#Created by Kurt Galbreath (kurt.galbreath@wwu.edu); copyright 2009

#This script tacks the charset commands for partitioning of codon sites onto the end of a set of files (e.g., nexus files)
#nreps<- the number of files that need to be modified
#matrixname<-the base name for a the nexus file replicates (e.g., 'CephA_bayestree_HKY.SS_')

nexusCodonSetAppend<- function(nreps, matrixname){

  for (i in 1:nreps){
    write('begin sets;', file=(paste(matrixname, (i-1), '.nex', sep='')), append=T)
    write('  charset first = 1-.\\3;', file=(paste(matrixname, (i-1), '.nex', sep='')), append=T)
    write('  charset second = 2-.\\3;', file=(paste(matrixname, (i-1), '.nex', sep='')), append=T)
    write('  charset third = 3-.\\3;', file=(paste(matrixname, (i-1), '.nex', sep='')), append=T)	
    write('  charpartition codons = first:first, second:second, third:third;', file=(paste(matrixname, (i-1), '.nex', sep='')), append=T)		
    write('end;', file=(paste(matrixname, (i-1), '.nex', sep='')), append=T)		
  }
}