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\import{mcx.zmm}
\begin{pud::man}{
{name}{clm close}
{html_title}{The clm close manual}
{author}{Stijn van Dongen}
{section}{1}
{synstyle}{long}
{defstyle}{long}
\man_share
}
\${html}{\"pud::man::maketoc"}
\sec{name}{NAME}
\NAME{clm_close}{Fetch connected components from graphs or subgraphs}
\disclaim_clm{close}
\sec{synopsis}{SYNOPSIS}
\par{
\clm{close} -imx <fname> [options]
}
\par{
\clm{close}
\synreqopt{-imx}{fname}{specify matrix input}
\synreqopt{-abc}{fname}{specify label input}
\synreqopt{-dom}{fname}{input domain/cluster file}
\synoptopt{-o}{fname}{output file}
\synoptopt{--is-undirected}{trust input graph to be undirected}
\synoptopt{--write-count}{output component count}
\synoptopt{--write-sizes}{output component sizes (default)}
\synoptopt{--write-cc}{output components as clustering}
\synoptopt{--write-block}{output graph restricted to -dom argument}
\synoptopt{--write-blockc}{output graph complement of -dom argument}
\synoptopt{-cc-bound}{num}{select components with size at least num}
\shared_synoptopt{-tf}
\stdsynopt
}
\sec{description}{DESCRIPTION}
\par{
Use \clm{close} to fetch the connected components from a graph. Different
output modes are supported (see below). In matrix mode (i.e. using
the \genopt{-imx} option) the output returned with
\genopt{--write-cc} can be used in conjunction with \mcxsubs
to retrieve individual subgraphs corresponding to connected components.
}
\sec{options}{OPTIONS}
\begin{itemize}{\mcx_itemopts}
\item{\defopt{-abc}{<fname>}{label input}}
\car{
The file name for input that is in label format.}
\item{\defopt{-imx}{<fname>}{input matrix}}
\car{
The file name for input that is in mcl native matrix format.}
\item{\defopt{-o}{fname}{output file}}
\car{
Specify the file where output is sent to. The default is STDOUT.
}
\item{\defopt{-dom}{fname}{input domain/cluster file}}
\car{
If this option is used, clm close will, as a first step,
for each of the domains in file\~\genarg{fname} retrieve the associated
subgraph from the input graph. These are then further decomposed into
connected components, and the program will process these in the normal
manner.
}
\items{
{\defopt{--write-count}{output component count}}
{\defopt{--write-sizes}{output component sizes (default)}}
{\defopt{--write-cc}{output components as clustering}}
{\defopt{--write-block}{output graph restricted to -dom argument}}
{\defopt{--write-blockc}{output graph complement of -dom argument}}
}
\car{
The default behaviour is currently to output the sizes of the
connected components. It is also possible to simply output
the number of components with \genopt{--write-count} or to
write the components as a clustering in mcl format with
\genopt{-write-cc}. Even more options exist: it is possible
to output the restriction of the input graph to a domain, or
to output the complement of this restriction.
}
\item{\defopt{--is-undirected}{omit graph undirected check}}
\car{
With this option the transformation to make sure
that the input is undirected is omitted. This will
be slightly faster. Using this option while the
input is directed may lead to erronenous results.
}
\item{\defopt{-cc-bound}{num}{select components with size at least num}}
\shared_defopt{-tf}
\stddefopt
\end{itemize}
\sec{author}{AUTHOR}
\par{
Stijn van Dongen.
}
\sec{seealso}{SEE ALSO}
\par{
\mysib{mclfamily} for an overview of all the documentation
and the utilities in the mcl family.
}
\end{pud::man}
|
