mcxmap(1)							  USER COMMANDS 							 mcxmap(1)

  NAME
      mcxmap - permute or remap the indices of graphs and matrices.

  SYNOPSIS
      mcxmap -imx fname (input) [-o fname (output)] [-make-map (output map file name)] [-make-mapc (output map file name)] [-make-mapr (output map
      file name)] [-cmul a (coefficient)] [-cshift b (translate)] [-rmul c (coefficient)] [-rshift d (translate)] [-mul e (coefficient)] [-shift f
      (translate)]  [-map  fname  (row/col  map file)] [-rmap fname (row map file)] [-cmap fname (column map file)] [-mapi fname (row/col map file
      (use inverse))] [-rmapi fname (row map file (use inverse))] [-cmapi fname (column map file (use inverse))] [-tab fname (read (and  map)  tab
      file)]

  DESCRIPTION
      This utility relabels graphs or matrices. Its main use is in applying a map file to a given matrix or graph. A map file contains a so called
      map matrix in mcl format that has some special properties (given further below). The functionality of mcxmap can also be provided by mcx, as
      a  mapped  matrix  (i.e.	the  result  of  applying a map matrix to another matrix) is simply the usual matrix product of a matrix and a map
      matrix. However, mcx will construct a new matrix and leave the original matrix to be mapped alone. When dealing with huge matrices,  consid-
      erable  gains  in  efficiency  memory-wise  and  time-wise  can be achieved by doing the mapping in-place.  This is what mcxmap does. In the
      future, its functionality may be embedded in mcx with new mcx operators.

      The special properties of a map matrix are

      o The column domain and row domain are of the same cardinality.
      o Each column has exactly one entry.
      o Each row domain index occurs in exactly one column.

      These properties imply that the matrix can be used as a map from the column domain onto the row domain.  An example map matrix is  found	in
      the EXAMPLES Section.

  OPTIONS
      -o fname (output file)
	Output file.

      -imx fname (input file)
	Input file.

      -map fname (row/col map file))
      -rmap fname (row map file)
      -cmap fname (column map file)
      -mapi fname (row/col map file (use inverse))
      -rmapi fname (row map fil (use inverse))
      -cmapi fname (column map fil (use inverse))
	Different ways to specify map files.

      -make-map (output map file name)
      -make-mapc (output map file name)
      -make-mapr (output map file name)
	Generate a map that maps the specified domain onto the appropriate canonical domain and write the map matrix to file.

      -cmul a (coefficient)
      -cshift b (translate)
	These  options	have  affect if neither a column map file nor column canonification is specified. If any of the first two options is used,
	column indices i are mapped to a*i+b.

      -rmul c (coefficient)
      -rshift d (translate)
	These options have affect if neither a row map file nor row canonification is specified.  If  any  of  the  first  two	options  is  used,
	indices i are mapped to c*i+d.

      -mul e (coefficient)
      -shift f (translate)
	If  a  map  file  is  specified for a given domain, neither a map file nor canonification is specified. If any of the first two options is
	used, the indices i will be mapped to e*i+f.

      -tab fname (read (and map) tab file)
	This option requires the -map option. mcxmap will output the mapped tab definition.

  EXAMPLES
      The matrix below has two canonical domains which are identical.  It denotes a map of the canonical domain onto itself, in which  node  0	is
      relabeled to 8, node 1 is relabeled to 5, et cetera.

      (mclheader
      mcltype matrix
      dimensions 12x12
      )
      (mclmatrix
      begin
      0  8  $
      1  5  $
      2  3  $
      3  2  $
      4  4  $
      5  6  $
      6  7  $
      7  9  $
      8  1  $
      9  10 $
      10 11 $
      11 0  $
      )

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcxmap 12-068 						      8 Mar 2012							   mcxmap(1)