allLines = 1;
commandName = commandString; //save command name to be used by other classes
- //set all non filename paramters to default values
+ //set all non filename paramters to default
reset();
//clears out data from previous read
clear();
gGroupmap = NULL;
gTree.clear();
+ labels.clear(); lines.clear(); groups.clear();
}
//saves help request
if (key == "freq" ) { freq = value; }
if (key == "method" ) { method = value; }
if (key == "fileroot" ) { fileroot = value; }
- if (key == "randomtree" ) { randomtree = value; }
+ if (key == "abund" ) { abund = value; }
+ if (key == "random" ) { randomtree = value; }
if (key == "groups" ) { groups = value; }
if (key == "calc") { calc = value; }
+
if (key == "line") {//stores lines to be used in a set
lines.clear();
splitAtDash(value, labels);
allLines = 0;
}
+
if (key == "groups") {//stores groups to be used in a vector
Groups.clear();
groups = value;
splitAtDash(value, Groups);
}
+
}
//saves the last parameter
if (key == "freq" ) { freq = value; }
if (key == "method" ) { method = value; }
if (key == "fileroot" ) { fileroot = value; }
- if (key == "randomtree" ) { randomtree = value; }
+ if (key == "abund" ) { abund = value; }
+ if (key == "random" ) { randomtree = value; }
if (key == "groups" ) { groups = value; }
if (key == "calc") { calc = value; }
string GlobalData::getIters() { return iters; }
string GlobalData::getJumble() { return jumble; }
string GlobalData::getFreq() { return freq; }
+string GlobalData::getAbund() { return abund; }
string GlobalData::getRandomTree() { return randomtree; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file;}
void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file;}
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.
+ randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
freq = "100";
method = "furthest";
fileroot = "";
- calc = "";
+ abund = "10";
}
-/*******************************************************/
+
+//*******************************************************/
/******************************************************/
void GlobalData::reset() {
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.
+ randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
freq = "100";
method = "furthest";
calc = "";
+ abund = "10";
}
/*******************************************************/
if(gorder != NULL) { delete gorder; }
}
/*******************************************************/
-
-/******************************************************/
-