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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
if (key == "name" ) { namefile = value; }
if (key == "order" ) { orderfile = value; }
if (key == "group" ) { groupfile = value; }
splitAtDash(value, lines);
allLines = 0;
}
- if (key == "label") {//stores lines to be used in a set
+ if (key == "label") {//stores labels to be used in a set
labels.clear();
label = value;
line = "";
splitAtDash(value, labels);
allLines = 0;
}
- if (key == "groups") {//stores lines to be used in a vector
+ if (key == "groups") {//stores groups to be used in a vector
Groups.clear();
groups = value;
splitAtDash(value, Groups);
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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
if (key == "name" ) { namefile = value; }
if (key == "order" ) { orderfile = value; }
if (key == "group" ) { groupfile = value; }
if (key == "method" ) { method = value; }
if (key == "fileroot" ) { fileroot = value; }
if (key == "randomtree" ) { randomtree = value; }
+ if (key == "groups" ) { groups = value; }
+
if (key == "single") {//stores estimators in a vector
singleEstimators.clear(); //clears out old values
splitAtDash(value, labels);
allLines = 0;
}
+ if (key == "groups") {//stores groups to be used in a vector
+ Groups.clear();
+ groups = value;
+ splitAtDash(value, Groups);
+ }
+
}
//set format for shared
iters = "1000";
line = "";
label = "";
+ groups = "";
jumble = "1"; //0 means don't jumble, 1 means jumble.
randomtree = "0"; //0 means user will enter some user trees, 1 means they just want the random tree distribution.
freq = "100";
/*******************************************************/
/******************************************************/
-//This function separates the key value from the option value i.e. distfile = "96_..."
+//This function separates the key value from the option value i.e. dist=96_...
void GlobalData::splitAtEquals(string& key, string& value){
try {
if(value.find_first_of('=') != -1){