Auxiliary funtions and structures. More...

#include <fstream>
#include <iostream>
#include <vector>
#include <deque>
#include <map>
#include <unordered_map>
#include <string>
#include <sstream>
#include <iomanip>
#include <cfloat>
#include <cmath>
#include <QString>
#include <QByteArray>
#include <QMetaType>
#include <QAbstractItemModel>
#include <QModelIndex>
#include <boost/regex.hpp>

Classes
struct	cCoordinateInfo
	Store aggregated information about a coordinate. More...

struct	compareStringBySize
	Compare items in a string vector by size. More...

Macros
#define	WIN 0

#define	UNX 1

#define	OSX 2

#define	OS_TYPE WIN

Enumerations
enum	eVendorType { unknownvendor = 0 , bruker = 1 , waters = 2 }
	Vendor types.

enum	eModeType { denovoengine = 0 , singlecomparison = 1 , databasesearch = 2 , dereplication = 3 , compoundsearch = 4 }
	Running modes of the application.

enum	ePeptideType { linear = 0 , cyclic = 1 , branched = 2 , branchcyclic = 3 , linearpolyketide = 4 , cyclicpolyketide = 5 , other = 6 }
	The types of peptides supported by the application.

Functions
void	storeIntVector (vector< int > &v, ofstream &os)
	Store a vector of integers into an output stream. More...

void	loadIntVector (vector< int > &v, ifstream &is)
	Load a vector of integers from an input stream. More...

void	storeDoubleVector (vector< double > &v, ofstream &os)
	Store a vector of doubles into an output stream. More...

void	loadDoubleVector (vector< double > &v, ifstream &is)
	Load a vector of doubles from an input stream. More...

void	storeString (string &s, ofstream &os)
	Store a string into an output stream. More...

void	loadString (string &s, ifstream &is)
	Load a string from an input stream. More...

void	storeStringVector (vector< string > &v, ofstream &os)
	Store a vector of strings into an output stream. More...

void	loadStringVector (vector< string > &v, ifstream &is)
	Load a vector of strings from an input stream. More...

void	storeStringIntMap (map< string, int > &map, ofstream &os)
	Store a map<string, int> into an output stream. More...

void	loadStringIntMap (map< string, int > &map, ifstream &is)
	Load a map<string, int> from an input stream. More...

void	storeStringIntMapVector (vector< map< string, int > > &vector, ofstream &os)
	Store a vector of map<string, int> into an output stream. More...

void	loadStringIntMapVector (vector< map< string, int > > &vector, ifstream &is)
	Load a vector of map<string, int> from an input stream. More...

void	storeIntStringMap (map< int, string > &map, ofstream &os)
	Store a map<int, string> into an output stream. More...

void	loadIntStringMap (map< int, string > &map, ifstream &is)
	Load a map<int, string> from an input stream. More...

void	convertStringIntUnorderedMapToStringVector (unordered_map< string, int > &map, vector< string > &vector)
	Convert an unordered_map<string, int> to a vector<string>. More...

bool	isWhiteSpace (char c)
	Check if c is a white space. More...

bool	isWhiteSpaceExceptSpace (char c)
	Check if c is a white space (except normal space). More...

string &	removeWhiteSpacesExceptSpaces (string &s)
	Remove white spaces except normal spaces from a string. More...

bool	checkRegex (ePeptideType peptidetype, string &sequence, string &errormessage)
	Check the syntax of a peptide sequence. More...

bool	checkFile (string filename)
	Check if a file exists. More...

bool	compareDoubles (double &first, double &second, double epsilon=0.0000001f)
	Check if two doubles are equal. More...

bool	compareStringVectors (vector< string > &first, vector< string > &second)
	Check if two vectors of strings are equal. More...

bool	compareMapsIntDouble (map< int, double > &first, map< int, double > &second, double epsilon=0.0000001f)
	Check if two maps of doubles are equal. More...

void	parseBranch (ePeptideType peptidetype, string &composition, vector< string > &vectorcomposition, int &branchstart, int &branchend)
	Parse a position of a branch from a peptide sequence. More...

ePeptideType	getPeptideTypeFromString (string &s)
	Convert a string to peptide type. More...

string	getStringFromPeptideType (ePeptideType peptidetype)
	Convert the peptide type to a string. More...

double	cropPrecisionToSixDecimals (double value)
	Crop a precision of a double to six decimal places. More...

QByteArray	cropDecimalsByteArray (double value)
	Crop decimals of a double. More...

QByteArray	cropPrecisionToSixDecimalsByteArray (double value)
	Crop a precision of a double to six decimal places. More...

string	getShortFileName (string filename)
	Get a short filename from a string. More...

	Q_DECLARE_METATYPE (vector< cCoordinateInfo >)
	Register vector<cCoordinateInfo> by Qt.

double	fact (int value)
	Get factorial of a value. More...

double	median (vector< double > &vector)
	Get median from a vector of doubles. More...

string	stripHTML (string &htmlstring)
	Strip HTML tags from a HTML string. More...

void	stripIsomers (string &peptidesequence)
	Strip isomers of building blocks from an input peptide sequence. More...

void	stripIsomersFromStringVector (vector< string > &acronyms)
	Strip isomers of building blocks from an input string vector. More...

bool	proxyModelCheckInt (QAbstractItemModel *model, int index, int row, int column, QString str, const QModelIndex &parent)
	Proxy model - int comparator. More...

bool	proxyModelCheckDouble (QAbstractItemModel *model, int index, int row, int column, QString str, const QModelIndex &parent)
	Proxy model - double comparator. More...

bool	proxyModelCheckString (QAbstractItemModel *model, int index, int row, int column, QString &itemstr, QString str, const QModelIndex &parent, bool wholeword, Qt::CaseSensitivity casesensitive)
	Proxy model - string comparator. More...

bool	isCompatibleVersion (int fileversionpart1, int fileversionpart2, int fileversionpart3, int lastcompatiblepart1, int lastcompatiblepart2, int lastcompatiblepart3)
	Check the compatibility of CycloBranch version. More...

string	fixLabelCharge (string &str, int sourcecharge, int targetcharge)
	Fix the name of a multiply charged ion in MS mode. More...

Variables
const double	pi = 3.141592653589793
	The pi value.

const double	econst = 2.718281828459045
	The e constant.

const int	defaultwinsizex = 1350
	Default window size x.

const int	defaultwinsizey = 875
	Default window size y.

QString	appname
	The name of the application.

QString	appversion
	The version of the application.

QString	lastcompatibleappversion
	Last compatible version of the application.

QString	installdir
	A directory where the application is installed under Linux or OSX.

Detailed Description

Auxiliary funtions and structures.

Function Documentation

◆ checkFile()

bool checkFile ( string filename )

Check if a file exists.

Parameters

filename filename

Return values

bool	true if the file exists, false otherwise

◆ checkRegex()

bool checkRegex	(	ePeptideType	peptidetype,
		string &	sequence,
		string &	errormessage
	)

Check the syntax of a peptide sequence.

Parameters

peptidetype	peptide type
sequence	peptide sequence
errormessage	an error message if false is returned

Return values

bool	true when the syntax is correct, false otherwise

◆ compareDoubles()

bool compareDoubles	(	double &	first,
		double &	second,
		double	epsilon = `0.0000001f`
	)

Check if two doubles are equal.

Parameters

first	first value
second	second value
epsilon	epsilon value for comparison

Return values

bool	true if the values are equal

◆ compareMapsIntDouble()

bool compareMapsIntDouble	(	map< int, double > &	first,
		map< int, double > &	second,
		double	epsilon = `0.0000001f`
	)

Check if two maps of doubles are equal.

Parameters

first	first map
second	second map
epsilon	epsilon value for double comparison

Return values

bool	true if the maps are equal

◆ compareStringVectors()

bool compareStringVectors	(	vector< string > &	first,
		vector< string > &	second
	)

Check if two vectors of strings are equal.

Parameters

first	first vector
second	second vector

Return values

bool	true if the vectors are equal

◆ convertStringIntUnorderedMapToStringVector()

void convertStringIntUnorderedMapToStringVector	(	unordered_map< string, int > &	map,
		vector< string > &	vector
	)

Convert an unordered_map<string, int> to a vector<string>.

Parameters

map	an input map
vector	an output vector

◆ cropDecimalsByteArray()

QByteArray cropDecimalsByteArray ( double value )

Crop decimals of a double.

Parameters

value an input value

Return values

QByteArray a value with the limited precision

◆ cropPrecisionToSixDecimals()

double cropPrecisionToSixDecimals ( double value )

Crop a precision of a double to six decimal places.

Parameters

value an input value

Return values

double a value with the limited precision

◆ cropPrecisionToSixDecimalsByteArray()

QByteArray cropPrecisionToSixDecimalsByteArray ( double value )

Crop a precision of a double to six decimal places.

Parameters

value an input value

Return values

QByteArray a value with the limited precision

◆ fact()

double fact ( int value )

Get factorial of a value.

Parameters

value value

Return values

double factorial of the value

◆ fixLabelCharge()

string fixLabelCharge	(	string &	str,
		int	sourcecharge,
		int	targetcharge
	)

Fix the name of a multiply charged ion in MS mode.

Parameters

str	original ion name
sourcecharge	source charge
targetcharge	target charge

Return values

string fixed name

◆ getPeptideTypeFromString()

ePeptideType getPeptideTypeFromString ( string & s )

Convert a string to peptide type.

Parameters

s string

Return values

ePeptideType type of peptide

◆ getShortFileName()

string getShortFileName ( string filename )

Get a short filename from a string.

Parameters

filename long filename

Return values

string short filename

◆ getStringFromPeptideType()

string getStringFromPeptideType ( ePeptideType peptidetype )

Convert the peptide type to a string.

Parameters

peptidetype type of peptide

Return values

string string

◆ isCompatibleVersion()

bool isCompatibleVersion	(	int	fileversionpart1,
		int	fileversionpart2,
		int	fileversionpart3,
		int	lastcompatiblepart1,
		int	lastcompatiblepart2,
		int	lastcompatiblepart3
	)

Check the compatibility of CycloBranch version.

Parameters

fileversionpart1	tested version (part 1)
fileversionpart2	tested version (part 2)
fileversionpart3	tested version (part 3)
lastcompatiblepart1	last compatible version (part 1)
lastcompatiblepart2	last compatible version (part 2)
lastcompatiblepart3	last compatible version (part 3)

Return values

bool	true if the versions are compatible

◆ isWhiteSpace()

bool isWhiteSpace ( char c )

Check if c is a white space.

Parameters

c char

Return values

bool	true if c is a white space; false otherwise.

◆ isWhiteSpaceExceptSpace()

bool isWhiteSpaceExceptSpace ( char c )

Check if c is a white space (except normal space).

Parameters

c char

Return values

bool	true if c is a white space (except normal space); false otherwise.

◆ loadDoubleVector()

void loadDoubleVector	(	vector< double > &	v,
		ifstream &	is
	)

Load a vector of doubles from an input stream.

Parameters

v	reference to a vector of doubles
is	reference to an input stream

◆ loadIntStringMap()

void loadIntStringMap	(	map< int, string > &	map,
		ifstream &	is
	)

Load a map<int, string> from an input stream.

Parameters

map	reference to a map
is	reference to an input stream

◆ loadIntVector()

void loadIntVector	(	vector< int > &	v,
		ifstream &	is
	)

Load a vector of integers from an input stream.

Parameters

v	reference to a vector of integers
is	reference to an input stream

◆ loadString()

void loadString	(	string &	s,
		ifstream &	is
	)

Load a string from an input stream.

Parameters

s	reference to a string
is	reference to an input stream

◆ loadStringIntMap()

void loadStringIntMap	(	map< string, int > &	map,
		ifstream &	is
	)

Load a map<string, int> from an input stream.

Parameters

map	reference to a map
is	reference to an input stream

◆ loadStringIntMapVector()

void loadStringIntMapVector	(	vector< map< string, int > > &	vector,
		ifstream &	is
	)

Load a vector of map<string, int> from an input stream.

Parameters

vector	reference to a vector
is	reference to an input stream

◆ loadStringVector()

void loadStringVector	(	vector< string > &	v,
		ifstream &	is
	)

Load a vector of strings from an input stream.

Parameters

v	reference to a vector of strings
is	reference to an input stream

◆ median()

double median ( vector< double > & vector )

Get median from a vector of doubles.

Parameters

vector vector of doubles

Return values

double median value

◆ parseBranch()

void parseBranch	(	ePeptideType	peptidetype,
		string &	composition,
		vector< string > &	vectorcomposition,
		int &	branchstart,
		int &	branchend
	)

Parse a position of a branch from a peptide sequence.

Parameters

peptidetype	peptide type
composition	a peptide sequence where all blocks "[blockX]-[blockY]" were replaced by ids "1-2"; but "\‍(" and "\‍)" are still included
vectorcomposition	an output vector with ids of blocks represented as strings
branchstart	start position of a branch (an output value)
branchend	end position of a branch (an output value)

◆ proxyModelCheckDouble()

bool proxyModelCheckDouble	(	QAbstractItemModel *	model,
		int	index,
		int	row,
		int	column,
		QString	str,
		const QModelIndex &	parent
	)

Proxy model - double comparator.

Parameters

model	model
index	index
row	row
column	column
str	query string
parent	parent

Return values

bool	true if the item is valid

◆ proxyModelCheckInt()

bool proxyModelCheckInt	(	QAbstractItemModel *	model,
		int	index,
		int	row,
		int	column,
		QString	str,
		const QModelIndex &	parent
	)

Proxy model - int comparator.

Parameters

model	model
index	index
row	row
column	column
str	query string
parent	parent

Return values

bool	true if the item is valid

◆ proxyModelCheckString()

bool proxyModelCheckString	(	QAbstractItemModel *	model,
		int	index,
		int	row,
		int	column,
		QString &	itemstr,
		QString	str,
		const QModelIndex &	parent,
		bool	wholeword,
		Qt::CaseSensitivity	casesensitive
	)

Proxy model - string comparator.

Parameters

model	model
index	index
row	row
column	column
itemstr	string of current item
str	query string
parent	parent
wholeword	wholeword
casesensitive	casesensitive

Return values

bool	true if the item is valid

◆ removeWhiteSpacesExceptSpaces()

string & removeWhiteSpacesExceptSpaces ( string & s )

Remove white spaces except normal spaces from a string.

Parameters

s	reference to a string

Return values

string reference to the input string

◆ storeDoubleVector()

void storeDoubleVector	(	vector< double > &	v,
		ofstream &	os
	)

Store a vector of doubles into an output stream.

Parameters

v	reference to a vector of doubles
os	reference to an output stream

◆ storeIntStringMap()

void storeIntStringMap	(	map< int, string > &	map,
		ofstream &	os
	)

Store a map<int, string> into an output stream.

Parameters

map	reference to a map
os	reference to an output stream

◆ storeIntVector()

void storeIntVector	(	vector< int > &	v,
		ofstream &	os
	)

Store a vector of integers into an output stream.

Parameters

v	reference to a vector of integers
os	reference to an output stream

◆ storeString()

void storeString	(	string &	s,
		ofstream &	os
	)

Store a string into an output stream.

Parameters

s	reference to a string
os	reference to an output stream

◆ storeStringIntMap()

void storeStringIntMap	(	map< string, int > &	map,
		ofstream &	os
	)

Store a map<string, int> into an output stream.

Parameters

map	reference to a map
os	reference to an output stream

◆ storeStringIntMapVector()

void storeStringIntMapVector	(	vector< map< string, int > > &	vector,
		ofstream &	os
	)

Store a vector of map<string, int> into an output stream.

Parameters

vector	reference to a vector
os	reference to an output stream

◆ storeStringVector()

void storeStringVector	(	vector< string > &	v,
		ofstream &	os
	)

Store a vector of strings into an output stream.

Parameters

v	reference to a vector of strings
os	reference to an output stream

◆ stripHTML()

string stripHTML ( string & htmlstring )

Strip HTML tags from a HTML string.

Parameters

htmlstring reference to a string with HTML tags

Return values

string stripped string

◆ stripIsomers()

void stripIsomers ( string & peptidesequence )

Strip isomers of building blocks from an input peptide sequence.

Parameters

peptidesequence a peptide sequence

◆ stripIsomersFromStringVector()

void stripIsomersFromStringVector ( vector< string > & acronyms )

Strip isomers of building blocks from an input string vector.

Parameters

acronyms vector of building block acronyms with isomers

Classes

Macros

Enumerations

Functions

Variables

Detailed Description

Function Documentation

◆ checkFile()

◆ checkRegex()

◆ compareDoubles()

◆ compareMapsIntDouble()

◆ compareStringVectors()

◆ convertStringIntUnorderedMapToStringVector()

◆ cropDecimalsByteArray()

◆ cropPrecisionToSixDecimals()

◆ cropPrecisionToSixDecimalsByteArray()

◆ fact()

◆ fixLabelCharge()

◆ getPeptideTypeFromString()

◆ getShortFileName()

◆ getStringFromPeptideType()

◆ isCompatibleVersion()

◆ isWhiteSpace()

◆ isWhiteSpaceExceptSpace()

◆ loadDoubleVector()

◆ loadIntStringMap()

◆ loadIntVector()

◆ loadString()

◆ loadStringIntMap()

◆ loadStringIntMapVector()

◆ loadStringVector()

◆ median()

◆ parseBranch()

◆ proxyModelCheckDouble()

◆ proxyModelCheckInt()

◆ proxyModelCheckString()

◆ removeWhiteSpacesExceptSpaces()

◆ storeDoubleVector()

◆ storeIntStringMap()

◆ storeIntVector()

◆ storeString()

◆ storeStringIntMap()

◆ storeStringIntMapVector()

◆ storeStringVector()

◆ stripHTML()

◆ stripIsomers()

◆ stripIsomersFromStringVector()