AutoAnnotate Class Reference

The AutoAnnotate class scans database(s) for known features in the current sequence. More...

#include <AutoAnnotate.h>

List of all members.

Public Member Functions
	AutoAnnotate (MyChild *_p=NULL)
	Constructor.
	~AutoAnnotate ()
bool	SettingsDialog ()
	Runs the dialog; returns wether to Run or not.
void	Run ()
	Runs the search.
Private Member Functions
bool	ScanDatabase (wxString database)
	Scans a database for matching features.
bool	addORFs (TVector *v)
	Adds open reading frames as features (that could not be identified).
bool	MatchItem (TVector *tv, TVectorItem &item, TVector *v, wxString &oseq)
	Compares two items to prevent double entries.
bool	RawMatch (TVectorItem &item, TVector *v, wxString &oseq, wxString &s)
	Tries to match the full item sequence against the current sequence.
void	machete (TVector *v)
	Reduces the number of identified items, so that one can actually read something in the map again :-).
bool	within (TVectorItem &i1, TVectorItem &i2, TVector *v)
	Checks if TVectorItem i2 lies within i1 (no need to add it then).
Private Attributes
MyChild *	p
	Pointer to the calling MyChild.
wxArrayString	alreadyin
	Cache of items already added.
wxString	commonVectorsDatabase
wxString	additionalDatabase
bool	useCommonDatabase
bool	useAdditionalDatabase
bool	useMachete
bool	doAddORFs
wxArrayString	dbname
wxArrayString	dbfile
Friends
class	TAutoAnnotateDialog

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Detailed Description

The AutoAnnotate class scans database(s) for known features in the current sequence.

It uses the TAutoAnnotateDialog class to display a settings dialog, then runs through one or two databases (depending on the settings), extracting DNA, and matching it to the current sequence. Finally, it will add all not-identified open reading frames as "unknown" features.

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Constructor & Destructor Documentation

AutoAnnotate::AutoAnnotate (  MyChild *  _p = NULL  )

Constructor.

AutoAnnotate::~AutoAnnotate (   )  [inline]

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Member Function Documentation

bool AutoAnnotate::addORFs (  TVector *  v  )  [private]

Adds open reading frames as features (that could not be identified).

void AutoAnnotate::machete (  TVector *  v  )  [private]

Reduces the number of identified items, so that one can actually read something in the map again :-).

bool AutoAnnotate::MatchItem (  TVector *  tv, TVectorItem &  item, TVector *  v, wxString &  oseq )  [private]

Compares two items to prevent double entries.

bool AutoAnnotate::RawMatch (  TVectorItem &  item, TVector *  v, wxString &  oseq, wxString &  s )  [private]

Tries to match the full item sequence against the current sequence.

void AutoAnnotate::Run (   )

Runs the search.

bool AutoAnnotate::ScanDatabase (  wxString  database  )  [private]

Scans a database for matching features.

bool AutoAnnotate::SettingsDialog (   )

Runs the dialog; returns wether to Run or not.

bool AutoAnnotate::within (  TVectorItem &  i1, TVectorItem &  i2, TVector *  v )  [private]

Checks if TVectorItem i2 lies within i1 (no need to add it then).

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Friends And Related Function Documentation

friend class TAutoAnnotateDialog [friend]

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Member Data Documentation

wxString AutoAnnotate::additionalDatabase [private]

wxArrayString AutoAnnotate::alreadyin [private]

Cache of items already added.

wxString AutoAnnotate::commonVectorsDatabase [private]

wxArrayString AutoAnnotate::dbfile [private]

wxArrayString AutoAnnotate::dbname [private]

bool AutoAnnotate::doAddORFs [private]

MyChild* AutoAnnotate::p [private]

Pointer to the calling MyChild.

bool AutoAnnotate::useAdditionalDatabase [private]

bool AutoAnnotate::useCommonDatabase [private]

bool AutoAnnotate::useMachete [private]

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

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

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