#include "sharedsobs.h"
#include "sharednseqs.h"
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getValidParameters(){
+ try {
+ string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RareFactSharedCommand::RareFactSharedCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedrarefaction"] = tempOutNames;
+ outputTypes["sharedr_nseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
RareFactSharedCommand::RareFactSharedCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedrarefaction"] = tempOutNames;
+ outputTypes["sharedr_nseqs"] = tempOutNames;
+
//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
else {
if (calc == "default") { calc = "sharedobserved"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
}
globaldata->Groups = Groups;
convert(temp, nIters);
temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; }
- if (isTrue(temp)) { jumble = true; }
+ if (m->isTrue(temp)) { jumble = true; }
else { jumble = false; }
globaldata->jumble = jumble;
if (abort == false) {
- string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
// format = globaldata->getFormat();
if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sharedobserved") {
rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
- outputNames.push_back(fileNameRoot+"shared.rarefaction");
+ outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
}else if (Estimators[i] == "sharednseqs") {
rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
- outputNames.push_back(fileNameRoot+"shared.r_nseqs");
+ outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
}
}
}
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }