Added matlab_bgl dependencies for mKymoUI code.

src/matlab/bgl_deps/check_matlab_bgl.m

+function check_matlab_bgl(A,options)
+% CHECK_MATLAB_BGL Checks the input A for various properties
+%
+% check_matlab_bgl(A,options) throws an input error if...
+%   A is not square
+%   if options.values and A is not double valued
+%   if options.sym = 1 and A is not symmetric
+%   if options.flow_graph = 1 and A is not a flow graph data structure
+%   if options.nosparse = 1 do not check if A is sparse
+%   if options.nodefault = 1 then do not check default cases
+%   if options.nodiag = 1 throw an error if A has any non-zero diagonal values
+
+% David Gleich
+% Copyright, Stanford University, 2006-2008
+
+%% History
+%  2007-04-20: Added nodefault option
+%  2007-07-22: Fixed empty array error for noneg check
+%  2008-09-23: Added no diagonal check, misc formatting fixes
+%% 
+
+if ~isfield(options, 'nodefault') || options.nodefault == 0
+    if size(A,1) ~= size(A,2)
+        error('matlab_bgl:invalidParameter', 'the matrix A must be square.');
+    end
+end
+
+if isfield(options, 'values') && options.values == 1
+    if ~isa(A,'double')
+        error('matlab_bgl:invalidParameter', 'the matrix A must have double values.');
+    end
+end
+
+if isfield(options, 'noneg') && options.noneg == 1
+    v=min(min(A));
+    if ~isempty(v) && v < 0
+        error('matlab_bgl:invalidParameter', 'the matrix A must have non-negative values.');
+    end
+end
+
+if isfield(options, 'sym') && options.sym == 1
+    if ~isequal(A,A')
+        error('matlab_bgl:invalidParameter', 'the matrix A must be symmetric.');
+    end
+end
+
+if isfield(options, 'nosparse') && options.nosparse == 1
+else
+    if ~issparse(A)
+        error('matlab_bgl:invalidParameter', 'the matrix A must be sparse.  (See set_matlab_bgl_default.)');
+    end
+end
+
+if isfield(options,'nodiag') && options.nodiag == 1
+    if any(diag(A))
+        error('matlab_bgl:invalidParameter',...
+            'the matrix A must not have any diagonal values')
+    end
+end
+

src/matlab/bgl_deps/get_matlab_bgl_options.m

+function [trans check full2sparse] = get_matlab_bgl_options(varargin)
+% 
+% Internal private function.
+%
+% Example:
+%    Don't use this function!
+%
+
+%% History
+%  2008-09-26: Changed to use merge_options instead
+%%
+
+doptions = set_matlab_bgl_default();
+if nargin>0
+    options = merge_options(doptions,varargin{:});
+else
+    options = doptions;
+end
+
+trans = ~options.istrans;
+check = ~options.nocheck;
+full2sparse = options.full2sparse;
+

src/matlab/bgl_deps/merge_options.m

+function options = merge_options(default_options,varargin)
+% MERGE_OPTIONS Merge a set of default options with options from varargin
+% The set of options in varargin can be a list of key,value pairs, or a
+% struct with the same information.
+
+% David F. Gleich
+% Copyright, Stanford University, 2008
+
+%% History
+%  2008-09-25: Initial coding
+%%
+
+if ~isempty(varargin) && mod(length(varargin),2) == 0
+    options = merge_structs(struct(varargin{:}),default_options);
+elseif length(varargin)==1 && isstruct(varargin{1})
+    options = merge_structs(varargin{1},default_options);
+elseif ~isempty(varargin)
+    error('matlag_bgl:optionsParsing',...
+        'There were an odd number of key-value pairs of options specified');
+else
+    options = default_options;
+end
\ No newline at end of file

src/matlab/bgl_deps/merge_structs.m

+function S = merge_structs(A, B)
+% MERGE_STRUCTS Merge two structures.
+%
+% S = merge_structs(A, B) makes the structure S have all the fields from A
+% and B.  Conflicts are resolved by using the value in A.
+%
+
+%
+% merge_structs.m
+% David Gleich
+%
+% Revision 1.00
+% 19 Octoboer 2005
+%
+
+S = A;
+
+fn = fieldnames(B);
+
+for ii = 1:length(fn)
+    if (~isfield(A, fn{ii}))
+        S.(fn{ii}) = B.(fn{ii});
+    end;
+end;
+

src/matlab/bgl_deps/set_matlab_bgl_default.m

+function old_default = set_matlab_bgl_default(varargin)
+% SET_MATLAB_BGL_DEFAULT Sets a default option for the Matlab BGL interface
+%
+% old_default = set_matlab_bgl_default(options) or
+% old_default = set_matlab_bgl_default(...) for key-value pair version
+% options.istrans: the input matrices are already transposed [{0} | 1]
+% options.nocheck: skip the input checking [{0} | 1]
+% options.full2sparse: convert full matrices to sparse [{0} | 1]
+%
+% to get the current set of default options, call
+% options = set_matlab_bgl_default()
+%
+% These options can make the Matlab BGL interface more efficient by
+% eliminating the copying operations that occur between Matlab's structures
+% and the BGL structures.  However, they are more difficult to use and are
+% disabled by default.
+%
+% Generally, they are best used when you want to perform a large series of
+% computations.
+%
+% Example:
+%   % tranpose the matrix initially...
+%   At = A'
+%   old_options = set_matlab_bgl_default(struct('istrans',1));
+%   % perform a bunch of graph work with At...
+%   d1 = dfs(At,1); d2 = dfs(At,2); ...
+%   % restore the old options 
+%   set_matlab_bgl_default(old_options);
+
+% David Gleich
+% Copyright, Stanford University, 2006-2008
+
+%% History
+%%
+
+persistent default_options;
+if ~isa(default_options,'struct')
+    % initial default options
+    default_options = struct('istrans', 0, 'nocheck', 0, 'full2sparse', 0);
+end
+
+if nargin == 0
+    old_default = default_options;
+else
+    old_default = default_options;
+    default_options = merge_options(default_options,varargin{:});
+end
+   

src/matlab/bgl_deps/shortest_paths.m

+function [d pred] = shortest_paths(A,u,varargin)
+% SHORTEST_PATHS Compute the weighted single source shortest path problem.
+%
+% [d pred] = shortest_paths(A,u) returns the distance (d) and the predecessor
+% (pred) for each of the vertices along the shortest path from u to every
+% other vertex in the graph.  
+% 
+% ... = shortest_paths(A,u,...) takes a set of
+% key-value pairs or an options structure.  See set_matlab_bgl_options
+% for the standard options. 
+%   options.algname: the algorithm to use 
+%       [{'auto'} | 'dijkstra' | 'bellman_ford' | 'dag']
+%   options.inf: the value to use for unreachable vertices 
+%       [double > 0 | {Inf}]
+%   options.target: a special vertex that will stop the search when hit
+%       [{'none'} | any vertex number besides the u]; target is ignored if
+%       visitor is set.
+%   options.visitor: a structure with visitor callbacks.  This option only
+%       applies to dijkstra or bellman_ford algorithms.  See dijkstra_sp or
+%       bellman_ford_sp for details on the visitors.
+%   options.edge_weight: a double array over the edges with an edge
+%       weight for each edge, see EDGE_INDEX and EXAMPLES/REWEIGHTED_GRAPHS
+%       for information on how to use this option correctly
+%       [{'matrix'} | length(nnz(A)) double vector]
+%
+% Note: if you need to compute shortest paths with 0 weight edges, you must
+% use an edge_weight vector, see the examples for details.
+%
+% Note: 'auto' cannot be used with 'nocheck' = 1.  The 'auto' algorithm
+% checks if the graph has negative edges and uses bellman_ford in that
+% case, otherwise, it uses 'dijkstra'.  In the future, it may check if the
+% graph is a dag and use 'dag'.  
+%
+% Example:
+%    load graphs/clr-25-2.mat
+%    shortest_paths(A,1)
+%    shortest_paths(A,1,struct('algname','bellman_ford'))
+%
+% See also DIJKSTRA_SP, BELLMAN_FORD_SP, DAG_SP
+
+% David Gleich
+% Copyright, Stanford University, 2006-2008
+
+%% History
+%  2006-04-19: Initial coding
+%  2007-04-18: Added edge_weight option.
+%  2007-04-19: Added target option.
+%    Added additional error checks.
+%  2007-07-12: Fixed edge_weight documentation
+%%
+
+[trans check full2sparse] = get_matlab_bgl_options(varargin{:});
+if full2sparse && ~issparse(A), A = sparse(A); end
+
+options = struct('algname', 'auto', 'inf', Inf, 'edge_weight', 'matrix', ...
+    'target', 'none');
+options = merge_options(options,varargin{:});    
+
+% edge_weights is an indicator that is 1 if we are using edge_weights
+% passed on the command line or 0 if we are using the matrix.
+edge_weights = 0;
+edge_weight_opt = 'matrix';
+
+if strcmp(options.edge_weight, 'matrix')
+    % do nothing if we are using the matrix weights
+else
+    edge_weights = 1;
+    edge_weight_opt = options.edge_weight;
+end
+
+if strcmp(options.target,'none')
+    target = 0; % a flag used to denote "no target" to the mex
+elseif isa(options.target, 'double')
+    target = options.target;
+else
+    error('matlab_bgl:invalidParameter', ...
+        'options.target is not ''none'' or a vertex number.');
+end
+
+if check
+    % check the values of the matrix
+    check_matlab_bgl(A,struct('values',edge_weights ~= 1));
+    
+    if edge_weights && nnz(A) ~= length(edge_weight_opt)
+        error('matlab_bgl:invalidParameter', 'the vector of edge weights must have length nnz(A)');
+    end
+    
+    % set the algname
+    if (strcmpi(options.algname, 'auto'))
+        if edge_weights
+            mv = min(edge_weights);
+        else
+            mv = min(min(A));
+        end
+        
+        if (mv < 0)
+            options.algname = 'bellman_ford';
+        else
+            options.algname = 'dijkstra';
+        end
+    else
+        % check the data provided to match the algorithm
+        if strcmpi(options.algname, 'dijkstra')
+            if edge_weights
+                mv = min(edge_weight_opt);
+            else
+                mv = min(min(A));
+            end
+            if mv < 0
+                error('matlab_bgl:invalidParameter', ...
+                    'dijkstra''s algorithm cannot be used with negative edge weights.');
+            end
+        end
+    end
+    
+else
+    if (strcmpi(options.algname, 'auto'))
+        error('shortest_paths:invalidParameter', ...
+            'algname auto is not compatible with no check');       
+    end
+end
+
+if options.inf < 0, error('options.inf must be larger than 0'); end
+
+if trans, A = A'; end
+
+if isfield(options,'visitor')
+    [d pred] = matlab_bgl_sp_mex(A,u,target,lower(options.algname),options.inf,...
+        edge_weight_opt, options.visitor);
+else
+    [d pred] = matlab_bgl_sp_mex(A,u,target,lower(options.algname),options.inf,...
+        edge_weight_opt);
+end
+

src/matlab/check_matlab_bgl.m

+function check_matlab_bgl(A,options)
+% CHECK_MATLAB_BGL Checks the input A for various properties
+%
+% check_matlab_bgl(A,options) throws an input error if...
+%   A is not square
+%   if options.values and A is not double valued
+%   if options.sym = 1 and A is not symmetric
+%   if options.flow_graph = 1 and A is not a flow graph data structure
+%   if options.nosparse = 1 do not check if A is sparse
+%   if options.nodefault = 1 then do not check default cases
+%   if options.nodiag = 1 throw an error if A has any non-zero diagonal values
+
+% David Gleich
+% Copyright, Stanford University, 2006-2008
+
+%% History
+%  2007-04-20: Added nodefault option
+%  2007-07-22: Fixed empty array error for noneg check
+%  2008-09-23: Added no diagonal check, misc formatting fixes
+%% 
+
+if ~isfield(options, 'nodefault') || options.nodefault == 0
+    if size(A,1) ~= size(A,2)
+        error('matlab_bgl:invalidParameter', 'the matrix A must be square.');
+    end
+end
+
+if isfield(options, 'values') && options.values == 1
+    if ~isa(A,'double')
+        error('matlab_bgl:invalidParameter', 'the matrix A must have double values.');
+    end
+end
+
+if isfield(options, 'noneg') && options.noneg == 1
+    v=min(min(A));
+    if ~isempty(v) && v < 0
+        error('matlab_bgl:invalidParameter', 'the matrix A must have non-negative values.');
+    end
+end
+
+if isfield(options, 'sym') && options.sym == 1
+    if ~isequal(A,A')
+        error('matlab_bgl:invalidParameter', 'the matrix A must be symmetric.');
+    end
+end
+
+if isfield(options, 'nosparse') && options.nosparse == 1
+else
+    if ~issparse(A)
+        error('matlab_bgl:invalidParameter', 'the matrix A must be sparse.  (See set_matlab_bgl_default.)');
+    end
+end
+
+if isfield(options,'nodiag') && options.nodiag == 1
+    if any(diag(A))
+        error('matlab_bgl:invalidParameter',...
+            'the matrix A must not have any diagonal values')
+    end
+end
+

src/matlab/get_matlab_bgl_options.m

+function [trans check full2sparse] = get_matlab_bgl_options(varargin)
+% 
+% Internal private function.
+%
+% Example:
+%    Don't use this function!
+%
+
+%% History
+%  2008-09-26: Changed to use merge_options instead
+%%
+
+doptions = set_matlab_bgl_default();
+if nargin>0
+    options = merge_options(doptions,varargin{:});
+else
+    options = doptions;
+end
+
+trans = ~options.istrans;
+check = ~options.nocheck;
+full2sparse = options.full2sparse;
+

src/matlab/merge_options.m

+function options = merge_options(default_options,varargin)
+% MERGE_OPTIONS Merge a set of default options with options from varargin
+% The set of options in varargin can be a list of key,value pairs, or a
+% struct with the same information.
+
+% David F. Gleich
+% Copyright, Stanford University, 2008
+
+%% History
+%  2008-09-25: Initial coding
+%%
+
+if ~isempty(varargin) && mod(length(varargin),2) == 0
+    options = merge_structs(struct(varargin{:}),default_options);
+elseif length(varargin)==1 && isstruct(varargin{1})
+    options = merge_structs(varargin{1},default_options);
+elseif ~isempty(varargin)
+    error('matlag_bgl:optionsParsing',...
+        'There were an odd number of key-value pairs of options specified');
+else
+    options = default_options;
+end
\ No newline at end of file

src/matlab/merge_structs.m

+function S = merge_structs(A, B)
+% MERGE_STRUCTS Merge two structures.
+%
+% S = merge_structs(A, B) makes the structure S have all the fields from A
+% and B.  Conflicts are resolved by using the value in A.
+%
+
+%
+% merge_structs.m
+% David Gleich
+%
+% Revision 1.00
+% 19 Octoboer 2005
+%
+
+S = A;
+
+fn = fieldnames(B);
+
+for ii = 1:length(fn)
+    if (~isfield(A, fn{ii}))
+        S.(fn{ii}) = B.(fn{ii});
+    end;
+end;
+

src/matlab/set_matlab_bgl_default.m

+function old_default = set_matlab_bgl_default(varargin)
+% SET_MATLAB_BGL_DEFAULT Sets a default option for the Matlab BGL interface
+%
+% old_default = set_matlab_bgl_default(options) or
+% old_default = set_matlab_bgl_default(...) for key-value pair version
+% options.istrans: the input matrices are already transposed [{0} | 1]
+% options.nocheck: skip the input checking [{0} | 1]
+% options.full2sparse: convert full matrices to sparse [{0} | 1]
+%
+% to get the current set of default options, call
+% options = set_matlab_bgl_default()
+%
+% These options can make the Matlab BGL interface more efficient by
+% eliminating the copying operations that occur between Matlab's structures
+% and the BGL structures.  However, they are more difficult to use and are
+% disabled by default.
+%
+% Generally, they are best used when you want to perform a large series of
+% computations.
+%
+% Example:
+%   % tranpose the matrix initially...
+%   At = A'
+%   old_options = set_matlab_bgl_default(struct('istrans',1));
+%   % perform a bunch of graph work with At...
+%   d1 = dfs(At,1); d2 = dfs(At,2); ...
+%   % restore the old options 
+%   set_matlab_bgl_default(old_options);
+
+% David Gleich
+% Copyright, Stanford University, 2006-2008
+
+%% History
+%%
+
+persistent default_options;
+if ~isa(default_options,'struct')
+    % initial default options
+    default_options = struct('istrans', 0, 'nocheck', 0, 'full2sparse', 0);
+end
+
+if nargin == 0
+    old_default = default_options;
+else
+    old_default = default_options;
+    default_options = merge_options(default_options,varargin{:});
+end
+   

src/matlab/shortest_paths.m

+function [d pred] = shortest_paths(A,u,varargin)
+% SHORTEST_PATHS Compute the weighted single source shortest path problem.
+%
+% [d pred] = shortest_paths(A,u) returns the distance (d) and the predecessor
+% (pred) for each of the vertices along the shortest path from u to every
+% other vertex in the graph.  
+% 
+% ... = shortest_paths(A,u,...) takes a set of
+% key-value pairs or an options structure.  See set_matlab_bgl_options
+% for the standard options. 
+%   options.algname: the algorithm to use 
+%       [{'auto'} | 'dijkstra' | 'bellman_ford' | 'dag']
+%   options.inf: the value to use for unreachable vertices 
+%       [double > 0 | {Inf}]
+%   options.target: a special vertex that will stop the search when hit
+%       [{'none'} | any vertex number besides the u]; target is ignored if
+%       visitor is set.
+%   options.visitor: a structure with visitor callbacks.  This option only
+%       applies to dijkstra or bellman_ford algorithms.  See dijkstra_sp or
+%       bellman_ford_sp for details on the visitors.
+%   options.edge_weight: a double array over the edges with an edge
+%       weight for each edge, see EDGE_INDEX and EXAMPLES/REWEIGHTED_GRAPHS
+%       for information on how to use this option correctly
+%       [{'matrix'} | length(nnz(A)) double vector]
+%
+% Note: if you need to compute shortest paths with 0 weight edges, you must
+% use an edge_weight vector, see the examples for details.
+%
+% Note: 'auto' cannot be used with 'nocheck' = 1.  The 'auto' algorithm
+% checks if the graph has negative edges and uses bellman_ford in that
+% case, otherwise, it uses 'dijkstra'.  In the future, it may check if the
+% graph is a dag and use 'dag'.  
+%
+% Example:
+%    load graphs/clr-25-2.mat
+%    shortest_paths(A,1)
+%    shortest_paths(A,1,struct('algname','bellman_ford'))
+%
+% See also DIJKSTRA_SP, BELLMAN_FORD_SP, DAG_SP
+
+% David Gleich
+% Copyright, Stanford University, 2006-2008
+
+%% History
+%  2006-04-19: Initial coding
+%  2007-04-18: Added edge_weight option.
+%  2007-04-19: Added target option.
+%    Added additional error checks.
+%  2007-07-12: Fixed edge_weight documentation
+%%
+
+[trans check full2sparse] = get_matlab_bgl_options(varargin{:});
+if full2sparse && ~issparse(A), A = sparse(A); end
+
+options = struct('algname', 'auto', 'inf', Inf, 'edge_weight', 'matrix', ...
+    'target', 'none');
+options = merge_options(options,varargin{:});    
+
+% edge_weights is an indicator that is 1 if we are using edge_weights
+% passed on the command line or 0 if we are using the matrix.
+edge_weights = 0;
+edge_weight_opt = 'matrix';
+
+if strcmp(options.edge_weight, 'matrix')
+    % do nothing if we are using the matrix weights
+else
+    edge_weights = 1;
+    edge_weight_opt = options.edge_weight;
+end
+
+if strcmp(options.target,'none')
+    target = 0; % a flag used to denote "no target" to the mex
+elseif isa(options.target, 'double')
+    target = options.target;
+else
+    error('matlab_bgl:invalidParameter', ...
+        'options.target is not ''none'' or a vertex number.');
+end
+
+if check
+    % check the values of the matrix
+    check_matlab_bgl(A,struct('values',edge_weights ~= 1));
+    
+    if edge_weights && nnz(A) ~= length(edge_weight_opt)
+        error('matlab_bgl:invalidParameter', 'the vector of edge weights must have length nnz(A)');
+    end
+    
+    % set the algname
+    if (strcmpi(options.algname, 'auto'))
+        if edge_weights
+            mv = min(edge_weights);
+        else
+            mv = min(min(A));
+        end
+        
+        if (mv < 0)
+            options.algname = 'bellman_ford';
+        else
+            options.algname = 'dijkstra';
+        end
+    else
+        % check the data provided to match the algorithm
+        if strcmpi(options.algname, 'dijkstra')
+            if edge_weights
+                mv = min(edge_weight_opt);
+            else
+                mv = min(min(A));
+            end
+            if mv < 0
+                error('matlab_bgl:invalidParameter', ...
+                    'dijkstra''s algorithm cannot be used with negative edge weights.');
+            end
+        end
+    end
+    
+else
+    if (strcmpi(options.algname, 'auto'))
+        error('shortest_paths:invalidParameter', ...
+            'algname auto is not compatible with no check');       
+    end
+end
+
+if options.inf < 0, error('options.inf must be larger than 0'); end
+
+if trans, A = A'; end
+
+if isfield(options,'visitor')
+    [d pred] = matlab_bgl_sp_mex(A,u,target,lower(options.algname),options.inf,...
+        edge_weight_opt, options.visitor);
+else
+    [d pred] = matlab_bgl_sp_mex(A,u,target,lower(options.algname),options.inf,...
+        edge_weight_opt);
+end
+