- 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 == "hard") { hard = value; }
- if (key == "soft") { soft = value; }
- if (key == "scale") { scale = value; }
- if (key == "countends" ) { countends = value; }
- if (key == "processors" ) { processors = value; }
- if (key == "size" ) { size = value; }
- if (key == "candidate") { candidatefile = 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; }
- if (key == "start" ) { startPos = value; }
- if (key == "end" ) { endPos = value; }
- if (key == "maxambig" ) { maxAmbig = value; }
- if (key == "maxhomop" ) { maxHomoPolymer = value; }
- if (key == "minlength" ) { minLength = value; }
- if (key == "maxlength" ) { maxLength = value; }
-
- if (key == "line") {//stores lines to be used in a vector
+ 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 == "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 == "hard") { hard = value; }
+ if(key == "soft") { soft = value; }
+ if(key == "scale") { scale = value; }
+ if(key == "countends") { countends = value; }
+ if(key == "processors") { processors = value; }
+ if(key == "size") { size = value; }
+ if(key == "candidate") { candidatefile = 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; }
+ if(key == "start") { startPos = value; }
+ if(key == "end") { endPos = value; }
+ if(key == "maxambig") { maxAmbig = value; }
+ if(key == "maxhomop") { maxHomoPolymer = value; }
+ if(key == "minlength") { minLength = value; }
+ if(key == "maxlength") { maxLength = value; }
+ if(key == "flip" ) { flip = value; }
+ if(key == "oligos" ) { oligoFile = value; }
+
+ if(key == "line") {//stores lines to be used in a vector