Staden Class Reference

Parser of Staden output format. More...

#include <Staden.hpp>

Static Public Member Functions
static Align	parse (const std::string &string, bool deleteConsensus=true)
	Parses a string. More...
static Align	parse (std::istream &stream, bool deleteConsensus=true)
	Parses an open stream. More...

Detailed Description

Parser of Staden output format.

The parser is available as a static method. It takes either a stream or a string containing data formatted by the program GAP4 of the Staden package (command 'dump contig to file').

Member Function Documentation

Align parse ( const std::string &  string, bool  deleteConsensus = true  )

static

Parses a string.

Parameters

string	a string containing an alignment formatted by the program GAP4 of the Staden package.
deleteConsensus	if true, the sequence named "CONSENSUS" is deleted from the file (if it is present).

Returns

An Align instance containing the data found in the Staden while, after recoding the character following the standard codes.

This method opens a stream to the string and calls the overloaded method.

The character replacement rules assume Staden default convention, as follows:

• "-" codes for an unknown base and is replaced by "N".
• "*" codes for an alignment gap and is replaced by "-".
• A white space represents missing data and is replaced by "?".

Align parse ( std::istream &  stream, bool  deleteConsensus = true  )

static

Parses an open stream.

Parameters

stream	the open containing an alignment formatted by the program GAP4 of the Staden package.
deleteConsensus	if true, the sequence named "CONSENSUS" is deleted from the file (if it is present).

Returns

An Align instance containing the data found in the Staden while, after recoding the character following the standard codes.

The character replacement rules assume Staden default convention, as follows:

• "-" codes for an unknown base and is replaced by "N".
• "*" codes for an alignment gap and is replaced by "-".
• A white space represents missing data and is replaced by "?".

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

• /home/stephane/Documents/devel/egglib2/egglib-cpp/Staden.hpp
• /home/stephane/Documents/devel/egglib2/egglib-cpp/Staden.cpp