DGel.hpp.

int pwiz::analysis::Pseudo2DGel::Config::binCount

histogram bin count.

Definition at line 77 of file Pseudo2DGel.hpp.

float pwiz::analysis::Pseudo2DGel::Config::zRadius

intensity z-score function radius.

Definition at line 80 of file Pseudo2DGel.hpp.

bool pwiz::analysis::Pseudo2DGel::Config::bry

flag for blue-red-yellow coloration.

Definition at line 83 of file Pseudo2DGel.hpp.

bool pwiz::analysis::Pseudo2DGel::Config::grey

flag for grey scale coloration.

Definition at line 86 of file Pseudo2DGel.hpp.

bool pwiz::analysis::Pseudo2DGel::Config::binSum

flag to sum intensity in bins.

This flag causes bins to be the sum of the underlying values. If it's false, then the maximum value for the region will be used.

Definition at line 91 of file Pseudo2DGel.hpp.

bool pwiz::analysis::Pseudo2DGel::Config::ms2

flag to set marks for ms2 locations.

Definition at line 94 of file Pseudo2DGel.hpp.

bool pwiz::analysis::Pseudo2DGel::Config::positiveMs2Only

flag to only draw ms2 locations that exist in the peptide_id object and have a score >= 0.

Definition at line 98 of file Pseudo2DGel.hpp.

bool pwiz::analysis::Pseudo2DGel::Config::binScan

flag to render linearly with scan.

This flag will switch between having a y-axis that's linear with scan or linear with time.

Definition at line 103 of file Pseudo2DGel.hpp.

boost::shared_ptr<pwiz::peptideid::PeptideID> pwiz::analysis::Pseudo2DGel::Config::peptide_id

PeptideID object to retrieve peptide id's from.

If the object exists, it will be queried for peptide locations.

Definition at line 108 of file Pseudo2DGel.hpp.

MarkupShape pwiz::analysis::Pseudo2DGel::Config::markupShape

The shape used for pseudo2d gel markups.

Definition at line 111 of file Pseudo2DGel.hpp.

int pwiz::analysis::Pseudo2DGel::Config::output_width

Optional user-specified bitmap width and height.

Normally width and height are automatically calculated.

Definition at line 115 of file Pseudo2DGel.hpp.

int pwiz::analysis::Pseudo2DGel::Config::output_height

Definition at line 116 of file Pseudo2DGel.hpp.

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The documentation for this struct was generated from the following file:

• /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/analysis/passive/Pseudo2DGel.hpp