TVector Class Reference

This class stores all sequence information, both DNA and amino acids. More...

#include <TVector.h>

List of all members.

Public Member Functions
	TVector (ChildBase *win=NULL)
	Constructor.
	~TVector ()
	Destructor.
void	init ()
	Set up basic values.
void	clear ()
	Reset internal state.
void	recalculateCuts ()
	Recalculate restriction enzyme cuts.
void	getCuts (TRestrictionEnzyme *e, vector< TRestrictionCut > &ret, bool clear_vector=true, int max=10000000)
	Gets the cuts of restriction enzyme in this sequence.
bool	reduceToFragment (TRestrictionCut left, TRestrictionCut right)
	Cuts off everything except what is betreen these two cuts.
void	doRestriction ()
	Performs restriction. See TRestrictionEditor.
void	sortRestrictionSites ()
	Sorts the restriction sites by point of cut.
int	countCuts (wxString enzyme)
	Counts the number of cuts for an enzyme in this sequence.
void	methylationSites (wxArrayInt &vi, int what=ALL_METHYLATION_ENZYMES)
	Finds methylation sites.
bool	basematch (char b1, char b2)
	matches DNA bases; b1 in IUPAC, b2 in SIUPAC. This is superior to the "=" operator :-)
void	setIUPAC (char b, wxString s, char *pac=NULL)
char	getNucleotide (int pos, bool complement=false)
	Returns the base at a certain position, or its complement.
void	setNucleotide (int pos, char t)
	Sets a base at a certain position.
char	getComplement (char c)
	Returns the complement of a given base.
void	ligate_right (TVector &v, bool inverted=false)
	Adds another TVector to the right of this one.
void	closeCircle ()
	Closes a linear sequence into a circular (intramolecular ligation).
void	turn (int off)
	Turns a circular sequence "off" bases.
TVector *	getAAvector (int from, int to, int dir=1)
	Returns part of the sequence translated into amino acids.
void	doAction ()
	Perform an action (restriction, usually). Internal use.
void	doRemove (int from, int to, bool update=true, bool enableUndo=true)
	Removes part of the sequence.
void	insert_char (char x, int pos, bool overwrite=false)
	Inserts a character into the sequence.
float	getAAmw (char aa)
	Returns the molecular weight of an amino acid.
float	getAApi (char aa)
	Returns the isoelectric point of an amino acid.
wxString	dna2aa (wxString codon, int translation_table=-1)
	Translates a codon into an amino acid.
void	setAction (wxString _action, int _action_value=0)
	Sets the action for doAction().
void	setDatabase (wxString s)
	Sets the database in which the sequence is stored.
wxString	getDatabase ()
	Returns the database name in which the sequence is stored.
TVector *	newFromMark (int from, int to)
	Generates a new sequence based on a part of this one.
void	setChanged (bool c=true)
	The sequence has been changed.
bool	isChanged ()
	Was the sequence changed?
void	ClearORFs ()
	Clear the found open reading frames.
void	addORFs (int off)
	Add open reading frames for a specific reading frame.
void	removeBlanksFromSequence ()
	Removes blank chars (spaces etc.) from the sequence.
void	removeBlanksFromVector ()
	Removes blank chars (spaces etc.) from the sequence, altering items if necessary.
wxString	getParams ()
	Return sequence parameters.
void	setParams (wxString t)
	Set sequence parameters.
wxString	getParam (wxString key)
	Return the value of a parameter.
void	setParam (wxString key, wxString value)
	Set a parameter key/value pair.
void	setWindow (ChildBase *c)
	Set the window which owns this sequence.
void	setCircular (bool c=true)
	This is a circular sequence (or linear, if c == false).
bool	isCircular ()
	Is this a circular sequence?
bool	isLinear ()
	Is this a linear sequence?
wxString	one2three (int a)
	Converts one letter amino acid code to three-letter acronym.
char	three2one (wxString s)
	Converts three-letter acronym to one letter amino acid code.
void	setStickyEnd (bool left, bool upper, wxString s)
	Sets one of the four possible sticky ends.
wxString	getStickyEnd (bool left, bool upper)
	Returns one of the possible sticky ends.
bool	hasStickyEnds ()
	Does this sequence have sticky ends?
void	callUpdateUndoMenu ()
	Refreshes the Undo menu.
void	setFromVector (TVector &v)
	Makes this sequence a copy of another one (v).
void	doRemoveNucleotide (int x)
	Removes single base at position x.
int	getItemLength (int a)
	Return the length of item a.
TVector *	backtranslate (wxString mode=_T(""))
	Generate a new DNA sequence from this amino acid sequence.
wxString	getStrand53 ()
	Returns the 5'->3' strand of the sequence.
wxString	getStrand35 ()
	Returns the 3'->5' strand of the sequence, as 5'->3'.
TAAProp	getAAprop (char a)
	Returns the properties of the one-letter code amino acid.
int	find_item (wxString s)
	Finds an item with that name.
bool	isEnzymeHidden (wxString s)
	Is enzyme "s" hidden?
void	hideEnzyme (wxString s, bool hideit=true)
	Set enzyme hidden state.
wxString	getSubstring (int mf, int mt)
	Returns a sequence substring.
wxString	transformSequence (bool inverse, bool reverse)
	Transforms the sequence.
wxString	getSequence ()
	Returns the sequence.
wxString *	getSequencePointer ()
	Internal use; only used by SequenceCanvas::OnCharHook.
char	getSequenceChar (int x)
	Gets base at position x.
void	setSequence (wxString ns)
	Sets the sequence.
void	addToSequence (wxString x)
	Appends to the sequence.
void	alterSequence (int pos, char c)
	Changes the base at position pos into c.
int	getSequenceLength ()
	Returns the sequence length.
void	eraseSequence (int from, int len)
	Removes part of the sequence.
void	removeAlignmentArtifacts (char what= '-')
	Removes alignment artifacts from the sequence.
wxString	getDescription ()
	Returns the sequence description.
void	setDescription (wxString s)
	Sets the sequence description.
void	addDescription (wxString s)
	Appends to the sequence description.
wxString	getName ()
	Returns the sequence name.
void	setName (wxString s)
	Sets the sequence name.
void	addName (wxString s)
	Appends to the sequence name.
void	setGenomeMode (bool gm=true)
	Turns genome mode on/off.
bool	getGenomeMode ()
	Returns the genome mode.
int	getMem ()
	Returns memory usage estimate for this sequence. Debugging use only.
bool	getVectorCuts (TVector *v)
	Returns wether or not isoenzymes should be joined.
TEnzymeRules *	getEnzymeRule ()
	Gets the enzyme rules to follow.
int	showGC ()
	Returns 0 for "no", otherwise the number of blocks.
TORF *	getORF (int a)
	Returns an open reading frame.
int	countORFs ()
	Returns the number of found open reading frames.
void	updateDisplay (bool update=true)
	Recalc visual information on next draw.
bool	displayUpdate ()
	Update the display?
void	setType (int newtype)
	Set the sequence type.
int	getType ()
	Returns the sequence type.
int	getMethylationSiteIndex (int pos)
	Returns the index of a potential methylation site.
int	getMethylationSite (int index)
	Returns the position of a methylation site.
int	countMethylationSites ()
	Returns the number of found methylation sites.
void	prepareFeatureEdit (int pos, bool overwrite)
	Changes feature names or cuts features that are about to be edited.
TEnzymeRules *	getEnzymeRules ()
	Returns the restriction enzyme display rules for this vector.
void	setEnzymeRules (TEnzymeRules *er)
	Sets the restriction enzyme display rules for this vector.
void	getItemsAtPosition (int pos, wxArrayInt &vi, bool limit=false)
	Retrieves a list of items at that position (pos is 0-based).
bool	hasItemsAtPosition (int pos)
	Returns wether there are items at that position (pos is 0-based).
int	countCodonTables ()
wxString	getCodonTableName (int x)
void	addRestrictionEnzyme (TRestrictionEnzyme *e)
void	resetTurn ()
	Sets the turned variable to zero.
Public Attributes
vector< TVectorItem >	items
	Items/features/annotations.
vector< TRestrictionCut >	rc
	Restriction enzyme cuts.
wxArrayTRestrictionEnzyme	re
	Manually specified restriction enzymes.
wxArrayTRestrictionEnzyme	re2
	Automatically added restriction enzymes.
wxArrayString	proteases
	Proteases used.
wxArrayString	cocktail
	Enzymes from the last restriction.
TUndo	undo
	Undo information.
Private Member Functions
wxString	invert (wxString s)
	Inverts a string.
wxString	vary_base (char b)
	Turns a SIUPAC into a string of A, C, G, T.
void	makeAA2DNA (wxString mode=_T(""))
	"Translate" amino acid sequence into DNA; can be specified for an organism
wxString	mergeCodons (wxString c1, wxString c2)
	Used by makeAA2DNA for generating "abstract" (SIUPAC) DNA.
void	setCodonTable (int table, wxString sequence, wxString name)
	Sets up the codon_tables variable.
void	evaluate_key_value (wxString key, wxString value)
	Used in setParam() and setParams().
wxString	get_translation_table (int translation_table)
Private Attributes
int	type
	The sequence type.
TEnzymeRules *	enzyme_rules
	Pointer to the restriction enzyme display rules.
bool	recalcvisual
	Recalculate the layout of the sequence?
vector< TORF >	worf
	Open Reading Frames.
wxArrayInt	methyl
	Methylation sites.
wxArrayString	hiddenEnzymes
	Enzymes that are not shown.
wxString	sequence
	The sequence that all this fuss is about.
wxString	_lu
	Left upper sticky end.
wxString	_ll
	Left lower sticky end.
wxString	_ru
	Right upper sticky end.
wxString	_rl
	Right lower sticky end.
wxString	name
	The name of the sequence.
wxString	desc
	The sequence description.
bool	circular
	Is this sequence circular?
bool	changed
	Was this sequence changed?
bool	genomeMode
	Is this a genome (using different display routines)?
ChildBase *	window
	The window this TVector belongs to (might be NULL for most methods).
int	turned
	A circular sequence can be turned; this is the number of bases (negative for "left").
int	action_value
	Used by doAction().
wxString	database
	The database this vector was loaded from.
wxString	action
	Used by doAction().
wxString	aa
	Hell if I remember what this is for.
wxString	AA2DNA [256]
	AA-to-DNA "translation" table; used by makeAA2DNA().
wxArrayString	paramk
	Parameter keys.
wxArrayString	paramv
	Parameter values.
Static Private Attributes
static char	IUPAC [256]
	The ACTG chars in binary encoding (IUPAC_A, IUPAC_C, IUPAC_T, IUPAC_G).
static char	SIUPAC [256]
	The extended IUPAC codes in binary encoding.
static char	COMPLEMENT [256]
	The complement to each SIUPAC base.
static char	ACGT [256]
	Different values for A, C, G, T; used in dna2aa().
static vector< TAAProp >	aaprop
	The 20 amino acids and their properties.
static wxArrayString	codon_tables
	The codon tables for different organisms.
static wxArrayString	codon_table_names
	The names of these codon tables.

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Detailed Description

This class stores all sequence information, both DNA and amino acids.

This class is of extreme importance. It carries sequence data, annotated items, methods for sequence manipulation, and static data, e.e., about amino acid properties and translation tables. So don't let the name fool you, this class does much more than storing vectors.

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Constructor & Destructor Documentation

TVector::TVector (  ChildBase *  win = NULL  )

Constructor.

TVector::~TVector (   )

Destructor.

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Member Function Documentation

void TVector::addDescription (  wxString  s  )

Appends to the sequence description.

void TVector::addName (  wxString  s  )

Appends to the sequence name.

void TVector::addORFs (  int  off  )

Add open reading frames for a specific reading frame.

void TVector::addRestrictionEnzyme (  TRestrictionEnzyme *  e  )

void TVector::addToSequence (  wxString  x  )

Appends to the sequence.

void TVector::alterSequence (  int  pos, char  c )

Changes the base at position pos into c.

TVector * TVector::backtranslate (  wxString  mode = _T("")  )

Generate a new DNA sequence from this amino acid sequence.

bool TVector::basematch (  char  b1, char  b2 )

matches DNA bases; b1 in IUPAC, b2 in SIUPAC. This is superior to the "=" operator :-)

void TVector::callUpdateUndoMenu (   )

Refreshes the Undo menu.

void TVector::clear (   )

Reset internal state.

void TVector::ClearORFs (   )

Clear the found open reading frames.

void TVector::closeCircle (   )

Closes a linear sequence into a circular (intramolecular ligation).

int TVector::countCodonTables (   )

int TVector::countCuts (  wxString  enzyme  )

Counts the number of cuts for an enzyme in this sequence.

int TVector::countMethylationSites (   )

Returns the number of found methylation sites.

int TVector::countORFs (   )

Returns the number of found open reading frames.

bool TVector::displayUpdate (   )

Update the display?

wxString TVector::dna2aa (  wxString  codon, int  translation_table = -1 )

Translates a codon into an amino acid.

void TVector::doAction (   )

Perform an action (restriction, usually). Internal use.

void TVector::doRemove (  int  from, int  to, bool  update = true, bool  enableUndo = true )

Removes part of the sequence.

void TVector::doRemoveNucleotide (  int  x  )

Removes single base at position x.

void TVector::doRestriction (   )

Performs restriction. See TRestrictionEditor.

void TVector::eraseSequence (  int  from, int  len )

Removes part of the sequence.

void TVector::evaluate_key_value (  wxString  key, wxString  value )  [private]

Used in setParam() and setParams().

int TVector::find_item (  wxString  s  )

Finds an item with that name.

wxString TVector::get_translation_table (  int  translation_table  )  [private]

float TVector::getAAmw (  char  aa  )

Returns the molecular weight of an amino acid.

float TVector::getAApi (  char  aa  )

Returns the isoelectric point of an amino acid.

TAAProp TVector::getAAprop (  char  a  )

Returns the properties of the one-letter code amino acid.

TVector * TVector::getAAvector (  int  from, int  to, int  dir = 1 )

Returns part of the sequence translated into amino acids.

wxString TVector::getCodonTableName (  int  x  )

char TVector::getComplement (  char  c  )

Returns the complement of a given base.

void TVector::getCuts (  TRestrictionEnzyme *  e, vector< TRestrictionCut > &  ret, bool  clear_vector = true, int  max = 10000000 )

Gets the cuts of restriction enzyme in this sequence.

wxString TVector::getDatabase (   )  [inline]

Returns the database name in which the sequence is stored.

wxString TVector::getDescription (   )

Returns the sequence description.

TEnzymeRules * TVector::getEnzymeRule (   )

Gets the enzyme rules to follow.

TEnzymeRules * TVector::getEnzymeRules (   )

Returns the restriction enzyme display rules for this vector.

bool TVector::getGenomeMode (   )

Returns the genome mode.

int TVector::getItemLength (  int  a  )

Return the length of item a.

void TVector::getItemsAtPosition (  int  pos, wxArrayInt &  vi, bool  limit = false )

Retrieves a list of items at that position (pos is 0-based).

int TVector::getMem (   )

Returns memory usage estimate for this sequence. Debugging use only.

int TVector::getMethylationSite (  int  index  )

Returns the position of a methylation site.

int TVector::getMethylationSiteIndex (  int  pos  )

Returns the index of a potential methylation site.

wxString TVector::getName (   )

Returns the sequence name.

char TVector::getNucleotide (  int  pos, bool  complement = false )

Returns the base at a certain position, or its complement.

TORF * TVector::getORF (  int  a  )

Returns an open reading frame.

wxString TVector::getParam (  wxString  key  )

Return the value of a parameter.

wxString TVector::getParams (   )

Return sequence parameters.

wxString TVector::getSequence (   )

Returns the sequence.

char TVector::getSequenceChar (  int  x  )

Gets base at position x.

int TVector::getSequenceLength (   )

Returns the sequence length.

wxString * TVector::getSequencePointer (   )

Internal use; only used by SequenceCanvas::OnCharHook.

wxString TVector::getStickyEnd (  bool  left, bool  upper )

Returns one of the possible sticky ends.

wxString TVector::getStrand35 (   )

Returns the 3'->5' strand of the sequence, as 5'->3'.

wxString TVector::getStrand53 (   )

Returns the 5'->3' strand of the sequence.

wxString TVector::getSubstring (  int  mf, int  mt )

Returns a sequence substring.

int TVector::getType (   )

Returns the sequence type.

bool TVector::getVectorCuts (  TVector *  v  )

Returns wether or not isoenzymes should be joined.

bool TVector::hasItemsAtPosition (  int  pos  )

Returns wether there are items at that position (pos is 0-based).

bool TVector::hasStickyEnds (   )

Does this sequence have sticky ends?

void TVector::hideEnzyme (  wxString  s, bool  hideit = true )

Set enzyme hidden state.

void TVector::init (   )

Set up basic values.

void TVector::insert_char (  char  x, int  pos, bool  overwrite = false )

Inserts a character into the sequence.

wxString TVector::invert (  wxString  s  )  [private]

Inverts a string.

bool TVector::isChanged (   )  [inline]

Was the sequence changed?

bool TVector::isCircular (   )

Is this a circular sequence?

bool TVector::isEnzymeHidden (  wxString  s  )

Is enzyme "s" hidden?

bool TVector::isLinear (   )

Is this a linear sequence?

void TVector::ligate_right (  TVector &  v, bool  inverted = false )

Adds another TVector to the right of this one.

void TVector::makeAA2DNA (  wxString  mode = _T("")  )  [private]

"Translate" amino acid sequence into DNA; can be specified for an organism

wxString TVector::mergeCodons (  wxString  c1, wxString  c2 )  [private]

Used by makeAA2DNA for generating "abstract" (SIUPAC) DNA.

void TVector::methylationSites (  wxArrayInt &  vi, int  what = ALL_METHYLATION_ENZYMES )

Finds methylation sites.

TVector * TVector::newFromMark (  int  from, int  to )

Generates a new sequence based on a part of this one.

wxString TVector::one2three (  int  a  )

Converts one letter amino acid code to three-letter acronym.

void TVector::prepareFeatureEdit (  int  pos, bool  overwrite )

Changes feature names or cuts features that are about to be edited.

void TVector::recalculateCuts (   )

Recalculate restriction enzyme cuts.

bool TVector::reduceToFragment (  TRestrictionCut  left, TRestrictionCut  right )

Cuts off everything except what is betreen these two cuts.

void TVector::removeAlignmentArtifacts (  char  what = '-'  )

Removes alignment artifacts from the sequence.

void TVector::removeBlanksFromSequence (   )

Removes blank chars (spaces etc.) from the sequence.

void TVector::removeBlanksFromVector (   )

Removes blank chars (spaces etc.) from the sequence, altering items if necessary.

void TVector::resetTurn (   )

Sets the turned variable to zero.

void TVector::setAction (  wxString  _action, int  _action_value = 0 )

Sets the action for doAction().

void TVector::setChanged (  bool  c = true  )

The sequence has been changed.

void TVector::setCircular (  bool  c = true  )

This is a circular sequence (or linear, if c == false).

void TVector::setCodonTable (  int  table, wxString  sequence, wxString  name )  [private]

Sets up the codon_tables variable.

void TVector::setDatabase (  wxString  s  )  [inline]

Sets the database in which the sequence is stored.

void TVector::setDescription (  wxString  s  )

Sets the sequence description.

void TVector::setEnzymeRules (  TEnzymeRules *  er  )

Sets the restriction enzyme display rules for this vector.

void TVector::setFromVector (  TVector &  v  )

Makes this sequence a copy of another one (v).

void TVector::setGenomeMode (  bool  gm = true  )

Turns genome mode on/off.

void TVector::setIUPAC (  char  b, wxString  s, char *  pac = NULL )

void TVector::setName (  wxString  s  )

Sets the sequence name.

void TVector::setNucleotide (  int  pos, char  t )

Sets a base at a certain position.

void TVector::setParam (  wxString  key, wxString  value )

Set a parameter key/value pair.

void TVector::setParams (  wxString  t  )

Set sequence parameters.

void TVector::setSequence (  wxString  ns  )

Sets the sequence.

void TVector::setStickyEnd (  bool  left, bool  upper, wxString  s )

Sets one of the four possible sticky ends.

void TVector::setType (  int  newtype  )

Set the sequence type.

void TVector::setWindow (  ChildBase *  c  )

Set the window which owns this sequence.

int TVector::showGC (   )

Returns 0 for "no", otherwise the number of blocks.

void TVector::sortRestrictionSites (   )

Sorts the restriction sites by point of cut.

char TVector::three2one (  wxString  s  )

Converts three-letter acronym to one letter amino acid code.

wxString TVector::transformSequence (  bool  inverse, bool  reverse )

Transforms the sequence.

void TVector::turn (  int  off  )

Turns a circular sequence "off" bases.

void TVector::updateDisplay (  bool  update = true  )

Recalc visual information on next draw.

wxString TVector::vary_base (  char  b  )  [private]

Turns a SIUPAC into a string of A, C, G, T.

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Member Data Documentation

wxString TVector::_ll [private]

Left lower sticky end.

wxString TVector::_lu [private]

Left upper sticky end.

wxString TVector::_rl [private]

Right lower sticky end.

wxString TVector::_ru [private]

Right upper sticky end.

wxString TVector::aa [private]

Hell if I remember what this is for.

wxString TVector::AA2DNA[256] [private]

AA-to-DNA "translation" table; used by makeAA2DNA().

vector< TAAProp > TVector::aaprop [static, private]

The 20 amino acids and their properties.

char TVector::ACGT [static, private]

Different values for A, C, G, T; used in dna2aa().

wxString TVector::action [private]

Used by doAction().

int TVector::action_value [private]

Used by doAction().

bool TVector::changed [private]

Was this sequence changed?

bool TVector::circular [private]

Is this sequence circular?

wxArrayString TVector::cocktail

Enzymes from the last restriction.

wxArrayString TVector::codon_table_names [static, private]

The names of these codon tables.

wxArrayString TVector::codon_tables [static, private]

The codon tables for different organisms.

char TVector::COMPLEMENT [static, private]

The complement to each SIUPAC base.

wxString TVector::database [private]

The database this vector was loaded from.

wxString TVector::desc [private]

The sequence description.

TEnzymeRules* TVector::enzyme_rules [private]

Pointer to the restriction enzyme display rules.

bool TVector::genomeMode [private]

Is this a genome (using different display routines)?

wxArrayString TVector::hiddenEnzymes [private]

Enzymes that are not shown.

vector<TVectorItem> TVector::items

Items/features/annotations.

char TVector::IUPAC [static, private]

The ACTG chars in binary encoding (IUPAC_A, IUPAC_C, IUPAC_T, IUPAC_G).

wxArrayInt TVector::methyl [private]

Methylation sites.

wxString TVector::name [private]

The name of the sequence.

wxArrayString TVector::paramk [private]

Parameter keys.

wxArrayString TVector::paramv [private]

Parameter values.

wxArrayString TVector::proteases

Proteases used.

vector<TRestrictionCut> TVector::rc

Restriction enzyme cuts.

wxArrayTRestrictionEnzyme TVector::re

Manually specified restriction enzymes.

wxArrayTRestrictionEnzyme TVector::re2

Automatically added restriction enzymes.

bool TVector::recalcvisual [private]

Recalculate the layout of the sequence?

wxString TVector::sequence [private]

The sequence that all this fuss is about.

char TVector::SIUPAC [static, private]

The extended IUPAC codes in binary encoding.

int TVector::turned [private]

A circular sequence can be turned; this is the number of bases (negative for "left").

int TVector::type [private]

The sequence type.

TUndo TVector::undo

Undo information.

ChildBase* TVector::window [private]

The window this TVector belongs to (might be NULL for most methods).

vector<TORF> TVector::worf [private]

Open Reading Frames.

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

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

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