helpRequest = optionText;
}
+ if (commandName == "libshuff") {
+ iters = "10000";
+ cutoff = "1.0";
+ }
+
string key, value;
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
if (key == "fileroot" ) { fileroot = value; }
if (key == "abund" ) { abund = value; }
if (key == "random" ) { randomtree = value; }
- if (key == "calc") { calc = value; }
+ if (key == "calc") { calc = value; }
+ if (key == "step") { step = value; }
+ if (key == "form") { form = value; }
+ if (key == "sorted") { sorted = value; }
+
if (key == "line") {//stores lines to be used in a set
lines.clear();
+ labels.clear();
line = value;
label = "";
splitAtDash(value, lines);
}
if (key == "label") {//stores labels to be used in a set
labels.clear();
+ lines.clear();
label = value;
line = "";
splitAtDash(value, labels);
if (key == "fileroot" ) { fileroot = value; }
if (key == "abund" ) { abund = value; }
if (key == "random" ) { randomtree = value; }
- if (key == "calc") { calc = value; }
-
+ if (key == "calc") { calc = value; }
+ if (key == "step") { step = value; }
+ if (key == "form") { form = value; }
+ if (key == "sorted") { sorted = value; }
if (key == "line") {//stores lines to be used in a vector
lines.clear();
+ labels.clear();
line = value;
label = "";
if (line != "all") { splitAtDash(value, lines); allLines = 0; }
}
if (key == "label") {//stores lines to be used in a vector
labels.clear();
+ lines.clear();
label = value;
line = "";
if (label != "all") { splitAtDash(value, labels); allLines = 0; }
//input defaults for calculators
if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
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"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
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"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
string GlobalData::getAbund() { return abund; }
string GlobalData::getRandomTree() { return randomtree; }
string GlobalData::getGroups() { return groups; }
+string GlobalData::getStep() { return step; }
+string GlobalData::getForm() { return form; }
+string GlobalData::getSorted() { return sorted; }
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;}
method = "furthest";
fileroot = "";
abund = "10";
+ step = "0.01";
+ form = "integral";
+ sorted = "1"; //0 means don't sort, 1 means sort.
}
//*******************************************************/
iters = "1000";
groups = "";
jumble = "1"; //0 means don't jumble, 1 means jumble.
+ sorted = "1"; //0 means don't sort, 1 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";
calc = "";
- abund = "10";
+ abund = "10";
+ step = "0.01";
+ form = "integral";
}
/*******************************************************/