Binalign object (Comparative Genomics Toolbox for Matlab®)

This object describes multiple alignment of binary data, usually interpreted as presence/absence of some character. Missing values are always described as NaN.

The basic data component is a matrix of size n-by-s, describing a length-s multiple alignment of n genes.

Navigate to:     General Description     Class Structure     Class Construction     Class Functions

Each field can be accessed by the dot (.) operation, or by the GET function. The GET function can work on multiple instances simultaneously. Most fields, except for those that are Dependent, can be modified using the dot (.) operation, or by the SET function.

		Field	Description	Type	Default	Dedicated Get/Set Function
		name	name of object, should be short and used as identifier. This field will never be empty.	string	'unnamed'
		description	verbal description of the class content.	string	''
		source	verbal description of the source of information.	string	''
		seq_names	names of the aligned seqeunces.	cell array of strings	{}
		patterns	list of all unique patterns. A matrix of size no_unique_patterns -by-pattern_length	double matrix	[]
		hist_patterns	number of times each unique pattern appears in the data. A vector of length no_unique_patterns.	integer vector	[]
		loc_patterns	the location of each pattern along the multiple alignment. A cell array of length no_unique_patterns, keeping in each cell the locations of each unique pattern.	cell of vectors of integers	[]
		consensus	concensus sequence. A vector of length no_unique_patterns.	vector on alpha-bet 0/1/NaN	[]
		reliability	reliability score of each position along the multiple alignment. A vector of length no_unique_patterns.	double vector	[]
	Dependent	no_sequences	number of sequences.	integer scalar	0
	Dependent	no_patterns	number of unique patterns.	integer scalar	0
	Dependent	no_sites	number of sites.	integer scalar	0

Empty instance (scalar)

an empty binalign instance, with all fields initialized to their default values.

syntax: bal = binalign;

Empty instance (matrix)

a vector of empty binalign instances.

syntax: bal = binalign(size);

Copy constructor

one binalign instance is copied into another.

syntax: bal_destination = binalign(bal_origin);

Construction by field names

an instance is formed by directly providing field values. Any field which is not dependent is permitted.

syntax: bal = binalign(field_name, field_value, ...);

Readin-in binary multiple alignment

Reading-in a matrix on 0/1/NaN representing a binary multiple alignment. Such a matrix is termed 'block'.

syntax: bal = binalign(block);

Display:

show

displays class content.

showstructure

displays positions with 1s.

I/O functions:

blockin

gets block input and transforms it into pattern input.

blockout

computes the block associated with a BINALIGN object.

dump

writes alignment information to disk.

Information extraction:

findpattern

locates a particular pattern in BINALIGN.

getfulllocpatterns

completes the first element of {loc_patterns}.

name2idx

finds the indices of sequence names.

Transformations:

deletesites

eliminate sites from an alignment.

join

merges several BINALIGN objects.