if (key == "step") { step = value; }
if (key == "form") { form = value; }
if (key == "sorted") { sorted = value; }
- if (key == "scaler") { scaler = value; }
+ if (key == "scale") { scale = value; }
if (key == "step") { step = value; }
if (key == "form") { form = value; }
if (key == "sorted") { sorted = value; }
- if (key == "scaler") { scaler = value; }
+ if (key == "scale") { scale = value; }
if (key == "line") {//stores lines to be used in a vector
//input defaults for calculators
if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
splitAtDash(calc, Estimators);
}
if (commandName == "collect.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "tree.groups") {
+ if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
if (calc != "") {
Estimators.clear();
splitAtDash(calc, Estimators);
string GlobalData::getStep() { return step; }
string GlobalData::getForm() { return form; }
string GlobalData::getSorted() { return sorted; }
-string GlobalData::getScaler() { return scaler; }
+string GlobalData::getScale() { return scale; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file;}
void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file;}
void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file;}
//option definitions should go here...
helpRequest = "";
clear();
+ gListVector == NULL;
+ gSparseMatrix == NULL;
}
/*******************************************************/
abund = "10";
step = "0.01";
form = "integral";
- sorted = "1"; //0 means don't sort, 1 means sort.
- scaler = "log2";
+ sorted = "T"; //F means don't sort, T means sort.
+ scale = "log10";
}
//*******************************************************/
iters = "1000";
groups = "";
jumble = "1"; //0 means don't jumble, 1 means jumble.
- sorted = "1"; //0 means don't sort, 1 means sort.
+ sorted = "T"; //F means don't sort, T means sort.
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";
//use nexus translation rather than parsing tree to save time
if ((holder == "translate") || (holder == "Translate")) {
-cout << "there is a translate " << endl;
+
string number, name, h;
h = ""; // so it enters the loop the first time
while((h != ";") && (number != ";")) {