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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

MyChildp
 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


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.


Constructor & Destructor Documentation

AutoAnnotate::AutoAnnotate MyChild _p = NULL  ) 
 

Constructor.

AutoAnnotate::~AutoAnnotate  )  [inline]
 


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).


Friends And Related Function Documentation

friend class TAutoAnnotateDialog [friend]
 


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]
 


The documentation for this class was generated from the following files:
Generated on Fri Aug 11 16:19:44 2006 for GENtle by  doxygen 1.4.1