- if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";}
- if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column";}
- if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "namefile" ) { namefile = value; }
- if (key == "orderfile" ) { orderfile = value; }
- if (key == "groupfile" ) { groupfile = value; }
- if (key == "cutoff" ) { cutoff = value; }
- if (key == "precision" ) { precision = value; }
- if (key == "iters" ) { iters = value; }
- if (key == "jumble" ) { jumble = value; }
- if (key == "freq" ) { freq = value; }
- if (key == "method" ) { method = value; }
- if (key == "fileroot" ) { fileroot = value; }
+ if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
+ if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
+ if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
+ if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
+ if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
+ if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
+ if (key == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; }
+ if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
+ if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
+ if (key == "name" ) { namefile = value; }
+ if (key == "order" ) { orderfile = value; }
+ if (key == "group" ) { groupfile = value; }
+ if (key == "cutoff" ) { cutoff = value; }
+ if (key == "precision" ) { precision = value; }
+ if (key == "iters" ) { iters = value; }
+ if (key == "jumble" ) { jumble = value; }
+ if (key == "freq" ) { freq = value; }
+ if (key == "method" ) { method = value; }
+ if (key == "fileroot" ) { fileroot = value; }
+ if (key == "abund" ) { abund = value; }
+ if (key == "random" ) { randomtree = value; }
+ if (key == "calc") { calc = value; }
+ if (key == "step") { step = value; }
+ if (key == "form") { form = value; }
+ if (key == "sorted") { sorted = value; }
+ if (key == "vertical") { vertical = value; }
+ if (key == "trump") { trump = value; }
+ if (key == "filter") { filter = value; }
+ if (key == "soft") { soft = value; }
+ if (key == "scale") { scale = value; }
+ if (key == "ends" ) { ends = value; }
+ if (key == "processors" ) { processors = value; }
+ if (key == "size" ) { size = value; }
+ if (key == "template") { templatefile = value; }
+ if (key == "search") { search = value; }
+ if (key == "ksize") { ksize = value; }
+ if (key == "align") { align = value; }
+ if (key == "match") { match = value; }
+ if (key == "mismatch") { mismatch = value; }
+ if (key == "gapopen") { gapopen = value; }
+ if (key == "gapextend" ) { gapextend = value; }