#  compile and run MSA evaluation program for all the proteins
#      which is listed in ../thinParam/proteinList
# Run Blackboard.java, runmax.java, MSAback.java and Compare.java

set paramSuffix = ".8.07"   #suffix for paramter files
set proteinSuffix = ".8.grid.c07"   #suffix for thinned protein file
set startProtein = "1a0b"   #start protein in proteinList. First one is 1a0b
set endProtein = "2cyp"   #end protein in proteinList. last one is 4pti
set paramDir = "/cis/msa1/hongzhi/thinParam/"   #Parameter file dir

set flag = "No"
echo MSA evaluation of proteins listed
echo in $paramDir"proteinList"
foreach x  (`cat $paramDir"proteinList"`)
  if ($x == $startProtein || $flag == "Yes") then
    set flag = "Yes"
    echo  ~~~~~~~~~~~~~~~~Start of $paramDir$x$paramSuffix ~~~~~~~~~~~~~~~~~
    echo MSA evaluation of parameter file $paramDir$x$paramSuffix ...
    echo  +++++++++++Evaluation of normal .peak file+++++++++++++++
    echo runmsa $x  $x$proteinSuffix  false
    runmsa $x  $x$proteinSuffix  false
    echo
    echo
    echo  +++++++Evaluation of faked branch-point .bpeak file++++++
    runmsa $x  $x$proteinSuffix  true
    echo  ~~~~~~~~~~~~~~~~End of $paramDir$x$paramSuffix ~~~~~~~~~~~~~~~~~~~
    echo
    echo 
    if ($x == $endProtein) then
      set flag = "No"
    endif  
  endif  
end