A base class to hold analytes. More...

#include "us_analyte.h"

Public Types
enum	analyte_t { PROTEIN, DNA, RNA, CARBOHYDRATE }
	The types of analytes used in UltraScan III. More...

Public Member Functions
	US_Analyte ()
	An analyte constructor with default values. More...

bool	operator== (const US_Analyte &) const
	A test for equality between two analytes. More...

int	load (bool, const QString &, US_DB2 *=0)

int	write (bool, const QString &, US_DB2 *=0)

void	dump (void)
	Dump the analyte values to stderr for debugging. More...

Static Public Member Functions
static bool	analyte_path (QString &)

static QString	get_filename (const QString &, const QString &)
	Find an analyte file on the disk. More...

Public Attributes
double	vbar20
	vbar at 20C More...

double	mw
	Molecular weight. More...

QString	description
	Description of the analyte. More...

QString	analyteGUID
	Global identifier of the analyte. More...

QString	sequence
	Coded sequnce of analyte. More...

analyte_t	type
	The type of analyte. More...

bool	grad_form
	Flag if gradient-forming. More...

bool	doubleStranded
	Single or double stranded analyte? More...

bool	complement
	Is the strand a complement? More...

bool	_3prime
	Hydroxyl or Phosphate. More...

bool	_5prime
	Hydroxyl or Phosphate. More...

double	sodium
	Counterion molar ratio/nucleotide. More...

double	potassium
	Counterion molar ratio/nucleotide. More...

double	lithium
	Counterion molar ratio/nucleotide. More...

double	magnesium
	Counterion molar ratio/nucleotide. More...

double	calcium
	Counterion molar ratio/nucleotide. More...

QMap< double, double >	extinction
	extinction[ wavelength ] <=> value More...

QMap< double, double >	refraction
	refraction[ wavelength ] <=> value More...

QMap< double, double >	fluorescence
	fluorescence[ wavelength ] <=> value More...

QString	message

QString	analyteID
	Current analyte DB ID. More...

Private Member Functions
int	load_db (const QString &, US_DB2 *)

int	load_disk (const QString &)

int	read_analyte (const QString &)

void	nucleotide (void)

int	write_disk (const QString &)

int	write_db (US_DB2 *)

void	set_spectrum (US_DB2 *)

void	write_nucleotide (US_DB2 *)

Detailed Description

A base class to hold analytes.

Definition at line 11 of file us_analyte.h.

Member Enumeration Documentation

enum US_Analyte::analyte_t

The types of analytes used in UltraScan III.

Enumerator
PROTEIN
DNA
RNA
CARBOHYDRATE

Definition at line 22 of file us_analyte.h.

Constructor & Destructor Documentation

US_Analyte::US_Analyte ( )

An analyte constructor with default values.

Definition at line 11 of file us_analyte.cpp.

Member Function Documentation

bool US_Analyte::analyte_path ( QString & path )

static

Parameters

path	- A reference where the path to ayalutes on the disk drive is written

Returns: - Success if the path is found or created and failure if the path cannot be created

Definition at line 468 of file us_analyte.cpp.

void US_Analyte::dump ( void )

Dump the analyte values to stderr for debugging.

Definition at line 856 of file us_analyte.cpp.

QString US_Analyte::get_filename	(	const QString &	path,
		const QString &	guid
	)

static

Find an analyte file on the disk.

Parameters

path	The full path of the directory to search
guid	The GUID of the desired analyte

Returns: The file name of the analyte.

Definition at line 830 of file us_analyte.cpp.

int US_Analyte::load	(	bool	db_access,
		const QString &	guid,
		US_DB2 *	db = `0`
	)

Read an analyte from the disk or database

Parameters

db_access	- A flag to indicate if the DB (true) or disk (false) should be searched for the analyte
guid	- The guid of the analyte to be loaded
db	- For DB access, an open database connection

Returns: - The US_DB2 retrun code for the operation

Definition at line 69 of file us_analyte.cpp.

int US_Analyte::load_db	(	const QString &	load_guid,
		US_DB2 *	db
	)

private

Definition at line 78 of file us_analyte.cpp.

int US_Analyte::load_disk ( const QString & guid )

private

Definition at line 186 of file us_analyte.cpp.

void US_Analyte::nucleotide ( void )

private

Definition at line 362 of file us_analyte.cpp.

bool US_Analyte::operator== ( const US_Analyte & a ) const

A test for equality between two analytes.

Definition at line 38 of file us_analyte.cpp.

int US_Analyte::read_analyte ( const QString & filename )

private

Definition at line 238 of file us_analyte.cpp.

void US_Analyte::set_spectrum ( US_DB2 * db )

private

Definition at line 635 of file us_analyte.cpp.

int US_Analyte::write	(	bool	db_access,
		const QString &	filename,
		US_DB2 *	db = `0`
	)

Write an analyte to the disk or database

Parameters

db_access	- A flag to indicate if the DB (true) or disk (false) should be used to save the analyte
filename	- The filename (with path) where the xml file be written if disk access is specified
db	- For DB access, an open database connection

Returns: - The US_DB2 retrun code for the operation

Definition at line 484 of file us_analyte.cpp.

int US_Analyte::write_db ( US_DB2 * db )

private

Definition at line 728 of file us_analyte.cpp.

int US_Analyte::write_disk ( const QString & filename )

private

Definition at line 493 of file us_analyte.cpp.

void US_Analyte::write_nucleotide ( US_DB2 * db )

private

Definition at line 836 of file us_analyte.cpp.

Member Data Documentation

bool US_Analyte::_3prime

Hydroxyl or Phosphate.

Definition at line 35 of file us_analyte.h.

bool US_Analyte::_5prime

Hydroxyl or Phosphate.

Definition at line 36 of file us_analyte.h.

QString US_Analyte::analyteGUID

Global identifier of the analyte.

Definition at line 27 of file us_analyte.h.

QString US_Analyte::analyteID

Current analyte DB ID.

Definition at line 55 of file us_analyte.h.

double US_Analyte::calcium

Counterion molar ratio/nucleotide.

Definition at line 41 of file us_analyte.h.

bool US_Analyte::complement

Is the strand a complement?

Definition at line 34 of file us_analyte.h.

QString US_Analyte::description

Description of the analyte.

Definition at line 26 of file us_analyte.h.

bool US_Analyte::doubleStranded

Single or double stranded analyte?

Definition at line 33 of file us_analyte.h.

QMap< double, double > US_Analyte::extinction

extinction[ wavelength ] <=> value

Definition at line 44 of file us_analyte.h.

QMap< double, double > US_Analyte::fluorescence

fluorescence[ wavelength ] <=> value

Definition at line 50 of file us_analyte.h.

bool US_Analyte::grad_form

Flag if gradient-forming.

Definition at line 30 of file us_analyte.h.

double US_Analyte::lithium

Counterion molar ratio/nucleotide.

Definition at line 39 of file us_analyte.h.

double US_Analyte::magnesium

Counterion molar ratio/nucleotide.

Definition at line 40 of file us_analyte.h.

QString US_Analyte::message

The following items are for internal use in memory. They are not written to the disk or DB

Definition at line 54 of file us_analyte.h.

double US_Analyte::mw

Molecular weight.

Definition at line 25 of file us_analyte.h.

double US_Analyte::potassium

Counterion molar ratio/nucleotide.

Definition at line 38 of file us_analyte.h.

QMap< double, double > US_Analyte::refraction

refraction[ wavelength ] <=> value

Definition at line 47 of file us_analyte.h.

QString US_Analyte::sequence

Coded sequnce of analyte.

Definition at line 28 of file us_analyte.h.

double US_Analyte::sodium

Counterion molar ratio/nucleotide.

Definition at line 37 of file us_analyte.h.

analyte_t US_Analyte::type

The type of analyte.

Definition at line 29 of file us_analyte.h.

double US_Analyte::vbar20

vbar at 20C

Definition at line 24 of file us_analyte.h.

The documentation for this class was generated from the following files:

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation