#!/bin/tcsh -f
#last edited JUNE 5 2008

setenv AFNI_DECONFLICT OVERWRITE

#count the total number of command line parameters
set al = $#argv
#echo $al

if ($al < 1) then
   goto HELP
endif

set starttime = `date`

PARSE:
   set Narg = $#
   set cnt = 1
   set vollist = ()
   set out = ''
   if ("$1" == '') goto HELP
   while ($cnt <= $Narg)
      set donext = 1;
      if ($donext && "$argv[$cnt]" == "-help" || "$argv[$cnt]" == "-h") then
         goto HELP
      endif
      
      if ($donext && "$argv[$cnt]" == "-out") then
         if ($cnt == $Narg) then
            echo "Need a filename after -out"
            goto END
         else
            @ cnt ++
            set out = "$argv[$cnt]"
            set donext = 0   
         endif   
      endif
      
      if ($donext && "$argv[$cnt]" == "-components") then
         if ($cnt == $Narg) then
            echo "Need at least one component file after -components"
            goto END
         else
            @ cnt ++
            set vollist = ($argv[$cnt-])
            goto PROCESS
         endif
      endif
      if ($donext) then
         set vollist = ($argv[$cnt-])
         goto PROCESS
      else 
         @ cnt ++
      endif
   end

PROCESS:
if ("out" == "") then
   set out = D_ALL_prepared4clust
   echo "Output filename defaults to $out"
endif
if ($#vollist == 0) then
   echo "Error: No component files given"
   goto END
endif
foreach ff ($vollist)
   if ( ! -f $ff ) then
      echo "Error: Component file $ff not found"
      goto END
   endif
end
echo "All component files are: ($vollist) "


   echo "Combining files and labeling the rows for later sorting"
   paste $vollist | nl -w 9 -n rz > $out
    #numbering lines is not needed any more with Aclustering, but if I change it here I should also change in Aclustering which columns to read... 
    #ZSS: I did that in 3dAclustering so no need for the extra column, and 
    #also, no need for 1D files either...

set endtime = `date`

echo $starttime
echo $endtime

goto END

HELP:
   echo "Catenates component files together to form signature file"
   echo "that can be used by cluster"
   echo "`basename $0` -out SIGNATURE_FILE -components COMP1 COMP2 ..."
   goto END

END: