}
/*******************************************************/
-/******************************************************/
-
-ListVector* GlobalData::getListVector() { return gListVector; }
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setListVector(ListVector* lv){
- try {
- if(gListVector != NULL){ delete gListVector; }
- gListVector = new ListVector(*lv);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-
-/******************************************************/
-
-SparseMatrix* GlobalData::getSparseMatrix() { return gSparseMatrix; }
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setSparseMatrix(SparseMatrix* sm){
- try{
- if(gSparseMatrix != NULL){ delete gSparseMatrix; }
- gSparseMatrix = new SparseMatrix(*sm);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-
/******************************************************/
//This function parses through the option string of the command to remove its parameters
void GlobalData::parseGlobalData(string commandString, string optionText){
try {
- 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
- if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree") || (commandName == "read.shared")) {
+ if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
clear();
gGroupmap = NULL;
gTree.clear();
+ labels.clear(); lines.clear(); groups.clear();
+ allLines = 1;
}
//saves help request
helpRequest = optionText;
}
+ if (commandName == "libshuff") {
+ iters = "10000";
+ cutoff = "1.0";
+ }
+
string key, value;
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
if (key == "freq" ) { freq = value; }
if (key == "method" ) { method = value; }
if (key == "fileroot" ) { fileroot = value; }
- if (key == "randomtree" ) { randomtree = value; }
- if (key == "groups" ) { groups = value; }
- if (key == "calc") { calc = 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 == "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 == "groups" ) { groups = 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 == "line") {//stores lines to be used in a vector
lines.clear();
line = value;
label = "";
- splitAtDash(value, lines);
- allLines = 0;
+ if (line != "all") { splitAtDash(value, lines); allLines = 0; }
+ else { allLines = 1; }
}
if (key == "label") {//stores lines to be used in a vector
labels.clear();
label = value;
line = "";
- splitAtDash(value, labels);
- allLines = 0;
+ if (label != "all") { splitAtDash(value, labels); allLines = 0; }
+ else { allLines = 1; }
}
+
if (key == "groups") {//stores groups to be used in a vector
Groups.clear();
groups = value;
//set format for shared
if ((listfile != "") && (groupfile != "")) { format = "shared"; }
+ if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
//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::getIters() { return iters; }
string GlobalData::getJumble() { return jumble; }
string GlobalData::getFreq() { return freq; }
+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; }
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;}
void GlobalData::setNameFile(string file) { namefile = file; }
void GlobalData::setFormat(string Format) { format = Format; }
void GlobalData::setRandomTree(string Random) { randomtree = Random; }
-void GlobalData::setCalc(string Calc) { calc = Calc; }
+void GlobalData::setGroups(string g) { groups = g; }
+void GlobalData::setCalc(string Calc) { calc = Calc; }
/*******************************************************/
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";
+ step = "0.01";
+ form = "integral";
}
-/*******************************************************/
+
+//*******************************************************/
/******************************************************/
void GlobalData::reset() {
cutoff = "10.00";
precision = "100";
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.
+ 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";
+ step = "0.01";
+ form = "integral";
}
/*******************************************************/
if(gorder != NULL) { delete gorder; }
}
/*******************************************************/
-
-/******************************************************/
-
projects / mothur.git / blobdiff