The Bioinformatics Template Library (BTL)  

Version 3.0 alpha

Description

The focus of this library is on the data structures and algorithms used within the fields of bioinformatics and molecular modelling. The approach used closely follows that of the Standard Template Library (STL) which is part of ISO/ANSI standard C++. This library uses templates to implement generic programming. Templates allow the development of efficient programming modules using compile-time mechanisms. Although the BTL has been designed with biomolecular applications in mind it contains classes of more general utility. For instance, the matrix container and associated algorithms could be used for matrix algebra in many contexts.

Floating Point Precision

The floating point precision of the library as a whole is defined as the user defined type BTL_REAL. A typedef statement in the BTL.h. e.g.

typedef double BTL_REAL;

To change the precision used simply alter this statement and recompile your code. Of course not all floating point variables in the library are of type BTL_REAL, some, for instance, are fixed at type double to avoid large round off errors. In spite of this, setting BTL_REAL to be of type float may well result significant round off problems in certain calculations such as those used by the eigen_solution() algorithm.

Debugging Version of Library

If the DEBUG_VERSION symbol is defined then the library will carry out extra error checking such as some array bounds checking. This checking will obviously make the library more robust but will also increase excecution times. Simply comment out the define statement in the BTL.h file, if the extra checking is not required.

Components

• ATOM_processor - reads PDB format files and extracts ATOM record data into vectors.
• pdb_sort - function object (functor) used for sorting objects into Protein Data Bank (pdb) format atom order
• amino_acid_property - functor that returns amino acid property values
• PIR_processor - simple class for parsing PIR format sequence files
• PPM_processor - simple class for parsing ascii PPM format image files
• XYZ_processor - reads xyz format coordinate files and puts the data in vectors
• needleman_wunsch_similarity
• needleman_wusch_align
• fourier_transform
• mean
• mean_absolute_deviation
• variance
• normal_statistics
• max_mismatch
• max_absolute_mismatch
• min_mismatch
• min_absolute_mismatch
• every_less_equal
• every_less
• less_absolute
• random_uniform
• random_normal
• random_exponential
• numeric_vector - a vector of real numbers of any size
• scalar_product
• direct_product
• triple_vector_product
• triple_scalar_product
• separation_squared
• separation
• sum
• sum_precise
• sum_of_squares
• sum_of_squares_precise
• magnitude
• magnitude_precise
• rotate
• translate
• matrix - a 2-dimensional array of real numbers of any size
• matrix_product
• matrixtranspose_matrix_product
• matrix_matrixtranspose_product
• transpose
• column_means
• copy_column
• determinant
• minor
• adjoint
• inverse_square
• eigen_solution
• inverse_cholesy
• lsqfit_rmsd
• centroid
• rotation_from_fit
• rmsd
• check_3d_data
• BTL_VertexWithEdges - template graph vertex for use with BTL_GraphWithEdges
• BTL_Edge - a template graph edge for use with BTL_GraphWithEdges
• BTL_GraphWithEdges - a template graph with two template parameters determining the type of vertices and edges
• BTL_Vertex - a template graph vertex for use with graph
• BTL_Graph - A template graph with edges as simple pointers to vertices.
• BTL_DFSIterator - an iterator for iterating over a connected sub-graph in depth first order.
• BTL_ConstDFSIterator - the const version of the BTL_DFSIterator.

 

 
 
 
 
 
 
 

Files

• The library source code
• Demo programs

ATOM_processor

This is simple class for reading ATOM records from clean PDB format files.
Friends: an output operator
Authors: M.A.Williams
Files: ATOM_processor.h
Dependencies: None

Operations
 
 

• CloseFile -
• Alternate -
• ATOM_processor - - Default constructor (does nothing)
• ~ATOM_processor - - Default destructor (does nothing)
• empty - - Returns true if no coordinates have been read
• ReadFile - - Read a PDB format file with the given name, selecting only those chains whose id letter occurs in a given string and using the alternate set of coordinates identified by the user-supplied character. The default reads records with any chain id and either no alternate id or the first encounterd alternate id.
• AtomNo - - Return a reference to the atom number in a STL vector of int.
• AtomName - - Return a reference to the atom n in a STL vector of char. Each name is stored as 4 chars.
• ResidueName - - Return a reference to the atom names in a STL vector of char. Each name is stored as 3 chars.
• ResidueNo - - Return a reference to the residue number in a STL vector of int.
• ChainName - - Return a reference to the chain names in a STL vector of char. Each name is stored as a single char.
• Coords - - Return a reference to the read coordinates in a STL vector of float. Coordinates are stored in the following order: x,y,z,x,y,z,x,...
• Occupancy - - Return a reference to the occupancy in a STL vector of float.
• BFactor - - Return a reference to the b_factor in a STL vector of float.

PDBSort

This class defines a functor or function object which can be used by a generic sort routine to sort atoms into the order used in Brookhaven pdb format files. Order is defined by strings, 2 or 3 characters long.
Authors: W.R.Pitt
Files: pdb_sort.h
Dependencies: none

Operations
 
 

• operator() - - Returns true is 1st string comes before the 2nd in pdb order. Returns false otherwise
• operator() - - The c style string version of the above function

AminoAcidProperty

This class defines a function object that will, given an amino acid single letter code with return a property value for that residue type.
Authors: W.R.Pitt
Files: amino_acid_property.h
Dependencies: none

Operations
 
 

• AminoAcidProperty - - Default constructor. The default property type is KyteHydropathy.
• AminoAcidProperty - - Construct function object which will return property values of a given type.
• operator() - - Operator that will return a property value given a single letter amino acid code.

PIR_processor

This class is a simple PIR sequence file processor. It is not complete and is only included for use by the demo programs that come with this library. It can parse a PIR format containing any number of sequences and provide the data as a vector or as individual strings.
Authors: W.R.Pitt
Files: PIR_processor.h
Dependencies: none

Operations
 
 

• PIR_processor - - Default constructor (does nothing)
• empty - - Return true if no sequences have been read in, false otherwise.
• ReadFile - - Read a file with a given name. If this function is called more than once, the new sequences are added to those already there.
• Seqs - - Return any sequences that been read in.
• Seq - - Return a single sequence, given a valid index number

PPM_processor

This class is a simple ascii PPM image file processor. It is not complete and is only included for use by the demo programs that come with this library.
Authors: W.R.Pitt
Friends: ostream operator
Files: PPM_processor.h
Dependencies: none

Operations
 
 

• ReadFile - - Read in a file with a given name.
• ReadImageData - - Get image data.
• WriteImageData - - Write image data.
• ReadWidth - - Read width of image.
• ReadHeight - - Read image height.

XYZ_processor

This is simple class for reading xyz format files. It is really only included in the library so that real data can be used in the test programs.
Friends: an output operator
Authors: W.R.Pitt
Files: XYZ_processor.h
Dependencies: None

Operations
 
 

• XYZ_processor - - Default constructor (does nothing)
• empty - - Returns true if no coordinates have been read
• ReadFile - - Read an xyz format file with the given name
• Coords - - Return a reference to the read coordinates in a STL vector of float. Coordinates are stored in the following order: x,y,z,x,y,z,x,...
• Elements - - Return a reference to the read atomic elements in a STL vector of char. Each element is stored as 2 chars.

needleman_wunsch_similarity

Pairwise similarity score for two sequences.
Restrictions: The containers holding the sequences must have at least forward iterators and an equality operator (==) should be defined for pairs of elements. The score for any pair of elements is match_score (or mismatch_score) - total gap penalty. The total gap penalty = gap_penalty + (length_of_gap * gap_length_multiplier)

Operations
 
 

• needleman_wunsch_similarity -

needleman_wusch_align

Pairwise alignment for two complete sequences. The score for any pair of elements is match_score (or mismatch_score) - total gap penalty. The total gap penalty = gap_penalty + (length_of_gap * gap_length_multiplier). The aligned sequence elements are placed alternately in the output container i.e with the odd elements representing the first sequence.
Restrictions: The containers holding the sequences must have at least forward iterators and an equality operator (==) should be defined for pairs of elements. The result container should either have no fixed size or be created at least twice the size of the longer sequence.

Operations
 
 

• needleman_wunsch_align -

fourier_transform

Two dimensional FFT. 1D and 3D versions also available

Operations
 
 

• fourier_transform -

mean

Calculate the mean value of the elements in a container.

Operations
 
 

• mean -

mean_absolute_deviation

Calculate mean absolute deviation from the mean of the elements in a container.

Operations
 
 

• mean_absolute_deviation -

variance

Calculate the sample variance of the elements in a container.

Operations
 
 

• variance -

normal_statistics

Calculate the mean, mean absolute deviation from mean, sample variance, skew and kurtosis of the distribution of the elements in a container.

Operations
 
 

• normal_statistics -

max_mismatch

Returns the maximum difference between equivalent elements in two containers in the sense of (a-b)

Operations
 
 

• max_mismatch -

max_absolute_mismatch

Returns the largest absolute difference between equivalent elements in two containers

Operations
 
 

• max_absolute_mismatch -

min_mismatch

Returns the minimum difference between equivalent elements in two containers in the sense of (a-b)

Operations
 
 

• min_mismatch -

min_absolute_mismatch

Returns the smallest absolute difference between equivalent elements in two containers

Operations
 
 

• min_absolute_mismatch -

every_less_equal

Returns true if every element of a is less than or equal to the equivalent element of b

Operations
 
 

• every_less_equal -

every_less

Returns true if every element of a is less than the equivalent element of b

Operations
 
 

• every_less -

less_absolute

Compare the absolute values of two arguements true if |x| < |y|

Operations
 
 

• operator() -

random_uniform

Portable random number generator that produces float,double, int and long random numbers. In the case of float & double the numbers are uniformly distributed in the range 0 to 1. In the case of long they are uniformly distributed in the range 0 to 2**31 and in the int case from 0 to 2**15. It is an implementation of Donald Knuth's floating point ranf_array generator, a lagged additive generator x(i) = (x(i-KK) + x(i-LL))mod 1.0 for float and double numbers and Knuth's lagged subtractive generator x(i) = (x(i-KK) - x(i-LL))mod 2**MM where MM = 15 for int and MM=30 for long. An object containing random numbers is constructed and used by random_uniform numbers(seed); T temp = numbers(); The seed integer should be < 1073741822 for float, double and long numbers and < 32765 in the case of of int data. N.B. it is best not to generate a sequence of more than 2**70 numbers using the same seed. This generator fails the birthday spacings test i.e some differences between pairs of numbers occur more often than desired. See Knuth's Art of Computer Programming 3rd Edition for solutions

Operations
 
 

• random_uniform -
• operator() -

random_normal

Portable random number generator that produces float or double precision random numbers from a normal distibution using the ratio method of Kinderman & Monahan (see Knuth TAOCP).

Operations
 
 

• random_normal -
• random_normal -
• operator() -

random_exponential

Portable random number generator that produces float or double precision random numbers from an exponential distibution.

Operations
 
 

• random_exponential -
• random_exponential -
• operator() -

numeric_vector

this template class represents a numerical vector of any size.

 V = xi + yj + zk + ...

 However, its primary use will probably in representing the position of atoms in three dimensions. The default contructor contructs a 3 element numeric_vector.

 There are several types associated with this class:

 value_type : by default the same as the type BTL_REAL which is defined in BTL.h

 iterator : this is a STL type iterator. It can be used to randomly access the elements of the numeric_vector e.g.

 numeric_vector<> v1; ... for (numeric_vector<>::iterator i = v1.begin(); i != v1.end(); i++) cout << *i;

const_iterator : used to access a const numeric_vector.

 size_type : this is an unsigned integer type that represents the size of any numeric_vector object.
Authors: D.S.Moss, W.R.Pitt, M.A.Williams
Files: btl_numeric_vector.h
Friends: Friend equivalents to some functions are available and are documented with these functions. Also available is: friend ostream& operator<<(ostream &os, const numeric_vector &m);
Dependencies: NumericLimits.h

Operations
 
 

• numeric_vector - - Constructs a 3D vector and initialises each value to zero.
• numeric_vector - - Constructs a 3D vector with initialization and initialises the values with the numbers given.
• numeric_vector - - Constructor for a vector of n elements. All n values initiated to a value v. The default value is zero .
• numeric_vector - - Construct from an array given a value_type*. This constructor is obsolete and will be deleted in future releases.
• numeric_vector - - Copy constructor.
• ~numeric_vector - - Destructor.
• begin - - Returns iterator that can be used to begin traversing through all elements of the numeric_vector. (There is also a const version of this function.)
• begin -
• end - - Returns an iterator can be used in comparison for ending traversal through the numeric_vector. (There is also a const version of this function.)
• end -
• operator[] - - Returns the element, i positions from the beginning of the numeric_vector, in constant time. (C-style i >= 0). (There is also a const version of this function.)
• operator[] -
• operator() - - Returns the i-th element in the numeric_vector (Fortran style i >= 1). (There is also a const version of this function).
• operator() -
• size - - Returns the number of elements in the numeric_vector.
• dim - - This function is added to give compatibility with TNT.
• operator= - - Vector assignment.
• operator+ - - Vector addition.
• operator+= - - Vector addition and assignment.
• operator- - - Vector subtraction.
• operator- - - Vector negation (unary minus operator).
• operator-= - - Vector subtraction and assignment.
• operator+ - - Add a scalar to each element in the numeric_vector.
• operator+= - - Add and assign a scalar to each element in the numeric_vector.
• operator- - - Subtract a scalar from each element in the numeric_vector.
• operator-= - - Subtract and assign a scalar from each element in the numeric_vector.
• operator* - - Vector scalar/dot product.
• operator% - - Vector cross product.
• operator* - - Vector multiplication by a scalar.
• operator*= - - Vector multiplication by a scalar and assignment.
• operator/ - - Vector division by a scalar.
• operator/= - - Vector division by a scalar and assignment.
• operator== - - Equality operator

scalar_product

Scalar/dot product of two vectors.

Operations
 
 

• scalar_product -

direct_product

Direct product of two matrices or vectors .

Operations
 
 

• direct_product -

triple_vector_product

Vector product of three triples.

Operations
 
 

• triple_vector_product -

triple_scalar_product

Scalar product of three triples.

Operations
 
 

• triple_scalar_product -

separation_squared

Calculate the squared distance between the points represented by two vectors.

Operations
 
 

• separation_squared -

separation

Calculate the distance between the points represented by two vectors.

Operations
 
 

• separation -

sum

Returns the sum of the vector elements.

Operations
 
 

• sum -

sum_precise

Returns the sum of the vector elements, but accumulates the elements in order of ascending value in order to minimise rounding errors.

Operations
 
 

• sum_precise -

sum_of_squares

Returns the sum of the squares of the vector elements.

Operations
 
 

• sum_of_squares -

sum_of_squares_precise

Returns the sum of the squares of the vector elements, but accumulates the elements in order of ascending value in order to minimise rounding errors.

Operations
 
 

• sum_of_squares_precise -

magnitude

Returns the length of a vector.

Operations
 
 

• magnitude -

magnitude_precise

Returns the precise length of a vector.

Operations
 
 

• magnitude_precise -

rotate

Rotates each triple in a container about a given axis and origin by a given number of radians.

Operations
 
 

• rotate -

translate

Translates a each triple in a container by a given vector

Operations
 
 

• translate -

matrix

This template class represents a numerical matrix of any dimension. Matrices of dimension 1 are more efficiently modelled using the numeric_vector.

 There are two types associated with this class:

 value_type : this type is the same as the numeric_vector::value_type and defines the type of the elements of the matrix.

 size_type : this type is the same as the numeric_vector::size_type and defines the type of the matrix indexes. It should always be an unsigned integer type.

Authors: D.S.Moss, W.R.Pitt, I.Tickle, M.A.Williams.
Files: btl_matrix.h
Friends: Friend equivalents to some functions are available and are documented with these functions. Also available is: friend ostream& operator<<(ostream &os, const matrix &m);
Dependencies: btl_numeric_vector.h, btl_vector_algorithms.h, NumericLimits.h

Operations
 
 

• matrix - - Constructor for default 3x3 matrix and initialise elements to zero.
• matrix - - Constructs an identity matrix of size p*p.
• matrix - - Constructs a matrix with p rows and q columns. Initialises each element to a value v. The default value is zero
• matrix - - Constructs a matrix with p rows and q columns. Elements are initialised to those in given array. This is obsolete and will be deleted in future releases
• matrix - - Constructor for a 3x3 Matrix with initialisation
• matrix - - Copy constructor
• ~matrix - - Destructor
• begin - - Returns an iterator that points to the first element in the Matrix. (There is also a const version of this function.)
• begin -
• end - - Returns an iterator that can be used in a comparison for ending a traversal through this Matrix. (There is also a const version of this function.)
• end -
• size - - Size of Matrix (the number of rows times the number of columns)
• lbound - - This function is added to give compatibility with TNT.
• num_rows - - Read number of rows (for compatability with TNT).
• num_cols - - Read number of columns (for compatability with TNT).
• rows - - Read number of rows.
• cols - - Set number of columns.
• rows - - Set number of rows.
• cols - - Read number of columns.
• dim - - This function is added to give compatibility with TNT.
• operator() - - Returns a matrix element given its indices e.g. x(i,j) i = row, j = col N.B. (i,j >= 1). (There is also a const (read only) version of this function.)
• operator() -
• operator[] - - Returns an iterator that points to the first element of a given row. N.B. ( 0 <= i < nrows ). (There is also a const (read only) version of this function.)
• operator[] -
• operator= - - Matrix assignment
• operator* - - Matrix multiplication e.g. matrix m1,m2,m3; .... m3 = m1 * m2;
• operator* - - Postmultiplication of a Matrix by a numeric_vector. e.g. matrix m; numeric_vector v1,v2; ... v2 = m * v1;
• operator*= - - Multiple each element by a number.
• operator* - - Multiple each element by a number
• operator/= - - Divide each element by a number
• operator/ - - Divide each element by a number
• operator-= - - Subtraction of a number from each element.
• operator- - - Subtraction of a number from each element.
• operator+= - - Addition of a number to each element.
• operator+ - - Addition of a number to each element.
• operator-= - - Subtraction of a vector from the rows of a matrix
• operator- - - Subtraction of a vector from the rows of a matrix
• operator+= - - Addition of a vector to the rows of a matrix
• operator+ - - Addition of a vector to the rows of a matrix
• operator-= - - matrix subtraction
• operator- - - Matrix subtraction
• operator+= - - Matrix addition
• operator+ - - Matrix addition
• operator& - - Matrix multiplication Transpose(m1) * m2 N.B. this is less efficient than (but not equivalent to) operator%
• operator% - - Matrix multiplication m1 * Transpose(m2) N.B. this is more efficient than (but not equivalent to) operator&
• operator== - - Equality operator

matrix_product

Matrix multiplication. The output matrix is nrows1*ncols2 in size.
Restrictions: ncols1 must equal nrows2.

Operations
 
 

• matrix_product -

matrixtranspose_matrix_product

Matrix multiplication: Transpose(M1)*M2. The output matrix is ncols1*ncols2 in size.
Restrictions: Both matrices must have the same number of rows

Operations
 
 

• matrixtranspose_matrix_product -

matrix_matrixtranspose_product

Matrix multiplication: M1*Transpose(M2) The output matrix is nrows1*nrows2 in size.
Restrictions: Both matrices must have the same number of columns

Operations
 
 

• matrix_matrixtranspose_product -

transpose

Matrix transpose. Can be used in-place.

Operations
 
 

• transpose -

column_means

Calculate the mean of each column of a matrix and store the answers in a container of size >= ncols.

Operations
 
 

• column_means -

copy_column

Copy a column of this matrix into another container. Columns are numbered from 1. in the FORTRAN manner.

Operations
 
 

• copy_column -

determinant

Calculates matrix determinant
Restrictions: Square matrices only.

Operations
 
 

• determinant -

minor

Find the minor of a matrix. The minor denoted by minor(.,.,,.,i,j) is found by eliminating the row i and column j from the parent matrix.

Operations
 
 

• minor -

adjoint

Matrix adjoint
Restrictions: Square matrices only.

Operations
 
 

• adjoint -

inverse_square

Calculate inverse of a small square matrix (inverse = adjoint/determinant). The result matrix should be of a floating point type.

Operations
 
 

• inverse_square -

eigen_solution

Eigenvalues and eigenvectors of a symmetric matrix
Restrictions: The input matrix must be real, square and symmetric, the output vector of eigen values will be nrows in size and the output matrix of eigenvectors will be nrows*nrows in size.

Operations
 
 

• eigen_solution -

inverse_cholesy

Inverts a symmetric positive definite matrix. Employs Cholesky decomposition in three steps:

 (1)M=LL(tr) (2)compute L(-1) (3)M(-1)=L(-1)(tr)L(-1) Input should contain numerical data that can be interpreted as a symmetric positive definite matrix. The output is the inverse of this matrix in the form of a matrix of the same size as the input and probably containing data of type BTL_REAL.

Operations
 
 

• inverse_cholesky -

lsqfit_rmsd

Calculate the root mean squared deviation after a least squares fit of the two sets of coordinates using the method of Kearsley(Acta Cryst. '89, A45, 208-10). Both sets of coordinates remain unchanged by this function
Restrictions: Each set must have the same number of coordinates. Each coordinate must be orthogonal and in three dimensions (i.e. normal x,y,z coordinates). WARNING: if coordinates with varying dimensions are input then this may well not be detected.

Operations
 
 

• lsqfit_rmsd -

centroid

Calculate the centroid of a set of x,y,z coordinates held in an n x 3 matrix.

Operations
 
 

• centroid -

rotation_from_fit

Create fitting rotation matrix from the eigen vector that corresponds to the smallest eigen vector of Kearsley's matrix.

Operations
 
 

• rotation_from_fit -

rmsd

Calculate the root mean squared deviation of two sets of coordinates.
Restrictions: Each set must have the same number of coordinates. There is no restriction on the number of dimensions which the coordinates represent (except that it must be the same in every case). WARNING: if coordinates with varying dimensions are input then this may well not be detected.

Operations
 
 

• rmsd -

check_3d_data

Check that both input containers have the same number of elements and that number is multiple of 3. Output the number of x,y,z positions.

Operations
 
 

• check_3d_data -

BTL_VertexWithEdges

This class represents an vertex that has links to edge objects. It is to be used in combination with class BTL_GraphWithEdges.
Authors: W.R.Pitt
Files: btl_graph_with_edges.h
Friends: friend class BTL_GraphWithEdges&ltT1,T2>>;

friend ostream& operator<<(ostream &os, const BTL_VertexWithEdges &m);
Dependencies: None, except by inheritance.

Generalizations

N.B. The graph classes command syntax will be revised in the 3.0beta version

• BTL_Vertex

• BTL_VertexWithEdges - - Constructor empty vertex.
• ~BTL_VertexWithEdges - - Delete vertex and its contents.
• begin_edge - - Return iterator that references first edge connected to Vertex. (There is also a const version of this function.)
• begin_edge -
• end_edge - - Return iterator that references the position in memory after the last edge connected to Vertex. (There is also a const version of this function.)
• end_edge -

BTL_Edge

This class represents an edge of a graph. It is to be used in combination with class BTL_GraphWithEdges.
Authors: W.R.Pitt
Files: btl_graph_with_edges.h
Friends: friend class BTL_GraphWithEdges&ltT1,T2>>;

friend ostream& operator<<(ostream &os, const BTL_Edge &m);
Dependencies: BTL_VertexWithEdges

Generalizations

N.B. The graph classes command syntax will be revised in the 3.0beta version
 

• BTL_EdgeBase

• BTL_Edge - - Construct empty edge
• BTL_Edge - - Copy constructor
• ~BTL_Edge - - Destructor
• GetIterator - - Returns an iterator that can be deferenced to obtain the data object associated with this edge (There is a const version of this function as well)
• GetIterator -
• LeftVertex - - Returns pointer to the first vertex connected to this edge.
• RightVertex - - Returns pointer to the second vertex connected to this edge.

BTL_GraphWithEdges

Graph container with any type of data at the vertices of the graph and any type of data at the edges. The default behaviour is have undirected edges. This can be changed to directed if specified in the constructor. No self links (edges from one vertex to itself) are allowed.
Authors: W.R.Pitt
Files: btl_graph_with_edges.h
Friends: friend ostream& operator<<<(ostream &os, const BTL_GraphWithEdges &m);
Dependencies: BTL_Vertex, BTL_II

Generalizations

N.B. The graph classes command syntax will be revised in the 3.0beta version
 

• BTL_Graph

• BTL_Graph3
• BTL_Graph4
• BTL_Graph5
• BTL_Graph6

• BTL_GraphWithEdges - - Construct empty undirected graph.
• BTL_GraphWithEdges - - Construct new undirected or directed graph i.e. BTL_GraphWithEdges g1(directed); or BTL_Graph g2(undirected);
• ~BTL_GraphWithEdges - - Delete graph and all vertices and edges in it.
• AddVertex - - Add new vertex to graph.
• RemoveVertex - - Delete vertex from graph. Return false if vertex not found in this graph.
• AddEdge - - Insert edge into this graph. Return endEdge() if input is invalid.
• RemoveEdge - - Remove edge from this graph. Return false if input is invalid.
• BeginEdgeData - - Return iterator that references first edge data item. (There is a const version of this function as well)
• BeginEdgeData -
• EndEdgeData - - Return iterator that references the position in memory after the last edge data item. (There is a const version of this function as well)
• EndEdgeData -
• begin_edge - - Return EdgeIterator that references first edge in graph. (There is a const version of this function as well)
• begin_edge -
• end_edge - - Return EdgeIterator that references the position in memory after the last edge in graph.(There is a const version of this function as well)
• end_edge -

BTL_Vertex

This class encapsulates a graph vertex and is designed for use with the graph class. Each vertex contains a reference to a data object and pointers to other vertices. It is a template class the single template parameter is a type of dereferencer.
Authors: W.R.Pitt
Files: btl_graph.h
Dependencies: BTL_II, and BTL_IteratorDerefencer, or BTL_InDencer

Generalizations

N.B. The graph classes command syntax will be revised in the 3.0beta version
 

• BTL_VertexBase

• BTL_VertexWithEdges

• BTL_Vertex - - Construct new empty Vertex
• BTL_Vertex - - Copy constructor.
• ~BTL_Vertex - - Destructor
• GetIterator - - Get an iterator that references the data item associated with this vertex. With graphs that use STL an vector or deque to store data items this iterator may become invalid after insertions or deletions of vertices. (There is also a const version of this function.)
• GetIterator -
• Visited - - Read/write access to visited flag. This can be used in Graph searching routines.
• begin_vertex - - Return iterator that references first vertex connected to this vertex.(There is a const version of this function as well)
• begin_vertex -
• end_vertex - - Return iterator that references the position in memory after the last vertex connected to this vertex.(There is a const version of this function as well)
• end_vertex -
• begin - - Return iterator that references first vertex connected to this vertex. (There is a const version of this function as well)
• begin -
• end - - Return iterator that references the position in memory after the last vertex connected to this vertex.(There is a const version of this function as well)
• end -

BTL_Graph

Graph container with any type of data at vertices of the graph and no data associated with edges. The default behaviour is have undirected edges. This can be changed to directed if specified in the constructor. No self links (edges from one vertex to itself) are allowed.
Authors: W.R.Pitt
Files: btl_graph.h
Friends: operator<<
Dependencies: BTL_VertexBase and its subclasses.

N.B. The graph classes command syntax will be revised in the 3.0beta version
 

Specializations
 
 

• BTL_GraphWithEdges
• BTL_Graph1
• BTL_Graph2

• BTL_Graph - - Construct new undirected graph
• BTL_Graph - - Construct new undirected or directed graph i.e. BTL_Graph g1(directed); or BTL_Graph g2(undirected);
• ~BTL_Graph - - Delete Graph and all the vertices in it
• GetDirectionality - - Get the edge directionality of this graph.
• AddVertex - - Add new vertex to graph.
• RemoveVertex - - Remove a vertex (and all pointers to it) from the graph. Return false if vertex was not found in the graph.
• AddLink - - Add a pointer between two vertices. Return false if either vertex is not in this graph or is link already present
• RemoveLink - - Remove pointer/link between two vertices. Return false if link not there
• SetAllVisited - - Set the visited field of all vertices in this graph.
• find - - Find a vertex within this Graph.(There is a const version of this function as well)
• find -
• begin - - Return iterator that references first data item.(There is a const version of this function as well)
• begin -
• end - - Return iterator that references the position in memory after the last data item. (There is a const version of this function as well)
• end -
• begin_vertex - - Return iterator that references the first Vertex. (There is a const version of this function as well)
• begin_vertex -
• end_vertex - - Return iterator that references the position in memory after the last Vertex. (There is a const version of this function as well)
• end_vertex -
• size - - Give the number of vertices within the Graph

BTL_DFSIterator

This is a an iterator for iterating over a connected sub-graph in depth first order. It is designed to work with the BTL_Graph and BTL_GraphWithEdges but takes that type of graph as its template parameter and could be used on any graph and vertex type if they have a given set of functions.
Authors: W.R.Pitt
Files: DFSIterator.h
Dependencies: None

N.B. The graph classes command syntax will be revised in the 3.0beta version
 

Operations
 
 

• BTL_DFSIterator - - Default constructor.
• BTL_DFSIterator - - Construct with iterator. This is essential if operator++ etc. is to be used.
• operator++ - - Move iterator forward one in depth first search order.
• operator! - - Returns false when current position is one past the end of the last element in the container.
• operator++ - - Move iterator forward one in depth first search order.
• operator== - - Equality operator
• operator* - - Dereference operator

BTL_ConstDFSIterator

The const version of the BTL_DFSIterator.
Authors: W.R.Pitt
Files: DFSIterator.h
Dependencies: None

N.B. The graph classes command syntax will be revised in the 3.0beta version
 

Operations
 
 

• BTL_ConstDFSIterator - - Default constructor.
• BTL_ConstDFSIterator - - Construct with iterator. This is essential if operator++ etc. is to be used.
• operator++ - - Move iterator forward one in depth first search order.
• operator! - - Returns false when current position is one past the end of the last element in the container.
• operator++ - - Move iterator forward one in depth first search order.
• operator== - - Equality operator
• operator* - - Dereference operator

  ATOM_processor

• void CloseFile(const char* fileName, ifstream& fileStream);

 

 
 
 
 
 

• NameStore& Alternate()

 

 
 
 
 
 

• ATOM_processor()

Default constructor (does nothing)
• ~ATOM_processor()

Default destructor (does nothing)
• bool empty() const

Returns true if no coordinates have been read
• void ReadFile(const char *fileName, const char *chains = " ", const char alternate = ' ');

Read a PDB format file with the given name, selecting only those chains whose id letter occurs in a given string and using the alternate set of coordinates identified by the user-supplied character. The default reads records with any chain id and either no alternate id or the first encounterd alternate id.
• IdStore& AtomNo()

Return a reference to the atom number in a STL vector of int.
• NameStore& AtomName()

Return a reference to the atom n in a STL vector of char. Each name is stored as 4 chars.
• NameStore& ResidueName()

Return a reference to the atom names in a STL vector of char. Each name is stored as 3 chars.
• IdStore& ResidueNo()

Return a reference to the residue number in a STL vector of int.
• NameStore& ChainName()

Return a reference to the chain names in a STL vector of char. Each name is stored as a single char.
• RealStore& Coords()

Return a reference to the read coordinates in a STL vector of float. Coordinates are stored in the following order: x,y,z,x,y,z,x,...
• RealStore& Occupancy()

Return a reference to the occupancy in a STL vector of float.
• RealStore& BFactor()

Return a reference to the b_factor in a STL vector of float.

  PDBSort

• bool operator()(const string& atomId1, const string& atomId2) const

Returns true is 1st string comes before the 2nd in pdb order. Returns false otherwise
• bool operator()(const char* atomId1, const char* atomId2) const

The c style string version of the above function

  AminoAcidProperty

• AminoAcidProperty()

Default constructor. The default property type is KyteHydropathy.
• AminoAcidProperty(const BTL_Scale whatScale)

Construct function object which will return property values of a given type.
• float operator()(const char aacode) const

Operator that will return a property value given a single letter amino acid code.

  PIR_processor

• PIR_processor()

Default constructor (does nothing)
• bool empty() const

Return true if no sequences have been read in, false otherwise.
• void ReadFile(const char *fileName);

Read a file with a given name. If this function is called more than once, the new sequences are added to those already there.
• vector& Seqs()

Return any sequences that been read in.
• string& Seq(const unsigned int iseq)

Return a single sequence, given a valid index number

  PPM_processor

• void ReadFile(const char *fileName);

Read in a file with a given name.
• vector& ReadImageData()

Get image data.
• void WriteImageData(const vector& idata, const unsigned int iwidth, const unsigned int iheight);

Write image data.
• unsigned int ReadWidth() const

Read width of image.
• unsigned int ReadHeight() const

Read image height.

  XYZ_processor

• XYZ_processor()

Default constructor (does nothing)
• bool empty() const

Returns true if no coordinates have been read
• void ReadFile(const char *fileName);

Read an xyz format file with the given name
• CoordStore& Coords()

Return a reference to the read coordinates in a STL vector of float. Coordinates are stored in the following order: x,y,z,x,y,z,x,...
• ElementStore& Elements()

Return a reference to the read atomic elements in a STL vector of char. Each element is stored as 2 chars.

  needleman_wunsch_similarity

• T needleman_wunsch_similarity(InputIterator first1, InputIterator last1, InputIterator first2, InputIterator last2, float match_score, float mismatch_score, float gap_penalty, float gap_length_multiplier, T init)

 

 
 
 
 
 
 
 

  needleman_wusch_align

• OutputIterator needleman_wunsch_align(InputIterator first1, InputIterator last1, InputIterator first2, InputIterator last2, float match_score, float mismatch_score, float gap_penalty, float gap_length_multiplier, OutputIterator result)

 

 
 
 
 
 
 
 

  fourier_transform

• void fourier_transform(const RandomAccessIterator start, const RandomAccessIterator result, const unsigned int nrows, const unsigned int ncols, const bool forward)

 

 
 
 
 
 
 
 

  mean

• T mean(InputIterator first, InputIterator last, T mean)

 

 
 
 
 
 
 
 

  mean_absolute_deviation

• T mean_absolute_deviation(InputIterator first, InputIterator last, T mad, T& mean)

 

 
 
 
 
 
 
 

  variance

• T variance(InputIterator first, InputIterator last, T var, T& mean)

 

 
 
 
 
 
 
 

  normal_statistics

• void normal_statistics(InputIterator first, InputIterator last, T& mean, T& mad, T& var, T& skew, T& kurtosis)

 

 
 
 
 
 
 
 

  max_mismatch

• T max_mismatch(ForwardIterator1 firsta, ForwardIterator1 lasta, ForwardIterator2 firstb, T init )

 

 
 
 
 
 
 
 

  max_absolute_mismatch

• T max_absolute_mismatch(ForwardIterator1 firsta, ForwardIterator1 lasta, ForwardIterator2 firstb, T init )

 

 
 
 
 
 
 
 

  min_mismatch

• T min_mismatch(ForwardIterator1 firsta, ForwardIterator1 lasta, ForwardIterator2 firstb, T init )

 

 
 
 
 
 
 
 

  min_absolute_mismatch

• T min_absolute_mismatch(ForwardIterator1 firsta, ForwardIterator1 lasta, ForwardIterator2 firstb, T init )

 

 
 
 
 
 
 
 

  every_less_equal

• bool every_less_equal(ForwardIterator1 firsta, ForwardIterator1 lasta, ForwardIterator2 firstb)

 

 
 
 
 
 
 
 

  every_less

• bool every_less(ForwardIterator1 firsta, ForwardIterator1 lasta, ForwardIterator2 firstb)

 

 
 
 
 
 
 
 

  less_absolute

• bool operator() (const T& x, const T& y) const

 

 
 
 
 
 
 
 

  random_uniform

• random_uniform(long seed)

 

 
 
 
 
 

• T operator() ()

 

 
 
 
 
 
 
 

  random_normal

• random_normal(long seed)

 

 
 
 
 
 

• random_normal(long seed, T mean, T standard_deviation)

 

 
 
 
 
 

• T operator() ()

 

 
 
 
 
 
 
 

  random_exponential

• random_exponential(long seed)

 

 
 
 
 
 

• random_exponential(long seed, T mean)

 

 
 
 
 
 

• T operator() ()

 

 
 
 
 
 
 
 

  numeric_vector

• numeric_vector()

Constructs a 3D vector and initialises each value to zero.
• numeric_vector(const value_type& p, const value_type& q, const value_type& r)

Constructs a 3D vector with initialization and initialises the values with the numbers given.
• numeric_vector(const size_type& n, const value_type& v = value_type(0))

Constructor for a vector of n elements. All n values initiated to a value v. The default value is zero .
• numeric_vector(const value_type* const array, const size_type& p)

Construct from an array given a value_type*. This constructor is obsolete and will be deleted in future releases.
• numeric_vector(const numeric_vector &v) : vec(v.vec)

Copy constructor.
• ~numeric_vector()

Destructor.
• iterator begin()

Returns iterator that can be used to begin traversing through all elements of the numeric_vector. (There is also a const version of this function.)
• const_iterator begin() const

 

 
 
 
 
 

• iterator end()

Returns an iterator can be used in comparison for ending traversal through the numeric_vector. (There is also a const version of this function.)
• const_iterator end() const

 

 
 
 
 
 

• value_type& operator[](const size_type& i)

Returns the element, i positions from the beginning of the numeric_vector, in constant time. (C-style i >= 0). (There is also a const version of this function.)
• value_type operator[](const size_type& i) const

 

 
 
 
 
 

• value_type& operator()(const size_type& i)

Returns the i-th element in the numeric_vector (Fortran style i >= 1). (There is also a const version of this function).
• value_type operator()(const size_type& i) const

 

 
 
 
 
 

• size_type size() const

Returns the number of elements in the numeric_vector.
• size_type dim() const

This function is added to give compatibility with TNT.
• numeric_vector& operator=(const numeric_vector &v)

Vector assignment.
• numeric_vector operator+(const numeric_vector &v) const

Vector addition.
• numeric_vector& operator+=(const numeric_vector &v)

Vector addition and assignment.
• numeric_vector operator-(const numeric_vector &v) const

Vector subtraction.
• numeric_vector operator-() const

Vector negation (unary minus operator).
• numeric_vector& operator-=(const numeric_vector &v)

Vector subtraction and assignment.
• numeric_vector operator+(const value_type &s) const

Add a scalar to each element in the numeric_vector.
• numeric_vector& operator+=(const value_type &s)

Add and assign a scalar to each element in the numeric_vector.
• numeric_vector operator-(const value_type &s) const

Subtract a scalar from each element in the numeric_vector.
• numeric_vector& operator-=(const value_type &s)

Subtract and assign a scalar from each element in the numeric_vector.
• value_type operator*(const numeric_vector &v) const

Vector scalar/dot product.
• numeric_vector operator%(const numeric_vector &v) const

Vector cross product.
• numeric_vector operator*(const value_type& y) const

Vector multiplication by a scalar.
• numeric_vector& operator*=(const value_type& y)

Vector multiplication by a scalar and assignment.
• numeric_vector operator/(const value_type& y) const

Vector division by a scalar.
• numeric_vector& operator/=(const value_type& y)

Vector division by a scalar and assignment.
• bool operator==(const numeric_vector& v) const

Equality operator

  scalar_product

• T scalar_product(InputIterator1 firsta, InputIterator1 lasta, InputIterator2 firstb, T init)

 

 
 
 
 
 
 
 

  direct_product

• OutputIterator direct_product(InputIterator1 firsta, InputIterator1 lasta, InputIterator2 firstb, OutputIterator result)

 

 
 
 
 
 
 
 

  triple_vector_product

• OutputIterator triple_vector_product(InputIterator1 firsta, InputIterator2 firstb, InputIterator3 firstc, OutputIterator result)

 

 
 
 
 
 
 
 

  triple_scalar_product

• T triple_scalar_product(InputIterator1 firsta, InputIterator2 firstb, InputIterator3 firstc, T init)

 

 
 
 
 
 
 
 

  separation_squared

• T separation_squared(InputIterator1 firsta, InputIterator1 lasta, InputIterator2 firstb, T init)

 

 
 
 
 
 
 
 

  separation

• T separation(InputIterator1 firsta, InputIterator1 lasta, InputIterator2 firstb, T init)

 

 
 
 
 
 
 
 

  sum

• T sum(InputIterator first, InputIterator last, T init)

 

 
 
 
 
 
 
 

  sum_precise

• T sum_precise(InputIterator first, InputIterator last, T init)

 

 
 
 
 
 
 
 

  sum_of_squares

• T sum_of_squares(InputIterator first, InputIterator last, T init)

 

 
 
 
 
 
 
 

  sum_of_squares_precise

• T sum_of_squares_precise(InputIterator first, InputIterator last, T init)

 

 
 
 
 
 
 
 

  magnitude

• T magnitude(InputIterator1 firsta, InputIterator1 lasta, T init )

 

 
 
 
 
 
 
 

  magnitude_precise

• T magnitude_precise(InputIterator1 firsta, InputIterator1 lasta, T init )

 

 
 
 
 
 
 
 

  rotate

• void rotate(ForwardIterator first, ForwardIterator last, ConstForwardIterator1 axis, ConstForwardIterator2 origin, T angle)

 

 
 
 
 
 
 
 

  translate

• void translate(ForwardIterator begin, ForwardIterator end, ConstForwardIterator trans)

 

 
 
 
 
 
 
 

  matrix

• matrix(): nrows(3), ncols(3)

Constructor for default 3x3 matrix and initialise elements to zero.
• matrix(BTL_INT p): nrows(p), ncols(p)

Constructs an identity matrix of size p*p.
• matrix(BTL_INT p, BTL_INT q, const value_type& v = value_type(0)) : nrows(p),ncols(q)

Constructs a matrix with p rows and q columns. Initialises each element to a value v. The default value is zero
• matrix(const value_type* const array, BTL_INT p, BTL_INT q): nrows(p), ncols(q)

Constructs a matrix with p rows and q columns. Elements are initialised to those in given array. This is obsolete and will be deleted in future releases
• matrix(const value_type& e1, const value_type& e2, const value_type& e3, const value_type& e4, const value_type& e5, const value_type& e6, const value_type& e7, const value_type& e8, const value_type& e9) : nrows(3), ncols(3)

Constructor for a 3x3 Matrix with initialisation
• matrix(const matrix &m) : mat(m.mat), nrows(m.nrows), ncols(m.ncols)

Copy constructor
• ~matrix()

Destructor
• iterator begin()

Returns an iterator that points to the first element in the Matrix. (There is also a const version of this function.)
• const_iterator begin() const

 

 
 
 
 
 

• iterator end()

Returns an iterator that can be used in a comparison for ending a traversal through this Matrix. (There is also a const version of this function.)
• const_iterator end() const

 

 
 
 
 
 

• size_type size() const

Size of Matrix (the number of rows times the number of columns)
• size_type lbound() const

This function is added to give compatibility with TNT.
• size_type num_rows() const

Read number of rows (for compatability with TNT).
• size_type num_cols() const

Read number of columns (for compatability with TNT).
• size_type rows() const

Read number of rows.
• void cols(BTL_INT n)

Set number of columns.
• void rows(BTL_INT n)

Set number of rows.
• size_type cols() const

Read number of columns.
• size_type dim(size_type d) const

This function is added to give compatibility with TNT.
• value_type& operator()(const size_type& i, const size_type& j)

Returns a matrix element given its indices e.g. x(i,j) i = row, j = col N.B. (i,j >= 1). (There is also a const (read only) version of this function.)
• value_type operator()(const size_type& i, const size_type& j) const

 

 
 
 
 
 

• iterator operator[](const size_type& i)

Returns an iterator that points to the first element of a given row. N.B. ( 0 <= i < nrows ). (There is also a const (read only) version of this function.)
• const_iterator operator[](const size_type& i) const

 

 
 
 
 
 

• matrix& operator=(const matrix &m)

Matrix assignment
• matrix operator*(const matrix& m) const

Matrix multiplication e.g. matrix m1,m2,m3; .... m3 = m1 * m2;
• numeric_vector operator*(const numeric_vector &v) const

Postmultiplication of a Matrix by a numeric_vector. e.g. matrix m; numeric_vector v1,v2; ... v2 = m * v1;
Restrictions: The size of v must equal the number of columns in this Matrix.
• matrix& operator*=(const value_type& v)

Multiple each element by a number.
• matrix operator*(const value_type& v) const

Multiple each element by a number
• matrix& operator/=(const value_type& v)

Divide each element by a number
• matrix operator/(const value_type& v) const

Divide each element by a number
• matrix& operator-=(const value_type &v)

Subtraction of a number from each element.
• matrix operator-(const value_type &v) const

Subtraction of a number from each element.
• matrix& operator+=(const value_type &v)

Addition of a number to each element.
• matrix operator+(const value_type &v) const

Addition of a number to each element.
• matrix& operator-=(const numeric_vector &v)

Subtraction of a vector from the rows of a matrix
Restrictions: The the size of numeric_vector v must equal the number of columns in this matrix.
• matrix operator-(const numeric_vector &v) const

Subtraction of a vector from the rows of a matrix
Restrictions: The the size of numeric_vector v must equal the number of columns in this matrix.
• matrix& operator+=(const numeric_vector &v)

Addition of a vector to the rows of a matrix
Restrictions: The the size of numeric_vector v must equal the number of columns in this matrix.
• matrix operator+(const numeric_vector &v) const

Addition of a vector to the rows of a matrix
Restrictions: The the size of numeric_vector v must equal the number of columns in this matrix.
• matrix& operator-=(const matrix &m)

matrix subtraction
Restrictions: The the size of matrix m must equal the size of this matrix.
• matrix operator-(const matrix &m) const

Matrix subtraction
Restrictions: The the size of Matrix m must equal the size of this Matrix.
• matrix& operator+=(const matrix &m)

Matrix addition
Restrictions: The the size of Matrix m must equal the size of this Matrix.
• matrix operator+(const matrix &m) const

Matrix addition
Restrictions: The the size of Matrix m must equal the size of this Matrix.
• matrix operator&(const matrix& m) const

Matrix multiplication Transpose(m1) * m2 N.B. this is less efficient than (but not equivalent to) operator%
Restrictions: Both *this and the input Matrix must have the same number of rows
• matrix operator%(const matrix& m) const

Matrix multiplication m1 * Transpose(m2) N.B. this is more efficient than (but not equivalent to) operator&
Restrictions: Both *this and the input Matrix must have the same number of columns
• bool operator==(const matrix& m) const

Equality operator

  matrix_product

• OutputIterator matrix_product(InputIterator1 first1, InputIterator1 last1, BTL_INT nrows1, InputIterator2 first2, InputIterator2 last2, BTL_INT nrows2, OutputIterator result)

 

 
 
 
 
 
 
 

  matrixtranspose_matrix_product

• OutputIterator matrixtranspose_matrix_product(InputIterator1 first1, InputIterator1 last1, BTL_INT nrows1, InputIterator2 first2, InputIterator2 last2, BTL_INT nrows2, OutputIterator result)

 

 
 
 
 
 
 
 

  matrix_matrixtranspose_product

• OutputIterator matrix_matrixtranspose_product(InputIterator1 first1, InputIterator1 last1, BTL_INT nrows1, InputIterator2 first2, InputIterator2 last2, BTL_INT nrows2, OutputIterator result)

 

 
 
 
 
 
 
 

  transpose

• OutputIterator transpose(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result)

 

 
 
 
 
 
 
 

  column_means

• OutputIterator column_means(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result)

 

 
 
 
 
 
 
 

  copy_column

• OutputIterator copy_column(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result, BTL_INT column_index)

 

 
 
 
 
 
 
 

  determinant

• T determinant(InputIterator first, InputIterator last, BTL_INT nrows, T det)

 

 
 
 
 
 
 
 

  minor

• OutputIterator minor(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result, BTL_INT i, BTL_INT j)

 

 
 
 
 
 
 
 

  adjoint

• OutputIterator adjoint(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result)

 

 
 
 
 
 
 
 

  inverse_square

• OutputIterator inverse_square(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result)

 

 
 
 
 
 
 
 

  eigen_solution

• void eigen_solution(InputIterator first, InputIterator last, BTL_INT nrows, OutputMatrixIterator eigenvectors, OutputVectorIterator eigenvalues)

 

 
 
 
 
 
 
 

  inverse_cholesy

• OutputIterator inverse_cholesky(InputIterator first, InputIterator last, BTL_INT nrows, OutputIterator result)

 

 
 
 
 
 
 
 

  lsqfit_rmsd

• T lsqfit_rmsd(ConstForwardIterator1 begin1, ConstForwardIterator1 end1, ConstForwardIterator2 begin2, ConstForwardIterator2 end2, T init)

 

 
 
 
 
 
 
 

  centroid

• OutputIterator centroid(ConstForwardIterator first, ConstForwardIterator last, OutputIterator result)

 

 
 
 
 
 
 
 

  rotation_from_fit

• OutputIterator rotation_from_fit(ForwardIterator eigenmatrix, OutputIterator rot)

 

 
 
 
 
 
 
 

  rmsd

• T rmsd(ConstForwardIterator begin1,ConstForwardIterator end1, ConstForwardIterator begin2, T init)

 

 
 
 
 
 
 
 

  check_3d_data

• BTL_INT check_3d_data(ForwardIterator1 begin1, ForwardIterator1 end1, ForwardIterator2 begin2, ForwardIterator2 end2)

 

 
 
 
 
 
 
 

  BTL_VertexWithEdges

• BTL_VertexWithEdges() : Base()

Constructor empty vertex.
• virtual ~BTL_VertexWithEdges()

Delete vertex and its contents.
• EdgeIterator begin_edge()

Return iterator that references first edge connected to Vertex. (There is also a const version of this function.)
• ConstEdgeIterator begin_edge() const

 

 
 
 
 
 

• EdgeIterator end_edge()

Return iterator that references the position in memory after the last edge connected to Vertex. (There is also a const version of this function.)
• ConstEdgeIterator end_edge() const

 

 
 
 
 
 
 
 

  BTL_Edge

• BTL_Edge() : BTL_EdgeBase()

Construct empty edge
• BTL_Edge(const BTL_Edge& e) : BTL_EdgeBase(e)

Copy constructor
• virtual ~BTL_Edge()

Destructor
• iterator GetIterator()

Returns an iterator that can be deferenced to obtain the data object associated with this edge (There is a const version of this function as well)
• const_iterator GetIterator() const

 

 
 
 
 
 

• VertexWEPtr LeftVertex() const

Returns pointer to the first vertex connected to this edge.
• VertexWEPtr RightVertex() const

Returns pointer to the second vertex connected to this edge.

  BTL_GraphWithEdges

• BTL_GraphWithEdges() : Base()

Construct empty undirected graph.
• BTL_GraphWithEdges(const Directionality& e) : Base(e)

Construct new undirected or directed graph i.e. BTL_GraphWithEdges g1(directed); or BTL_Graph g2(undirected);
• virtual ~BTL_GraphWithEdges()

Delete graph and all vertices and edges in it.
• virtual VertexIterator AddVertex(const value_type& v)

Add new vertex to graph.
• virtual bool RemoveVertex(VertexIterator in)

Delete vertex from graph. Return false if vertex not found in this graph.
• EdgeIterator AddEdge(VertexIterator i1, VertexIterator i2, const EdgeData& d)

Insert edge into this graph. Return endEdge() if input is invalid.
• bool RemoveEdge(EdgeIterator edgeIter)

Remove edge from this graph. Return false if input is invalid.
• EdgeDataIterator BeginEdgeData()

Return iterator that references first edge data item. (There is a const version of this function as well)
• EdgeDataConstIterator BeginEdgeData() const

 

 
 
 
 
 

• EdgeDataIterator EndEdgeData()

Return iterator that references the position in memory after the last edge data item. (There is a const version of this function as well)
• EdgeDataConstIterator EndEdgeData() const

 

 
 
 
 
 

• EdgeIterator begin_edge()

Return EdgeIterator that references first edge in graph. (There is a const version of this function as well)
• ConstEdgeIterator begin_edge() const

 

 
 
 
 
 

• EdgeIterator end_edge()

Return EdgeIterator that references the position in memory after the last edge in graph.(There is a const version of this function as well)
• ConstEdgeIterator end_edge() const

 

 
 
 
 
 
 
 

  BTL_Vertex

• BTL_Vertex() : BTL_VertexBase()

Construct new empty Vertex
• BTL_Vertex(const BTL_Vertex& v) : BTL_VertexBase(v)

Copy constructor.
• virtual ~BTL_Vertex()

Destructor
• iterator GetIterator()

Get an iterator that references the data item associated with this vertex. With graphs that use STL an vector or deque to store data items this iterator may become invalid after insertions or deletions of vertices. (There is also a const version of this function.)
• const_iterator GetIterator() const

 

 
 
 
 
 

• bool& Visited()

Read/write access to visited flag. This can be used in Graph searching routines.
• virtual VertexIterator begin_vertex()

Return iterator that references first vertex connected to this vertex.(There is a const version of this function as well)
• virtual ConstVertexIterator begin_vertex() const

 

 
 
 
 
 

• virtual VertexIterator end_vertex()

Return iterator that references the position in memory after the last vertex connected to this vertex.(There is a const version of this function as well)
• virtual ConstVertexIterator end_vertex() const

 

 
 
 
 
 

• VertexIterator begin()

Return iterator that references first vertex connected to this vertex. (There is a const version of this function as well)
• ConstVertexIterator begin() const

 

 
 
 
 
 

• VertexIterator end()

Return iterator that references the position in memory after the last vertex connected to this vertex.(There is a const version of this function as well)
• ConstVertexIterator end() const

 

 
 
 
 
 
 
 

  BTL_Graph

• BTL_Graph()

Construct new undirected graph
• BTL_Graph(const Directionality& e) : directionality(e)

Construct new undirected or directed graph i.e. BTL_Graph g1(directed); or BTL_Graph g2(undirected);
• virtual ~BTL_Graph()

Delete Graph and all the vertices in it
• Directionality GetDirectionality() const

Get the edge directionality of this graph.
• virtual VertexIterator AddVertex(const value_type& v)

Add new vertex to graph.
• virtual bool RemoveVertex(VertexIterator in)

Remove a vertex (and all pointers to it) from the graph. Return false if vertex was not found in the graph.
• bool AddLink(VertexIterator i1, VertexIterator i2)

Add a pointer between two vertices. Return false if either vertex is not in this graph or is link already present
• bool RemoveLink(VertexIterator i1, VertexIterator i2)

Remove pointer/link between two vertices. Return false if link not there
• virtual void SetAllVisited(bool truth)

Set the visited field of all vertices in this graph.
• virtual VertexIterator find(Vertex& v)

Find a vertex within this Graph.(There is a const version of this function as well)
• virtual ConstVertexIterator find(Vertex& v) const

 

 
 
 
 
 

• iterator begin()

Return iterator that references first data item.(There is a const version of this function as well)
• const_iterator begin() const

 

 
 
 
 
 

• iterator end()

Return iterator that references the position in memory after the last data item. (There is a const version of this function as well)
• const_iterator end() const

 

 
 
 
 
 

• virtual VertexIterator begin_vertex()

Return iterator that references the first Vertex. (There is a const version of this function as well)
• virtual ConstVertexIterator begin_vertex() const

 

 
 
 
 
 

• virtual VertexIterator end_vertex()

Return iterator that references the position in memory after the last Vertex. (There is a const version of this function as well)
• virtual ConstVertexIterator end_vertex() const

 

 
 
 
 
 

• size_type size() const

Give the number of vertices within the Graph

  BTL_DFSIterator

• BTL_DFSIterator()

Default constructor.
• BTL_DFSIterator(const iterator& i)

Construct with iterator. This is essential if operator++ etc. is to be used.
• BTL_DFSIterator& operator++()

Move iterator forward one in depth first search order.
• bool operator!() const

Returns false when current position is one past the end of the last element in the container.
• BTL_DFSIterator operator++(int)

Move iterator forward one in depth first search order.
• bool operator==(BTL_DFSIterator i) const

Equality operator
• value_type& operator*()

Dereference operator

  BTL_ConstDFSIterator

• BTL_ConstDFSIterator()

Default constructor.
• BTL_ConstDFSIterator(const iterator& i)

Construct with iterator. This is essential if operator++ etc. is to be used.
• BTL_ConstDFSIterator& operator++()

Move iterator forward one in depth first search order.
• bool operator!() const

Returns false when current position is one past the end of the last element in the container.
• BTL_ConstDFSIterator operator++(int)

Move iterator forward one in depth first search order.
• bool operator==(BTL_ConstDFSIterator i) const

Equality operator
• value_type operator*() const

Dereference operator

Questions or comments are welcome, please send them to Mark A. Williams.

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