.\" Copyright (c) 2014 Stijn van Dongen
.TH "clm close" 1 "16 May 2014" "clm close 14-137" "USER COMMANDS "
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.SH NAME
clm_close \- Fetch connected components from graphs or subgraphs

clmclose is not in actual fact a program\&. This manual
page documents the behaviour and options of the clm program when
invoked in mode \fIclose\fP\&. The options \fB-h\fP, \fB--apropos\fP,
\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
in all \fBclm\fP modes\&. They are described
in the \fBclm\fP manual page\&.
.SH SYNOPSIS

\fBclm close\fP -imx <fname> [options]

\fBclm close\fP
\fB-imx\fP fname (\fIspecify matrix input\fP)
\fB-abc\fP fname (\fIspecify label input\fP)
\fB-dom\fP fname (\fIinput domain/cluster file\fP)
\fB[-o\fP fname (\fIoutput file\fP)\fB]\fP
\fB[--is-undirected\fP (\fItrust input graph to be undirected\fP)\fB]\fP
\fB[--write-count\fP (\fIoutput component count\fP)\fB]\fP
\fB[--write-sizes\fP (\fIoutput component sizes (default)\fP)\fB]\fP
\fB[--write-cc\fP (\fIoutput components as clustering\fP)\fB]\fP
\fB[--write-block\fP (\fIoutput graph restricted to -dom argument\fP)\fB]\fP
\fB[--write-blockc\fP (\fIoutput graph complement of -dom argument\fP)\fB]\fP
\fB[-cc-bound\fP num (\fIselect components with size at least num\fP)\fB]\fP
\fB[-tf\fP spec (\fIapply tf-spec to input matrix\fP)\fB]\fP
\fB[-h\fP (\fIprint synopsis, exit\fP)\fB]\fP
\fB[--apropos\fP (\fIprint synopsis, exit\fP)\fB]\fP
\fB[--version\fP (\fIprint version, exit\fP)\fB]\fP
.SH DESCRIPTION

Use \fBclm close\fP to fetch the connected components from a graph\&. Different
output modes are supported (see below)\&. In matrix mode (i\&.e\&. using
the \fB-imx\fP option) the output returned with
\fB--write-cc\fP can be used in conjunction with \fBmcxsubs\fP
to retrieve individual subgraphs corresponding to connected components\&.
.SH OPTIONS

.ZI 2m "\fB-abc\fP <fname> (\fIlabel input\fP)"
\&
.br
The file name for input that is in label format\&.
.in -2m

.ZI 2m "\fB-imx\fP <fname> (\fIinput matrix\fP)"
\&
.br
The file name for input that is in mcl native matrix format\&.
.in -2m

.ZI 2m "\fB-o\fP fname (\fIoutput file\fP)"
\&
.br
Specify the file where output is sent to\&. The default is STDOUT\&.
.in -2m

.ZI 2m "\fB-dom\fP fname (\fIinput domain/cluster file\fP)"
\&
.br
If this option is used, clm close will, as a first step,
for each of the domains in file\ \&\fIfname\fP 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\&.
.in -2m

.ZI 2m "\fB--write-count\fP (\fIoutput component count\fP)"
\&
'in -2m
.ZI 2m "\fB--write-sizes\fP (\fIoutput component sizes (default)\fP)"
\&
'in -2m
.ZI 2m "\fB--write-cc\fP (\fIoutput components as clustering\fP)"
\&
'in -2m
.ZI 2m "\fB--write-block\fP (\fIoutput graph restricted to -dom argument\fP)"
\&
'in -2m
.ZI 2m "\fB--write-blockc\fP (\fIoutput graph complement of -dom argument\fP)"
\&
'in -2m
'in +2m
\&
.br
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 \fB--write-count\fP or to
write the components as a clustering in mcl format with
\fB-write-cc\fP\&. 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\&.
.in -2m

.ZI 2m "\fB--is-undirected\fP (\fIomit graph undirected check\fP)"
\&
.br
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\&.
.in -2m

.ZI 2m "\fB-cc-bound\fP num (\fIselect components with size at least num\fP)"
\&
.br
Transform the input matrix values according
to the syntax described in \fBmcxio(5)\fP\&.
.in -2m
.SH AUTHOR

Stijn van Dongen\&.
.SH SEE ALSO

\fBmclfamily(7)\fP for an overview of all the documentation
and the utilities in the mcl family\&.