TGenBank Class Reference

GenBank format import/export class. More...

#include <GenBank.h>

List of all members.

Public Member Functions
	TGenBank ()
	Constructor.
	~TGenBank ()
	Destructor, empty.
void	load (wxString s)
	Loads text from file, calles parser.
void	paste (wxString s)
	Calls parser for text.
void	remap (TVector *v)
	Wrapper to map the current sequence to a TVector.
void	remap (TVector *v, const wxArrayString &vs, const wxArrayInt &vi)
	Remaps the given data to a TVector.
void	doExport (TVector *v, wxArrayString &ex)
	Create a GenBank-format list of lines from a TVector.
wxString	trim (wxString s)
	Removes the leading blanks from a string.
void	itrim (wxString &s)
	Removes the leading blanks from a string.
void	multitrim (wxString &s, bool quotes=true)
	Removes the leading and ending blanks and/or quotes from a string.
wxString	trimQuotes (wxString s)
	Removes the leading and ending quotes from a string.
wxString	quote (wxString pre, wxString q)
	???
void	wrapit (wxArrayString &ex, wxString init, wxString data, int limit=80)
	Formats a new GenBank entry to a certein width.
wxString	expand (wxString init, int to, wxString with=_T(" "))
	Sets a string to a certain width, and fills it up if necessary.
int	count_blanks (wxString &s)
	Counts the leading blanks in a string.
Public Attributes
bool	success
	Did we encounter any errors while parsing?
Private Member Functions
void	parseLines ()
	The parser.
void	addItem (TVector *v, wxArrayString &va)
	Adds an item to a TVector.
void	iterateItem (TVector *v, TVectorItem &i, wxString l, int tag=0)
	Used for generating multiple items from a single GenBank item entry.
bool	isValidSequence (char a)
	Checks if the given char is "-", A-Z, or a-z.
Private Attributes
vector< wxArrayString >	vs_l
	All the lines, grouped by sequences.
vector< wxArrayInt >	vi_l
	All the line indentations.
wxArrayString	vs
	Current sequence.
wxArrayInt	vi
	Current line indentations.
wxString	params
	???
wxString	title
	Sequence title.
wxString	description
	Sequence description.
bool	perm [256]
	Allowed chars.
bool	validseq [256]
	Allowed sequence chars.
bool	isblank [256]
	Blank chars.
bool	isblankorquote [256]
	Blank or quote chars.
Friends
class	TAlignment
class	MyFrame

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Detailed Description

GenBank format import/export class.

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Constructor & Destructor Documentation

TGenBank::TGenBank (   )

Constructor.

TGenBank::~TGenBank (   )

Destructor, empty.

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Member Function Documentation

void TGenBank::addItem (  TVector *  v, wxArrayString &  va )  [private]

Adds an item to a TVector. Parameters: v  Pointer to the TVector va  Array of lines containing the item, GenBank-encoded

int TGenBank::count_blanks (  wxString &  s  )

Counts the leading blanks in a string. Parameters: s  The string

void TGenBank::doExport (  TVector *  v, wxArrayString &  ex )

Create a GenBank-format list of lines from a TVector. Parameters: v  The TVector ex  The array of lines (as reference)

wxString TGenBank::expand (  wxString  init, int  to, wxString  with = _T(" ") )

Sets a string to a certain width, and fills it up if necessary. Parameters: init  The string to expand/cut to  The desired length with  To fill the string with, if needed

bool TGenBank::isValidSequence (  char  a  )  [private]

Checks if the given char is "-", A-Z, or a-z. Parameters: a  The char to check

void TGenBank::iterateItem (  TVector *  v, TVectorItem &  i, wxString  l, int  tag = 0 )  [private]

Used for generating multiple items from a single GenBank item entry. Parameters: Pointer  to the TVector i  The TVectorItem new items should be based on l  ??? tag  ???

void TGenBank::itrim (  wxString &  s  )

Removes the leading blanks from a string. Parameters: s  The string (as reference)

void TGenBank::load (  wxString  s  )

Loads text from file, calles parser. Parameters: s  Filename

void TGenBank::multitrim (  wxString &  s, bool  quotes = true )

Removes the leading and ending blanks and/or quotes from a string. Parameters: s  The string (as reference)

void TGenBank::parseLines (   )  [private]

The parser.

void TGenBank::paste (  wxString  s  )

Calls parser for text. Parameters: s  The text in GenBank format

wxString TGenBank::quote (  wxString  pre, wxString  q )

??? Parameters: pre  ??? q  ???

void TGenBank::remap (  TVector *  v, const wxArrayString &  vs, const wxArrayInt &  vi )

Remaps the given data to a TVector. Parameters: v  Pointer to the TVector vs  The lines vi  The line indentations

void TGenBank::remap (  TVector *  v  )

Wrapper to map the current sequence to a TVector.

wxString TGenBank::trim (  wxString  s  )

Removes the leading blanks from a string. Parameters: s  The string

wxString TGenBank::trimQuotes (  wxString  s  )

Removes the leading and ending quotes from a string. Parameters: s  The string

void TGenBank::wrapit (  wxArrayString &  ex, wxString  init, wxString  data, int  limit = 80 )

Formats a new GenBank entry to a certein width. Parameters: ex  The output init  The GenBank "command" data  The data (to be wrapped) limit  The maximum line width

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Friends And Related Function Documentation

friend class MyFrame [friend]

friend class TAlignment [friend]

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Member Data Documentation

wxString TGenBank::description [private]

Sequence description.

bool TGenBank::isblank[256] [private]

Blank chars.

bool TGenBank::isblankorquote[256] [private]

Blank or quote chars.

wxString TGenBank::params [private]

???

bool TGenBank::perm[256] [private]

Allowed chars.

bool TGenBank::success

Did we encounter any errors while parsing?

wxString TGenBank::title [private]

Sequence title.

bool TGenBank::validseq[256] [private]

Allowed sequence chars.

wxArrayInt TGenBank::vi [private]

Current line indentations.

vector<wxArrayInt> TGenBank::vi_l [private]

All the line indentations.

wxArrayString TGenBank::vs [private]

Current sequence.

vector<wxArrayString> TGenBank::vs_l [private]

All the lines, grouped by sequences.

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

• C:/Programme/Dev-Cpp/Mine/GENtle/GenBank.h
• C:/Programme/Dev-Cpp/Mine/GENtle/GenBank.cpp

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