A class to define a model and provide Disk/DB IO for models. More...

#include "us_model.h"

Classes
class	Association
	Reversible association class The chemical constants associated with a reaction. More...

class	MfemInitial

class	SimulationComponent
	Simulation component (solute/analyte) class Each analyte in the model is a component. A sedimenting solute can also be a component. More...

Public Types
enum	ShapeType { SPHERE, PROLATE, OBLATE, ROD }
	Enumeration of the general shapes of molecules. More...

enum	OpticsType { ABSORBANCE, INTERFERENCE, FLUORESCENCE }
	The type of optics used to acquire data for the current model. More...

enum	AnalysisType { MANUAL, TWODSA, TWODSA_MW, GA, GA_MW, PCSA, COFS, FE, CUSTOMGRID, DMGA, DMGA_CONSTR }
	The type of analysis used with the model. More...

enum	GlobalType { NONE, MENISCUS, GLOBAL, SUPERGLOBAL }
	The type of global analysis used with the model. More...

Public Member Functions
	US_Model ()
	Constructor for the US_Model class. More...

int	load (bool, const QString &, US_DB2 *=0)
	Read a model from the disk or database. More...

int	load (const QString &, US_DB2 *)
	An overloaded function to read a model from a database. More...

int	load (const QString &)
	An overloaded function to read a model from the disk. More...

int	load_string (const QString &)
	A function to load a model from an XML string. More...

bool	operator== (const US_Model &) const
	A test for model equality. More...

bool	operator!= (const US_Model &m) const
	A test for model inequality. More...

int	write (bool, const QString &, US_DB2 *=0)
	Write a model to the disk or database. More...

int	write (US_DB2 *)
	An overloaded function to write a model to the DB. More...

int	write (const QString &)
	An overloaded function to write a model to a file on disk. More...

bool	update_coefficients (void)
	Update any missing analyte coefficient values. More...

QString	typeText (int=0)
	Model type text. More...

bool	constant_ff0 (void)
	Flag constant f/f0. More...

bool	constant_vbar (void)
	Flag constant vbar. More...

bool	is_reactant (const int compx)
	Flag if a specified component is a reactant. More...

bool	is_product (const int compx)
	Flag if a specified component is a product of a reaction. More...

int	mc_iter_xmls (QStringList &)
	Get count and list of MonteCarlo iteration xml contents. More...

void	debug (void)
	Dump model data for debugging. More...

Static Public Member Functions
static bool	calc_coefficients (SimulationComponent &)
	Calculate any missing coefficient values in an analyte component. More...

static bool	model_path (QString &, bool=true)
	Model directory path existence test and creation. More...

static QString	get_filename (const QString &, const QString &, bool &)
	Find a model file on the disk. More...

static QString	composite_mc_file (QStringList &, const bool)
	Create or append to a composite MC model file. More...

Public Attributes
bool	monteCarlo
	Model was generated by MC Analysis. More...

double	wavelength
	Wavelength of the data acquisition. More...

double	variance
	Variance of model fit. More...

double	meniscus
	Meniscus value for model meniscus fit. More...

double	alphaRP
	Alpha (Regularization Parameter) value. More...

QString	description
	Text description of the model. More...

QString	modelGUID
	Identifier of the model. More...

QString	editGUID
	Identifier of the edit data. More...

QString	requestGUID
	Identifier of the LIMS request. More...

QString	dataDescrip
	Raw data triple description string. More...

OpticsType	optics
	The optics used for the data acquisition. More...

AnalysisType	analysis
	The analysis used with this model. More...

GlobalType	global
	Global params used for model generation. More...

QStringList	mcixmls
	Component MC iteration XML contents. More...

int	nmcixs
	Number of MC component xmls (iterations) More...

int	subGrids

int	coSedSolute

QVector< SimulationComponent >	components
	The components being analyzed. More...

QVector< Association >	associations
	The association constants for interacting solutes. More...

QString	message
	Used internally for communication. More...

Private Member Functions
int	load_db (const QString &, US_DB2 *)
	Load a model from the database. More...

int	load_disk (const QString &)
	Load a model from a local disk file. More...

void	mfem_scans (QXmlStreamReader &, SimulationComponent &)
	Parse and load an initial concentration vector. More...

void	get_associations (QXmlStreamReader &, Association &)
	Parse the associations part of a model XML. More...

int	load_stream (QXmlStreamReader &)
	Load a model from an XML stream. More...

int	load_multi_model (QTextStream &)
	Load a multi-iteration model from a text stream. More...

void	write_stream (QXmlStreamWriter &)
	Write to an XML stream. More...

void	write_mm_stream (QTextStream &)
	Write to a multiple model text stream. More...

Detailed Description

A class to define a model and provide Disk/DB IO for models.

Definition at line 9 of file us_model.h.

Member Enumeration Documentation

enum US_Model::AnalysisType

The type of analysis used with the model.

Enumerator
MANUAL
TWODSA
TWODSA_MW
GA
GA_MW
PCSA
COFS
FE
CUSTOMGRID
DMGA
DMGA_CONSTR

Definition at line 27 of file us_model.h.

enum US_Model::GlobalType

The type of global analysis used with the model.

Enumerator
NONE
MENISCUS
GLOBAL
SUPERGLOBAL

Definition at line 31 of file us_model.h.

enum US_Model::OpticsType

The type of optics used to acquire data for the current model.

Enumerator
ABSORBANCE
INTERFERENCE
FLUORESCENCE

Definition at line 24 of file us_model.h.

enum US_Model::ShapeType

Enumeration of the general shapes of molecules.

Enumerator
SPHERE
PROLATE
OBLATE
ROD

Definition at line 21 of file us_model.h.

Constructor & Destructor Documentation

US_Model::US_Model ( )

Constructor for the US_Model class.

Definition at line 78 of file us_model.cpp.

Member Function Documentation

bool US_Model::calc_coefficients ( SimulationComponent & component )

static

Calculate any missing coefficient values in an analyte component.

Returns: - Success if values already existed or were successfully filled in by calculations.

Definition at line 146 of file us_model.cpp.

QString US_Model::composite_mc_file	(	QStringList &	mcfiles,
		const bool	rmvi
	)

static

Create or append to a composite MC model file.

Parameters

mcfiles	A list of MC iteration files to concatenate
rmvi	Flag to remove iteration files

Returns: The file name of the created/appended model.

Definition at line 1294 of file us_model.cpp.

bool US_Model::constant_ff0 ( void )

Flag constant f/f0.

Returns: - A boolean flag of whether component f/f0's are constant

Definition at line 446 of file us_model.cpp.

bool US_Model::constant_vbar ( void )

Flag constant vbar.

Returns: - A boolean flag of whether component vbar's are constant

Definition at line 461 of file us_model.cpp.

void US_Model::debug ( void )

Dump model data for debugging.

Definition at line 1596 of file us_model.cpp.

void US_Model::get_associations	(	QXmlStreamReader &	xml,
		Association &	as
	)

private

Parse the associations part of a model XML.

Definition at line 898 of file us_model.cpp.

QString US_Model::get_filename	(	const QString &	path,
		const QString &	guid,
		bool &	newFile
	)

static

Find a model file on the disk.

Parameters

path	The full path of the directory to search
guid	The GUID of the desired model
newFile	A reference to a boolean variable. Sets false if the model exist, true otherwise.

Returns: The file name of the model. If newFile is true, the name is the next in the M????????.xml numeric sequence but does not yet exist.

Definition at line 1230 of file us_model.cpp.

bool US_Model::is_product ( const int compx )

Flag if a specified component is a product of a reaction.

Parameters

compx Index of component to interrogate

Returns: A boolean flag whether specified component is a product

Definition at line 496 of file us_model.cpp.

bool US_Model::is_reactant ( const int compx )

Flag if a specified component is a reactant.

Parameters

compx Index of component to interrogate

Returns: A boolean flag whether specified component is a reactant

Definition at line 476 of file us_model.cpp.

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

Read a model from the disk or database.

Parameters

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

Returns: - The US_DB2 return code for the operation

Definition at line 516 of file us_model.cpp.

int US_Model::load	(	const QString &	id,
		US_DB2 *	db
	)

An overloaded function to read a model from a database.

Parameters

id	- Database ModelID
db	- For DB access, pointer to open database connection

Returns: - The US_DB2 return code for the operation

Definition at line 956 of file us_model.cpp.

int US_Model::load ( const QString & filename )

An overloaded function to read a model from the disk.

Parameters

filename The name, including full path, of the analyte file

Returns: - The US_DB2 return code for the operation

Definition at line 577 of file us_model.cpp.

int US_Model::load_db	(	const QString &	guid,
		US_DB2 *	db
	)

private

Load a model from the database.

Definition at line 941 of file us_model.cpp.

int US_Model::load_disk ( const QString & guid )

private

Load a model from a local disk file.

Definition at line 523 of file us_model.cpp.

int US_Model::load_multi_model ( QTextStream & tsi )

private

Load a multi-iteration model from a text stream.

Definition at line 736 of file us_model.cpp.

int US_Model::load_stream ( QXmlStreamReader & xml )

private

Load a model from an XML stream.

Definition at line 611 of file us_model.cpp.

int US_Model::load_string ( const QString & mcont )

A function to load a model from an XML string.

Parameters

mcont The XML string model contents

Returns: - The US_DB2 return code for the operation

Definition at line 603 of file us_model.cpp.

int US_Model::mc_iter_xmls ( QStringList & mcixs )

Get count and list of MonteCarlo iteration xml contents.

Parameters

mcixs Reference for return of MC xml contents

Returns: Count of MC iteration xml content strings

Definition at line 1588 of file us_model.cpp.

void US_Model::mfem_scans	(	QXmlStreamReader &	xml,
		SimulationComponent &	sc
	)

private

Parse and load an initial concentration vector.

Definition at line 876 of file us_model.cpp.

bool US_Model::model_path	(	QString &	path,
		bool	is_perm = `true`
	)

static

Model directory path existence test and creation.

Parameters

path	- A reference to the directory path on the disk where model files are to be written
is_perm	- An optional flag if the files are non-temporary

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

Definition at line 338 of file us_model.cpp.

bool US_Model::operator!= ( const US_Model & m ) const

inline

A test for model inequality.

Definition at line 95 of file us_model.h.

bool US_Model::operator== ( const US_Model & m ) const

A test for model equality.

Definition at line 103 of file us_model.cpp.

QString US_Model::typeText ( int subtype = 0 )

Model type text.

Parameters

subtype Optional PCSA subtype (1,2,4...->SL,IS,DS...)

Returns: - A short text string describing the type of model

Definition at line 360 of file us_model.cpp.

bool US_Model::update_coefficients ( void )

Update any missing analyte coefficient values.

Returns: - Success if values already existed or were successfully filled in by calculations.

Definition at line 134 of file us_model.cpp.

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

Write a model 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 model
filename	- The filename (with path) where the xml file be written if disk access is specified
db	- For DB access, pointer to open database connection

Returns: - The US_DB2 return code for the operation

Definition at line 984 of file us_model.cpp.

int US_Model::write ( US_DB2 * db )

An overloaded function to write a model to the DB.

Parameters

db	- A pointer to an open database connection

Returns: - The US_DB2 return code for the operation

Definition at line 991 of file us_model.cpp.

int US_Model::write ( const QString & filename )

An overloaded function to write a model to a file on disk.

Parameters

filename - The filename to write

Returns: - The US_DB2 return code for the operation

Definition at line 1055 of file us_model.cpp.

void US_Model::write_mm_stream ( QTextStream & tso )

private

Write to a multiple model text stream.

Definition at line 856 of file us_model.cpp.

void US_Model::write_stream ( QXmlStreamWriter & xml )

private

Write to an XML stream.

Definition at line 1080 of file us_model.cpp.

Member Data Documentation

double US_Model::alphaRP

Alpha (Regularization Parameter) value.

Definition at line 38 of file us_model.h.

AnalysisType US_Model::analysis

The analysis used with this model.

Definition at line 45 of file us_model.h.

QVector< Association > US_Model::associations

The association constants for interacting solutes.

Definition at line 62 of file us_model.h.

QVector< SimulationComponent > US_Model::components

The components being analyzed.

Definition at line 59 of file us_model.h.

int US_Model::coSedSolute

An index into components (-1 means none). Generally buffer data in the form of a component that affects the data readings.

Definition at line 56 of file us_model.h.

QString US_Model::dataDescrip

Raw data triple description string.

Definition at line 43 of file us_model.h.

QString US_Model::description

Text description of the model.

Definition at line 39 of file us_model.h.

QString US_Model::editGUID

Identifier of the edit data.

Definition at line 41 of file us_model.h.

GlobalType US_Model::global

Global params used for model generation.

Definition at line 46 of file us_model.h.

QStringList US_Model::mcixmls

Component MC iteration XML contents.

Definition at line 47 of file us_model.h.

double US_Model::meniscus

Meniscus value for model meniscus fit.

Definition at line 37 of file us_model.h.

QString US_Model::message

Used internally for communication.

Definition at line 64 of file us_model.h.

QString US_Model::modelGUID

Identifier of the model.

Definition at line 40 of file us_model.h.

bool US_Model::monteCarlo

Model was generated by MC Analysis.

Definition at line 34 of file us_model.h.

int US_Model::nmcixs

Number of MC component xmls (iterations)

Definition at line 48 of file us_model.h.

OpticsType US_Model::optics

The optics used for the data acquisition.

Definition at line 44 of file us_model.h.

QString US_Model::requestGUID

Identifier of the LIMS request.

Definition at line 42 of file us_model.h.

int US_Model::subGrids

An integer to define the number of subgrids for a CUSTOMGRID needed for the 2DSA initialization or output components for DISCRETEGA

Definition at line 52 of file us_model.h.

double US_Model::variance

Variance of model fit.

Definition at line 36 of file us_model.h.

double US_Model::wavelength

Wavelength of the data acquisition.

Definition at line 35 of file us_model.h.

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

Classes

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