File: mcx.zmm

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mcl 1%3A14-137-1
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\'set{reqver}{2009-250}
\'if{\'cmp{gq}{\__version__}{\reqver}}{}{
\'write{stderr}{txt}{Requires zoem version >= \reqver\|}\'exit}

   \: \setx{__searchpath__}{\__searchpath__\!{}{../../../zoem/mac}}
   \: Used this when using relative path through the micans tree.
   \: Nowadays I oblige myself to use the zoem installed on my system. 

\'input{pud/man.zmm}

   \: The three definitions below are for options defined in
   \: an \items{ .. } macro.
   \: The first option is the only one with a genuine \defopt
   \: and creates the anchor for those  options.
   \: Use the dummy macros on the other options so that documentation
   \: analysis tools (like Stijn's docme) can pick them up
   \: as definition instances and reconcile them with `prog --apropos`.

\'set{defoptdummy#2}{\genopt{\1}{\2}}
\'set{defoptdummy#3}{\genopt{\1}{\2}{\3}}
\'set{defkvpdummy#3}{\defkvp{\1}{\2}{\3}}

\'setx{"man::year"}{\'zinsert{stamp.year}}
\'setx{"man::month"}{\'zinsert{stamp.month}}
\'setx{"man::day"}{\'zinsert{stamp.day}}
\'setx{"mcx::stamp"}{\'zinsert{stamp.stamp}}

\'setx{"man::year"}{\'tr{{delete}{[:space:]}}{\"man::year"}}
\'setx{"man::month"}{\'tr{{delete}{[:space:]}}{\"man::month"}}
\'setx{"man::day"}{\'tr{{delete}{[:space:]}}{\"man::day"}}
\'setx{"mcx::stamp"}{\'tr{{delete}{[:space:]}}{\"mcx::stamp"}}

\setx{man_share}{
   {year}    {\"man::year"}
   {month}   {\"man::month"}
   {day}     {\"man::day"}
   {tag}     {\"mcx::stamp"}
   {stamp}   {\"mcx::stamp"}
}

\'setx{"mcx::date"}{\"man::day" \"man::month" \"man::year"}

\'def{mcl}{\bf{mcl}}
\'def{mcle}{\bf{mcl-edge}}
\'def{mclcm}{\bf{mclcm}}
\'def{mcx}{\bf{mcx}}
\'def{mcxi}{\bf{mcxi}}

\set{{modes}{vw}}{}{
   {clm}       {\bf{clm}}
   {clmdist}   {\bf{clm dist}}
   {clmvol}    {\bf{clm vol}}
   {clmstable}    {\bf{clm vol}}
   {clminfo}   {\bf{clm info}}
   {clmmeet}   {\bf{clm meet}}
   {clmclose}  {\bf{clm close}}
   {clmformat} {\bf{clm format}}
   {clmimac}   {\bf{clm imac}}
   {clmmate}   {\bf{clm mate}}
   {clmresidue}{\bf{clm residue}}
   {clmorder}  {\bf{clm order}}
}

\'def{disclaim_mcx#1}{\par{mcx\1 is not in actual fact a program. This manual
page documents the behaviour and options of the mcx program when
invoked in mode \it{\1}. The options \genopt{-h}, \genopt{--apropos},
\genopt{--version}, \genopt{-set}, \genopt{--nop}, \genopt{-progress}{<num>}
are accessible
in all \bf{mcx} modes. They are described
in the \sibref{mcx} manual page.}}

\'def{disclaim_clm#1}{\par{clm\1 is not in actual fact a program. This manual
page documents the behaviour and options of the clm program when
invoked in mode \it{\1}. The options \genopt{-h}, \genopt{--apropos},
\genopt{--version}, \genopt{-set}, \genopt{--nop} are accessible
in all \bf{clm} modes. They are described
in the \sibref{clm} manual page.}}

\'def{stddefopt}{
   \if{0}{
\items{
   {\defopt{-h}{print synopsis, exit}}
   {\defopt{--apropos}{print synopsis, exit}}
}
\item{\defopt{--version}{print version, exit}}
      }{
   }
}

\'def{stdsynopt}{\:/
   \synoptopt{-h}{print synopsis, exit}
   \synoptopt{--apropos}{print synopsis, exit}
   \synoptopt{--version}{print version, exit}}


\def{shared_synoptopt#1}{
   \switch{\1}{
      {-tf}
         {\synoptopt{-tf}{spec}{apply tf-spec to input matrix}}
      {-ceil-nb}
         {\synoptopt{-ceil-nb}{n}{reduce neighbourhoods}}
      {-knn}
         {\synoptopt{-knn}{n}{keep mutually close neighbours}}
      {-t}
         {\synoptopt{-t}{<int>}{use <int> threads}}
      {-J}
         {\synoptopt{-J}{<intJ>}{a total of <intJ> jobs are used}}
      {-j}
         {\synoptopt{-j}{<intj>}{this job has index <intj>}}
      {\inform{not supported for shared_synoptopt#1: \1}\exit}
   }
}

\def{shared_itemopt#1}{
   \switch{\1}{
      {-tf}
         {\item{\defopt{-tf}{<tf-spec>}{transform input matrix values}}}
      {-ceil-nb}
         {\item{\defopt{-ceil-nb}{n}{reduce neighbourhoods}}}
      {-knn}
         {\item{\defopt{-knn}{<num>}{keep mutually close neighbours}}}

      {\inform{not supported for shared_itemopt#1: \1}\exit}
   }
}


\def{shared_defopt#1}{
   \switch{\1}{
      {-tf}{
Transform the input matrix values according
to the syntax described in \mysib{mcxio}.
      }
      {-ceil-nb}{
The nodes of the input graph are considered in descending order of the
number of neighbours they posses.  The first nodes has it neighbours of
lowest edge weight removed until no more than \genopt{N} remain.  The
corresponding reciprocal edges from nodes further down the list are removed
as well.  Subsequent nodes are treated in the same way until all nodes in
the graph have at most \genopt{N} neighbours.  This may be considered a poor
man's hub removal.
      }
      {-knn}{
This considers the \genarg{<num>} best neighbours for each node, then only keeps
edges that occur in both best-neighbour lists for the two incident nodes.
      }
      {\inform{not supported for shared_defopt#1: \1}\exit}
   }
}


\'def{mcxload}{\bf{mcxload}}
\'def{mcxconvert}{\bf{mcxconvert}}
\'def{mcxarray}{\bf{mcxarray}}
\'def{mcxdump}{\bf{mcxdump}}
\'def{mcxdiameter}{\bf{mcxdiameter}}
\'def{mcxclcf}{\bf{mcxclcf}}
\'def{mcxquery}{\bf{mcxquery}}
\'def{mcxrand}{\bf{mcxrand}}
\'def{mcxdeblast}{\bf{mcxdeblast}}
\'def{mclblastline}{\bf{mclblastline}}
\'def{mclpipeline}{\bf{mclpipeline}}
\'def{zoem}{\bf{zoem}}
\'def{mcxsubs}{\bf{mcxsubs}}
\'def{mcxmap}{\bf{mcxmap}}
\'def{mcxalter}{\bf{mcxalter}}
\'def{mcxassemble}{\bf{mcxassemble}}

\'def{mcx_itemopts}{{flow}{cascade}{interitem}{1}{$w1}{2}{$w2}{1}{textindent}{2}{itemmargin}{1}}

\: different conventions for html and roff.
\: in roff I use 'section 5' of the manual pages.

\'def{sib#1}{\sibref{\1}{\1}}

\'set{%{sibroffmap}}{
   {mcxio}{5}
   {clmprotocols}{5}
   {mclfaq}{7}
   {mclfamily}{7}
   {tingea.log}{7}

   {mcl}{1}
   {mclcm}{1}
   {mcx}{1}
   {mcxi}{1}

   {mcxconvert}{1}
   {mcxarray}{1}
   {mcxrand}{1}
   {mcxdiameter}{1}
   {mcxclcf}{1}
   {mcxquery}{1}
   {mcxdump}{1}
   {mcxload}{1}
   {mcxsubs}{1}
   {mcxmap}{1}
   {mcxalter}{1}
   {mcxassemble}{1}

   {clm}{1}
   {clmimac}{1}
   {clmclose}{1}
   {clmresidue}{1}
   {clmdist}{1}
   {clminfo}{1}
   {clmvol}{1}
   {clmstable}{1}
   {clmmate}{1}
   {clmmeet}{1}
   {clmformat}{1}
   {clmorder}{1}

   {mclpipeline}{1}
   {mclblastline}{1}
   {mcxdeblast}{1}
}

\'def{clm#1}{\bf{clm \1}}
\'def{clmref#1}{\sibref{clm\1}{clm\~\1}}
\'def{clmref#2}{\sibref{clm\1}{\2}}

\'def{mcx#1}{\bf{mcx\~\1}}
\'def{mcxref#1}{\sibref{mcx\1}{mcx\~\1}}
\'def{mcxref#2}{\sibref{mcx\1}{\2}}

\'def{mysib#1}{\sibref{\1}{\1\'${roff}{(\%{sibroffmap}{\1})}}}
\'def{mysib#2}{\sibref{\1}{\2}{\1\'${roff}{(\%{sibroffmap}{\1})}}}

\def{abc}{\sc{ABC}}
\def{MCL}{\sc{MCL}}