#include "coverage.h"
//**********************************************************************************************************************
-
-
+vector<string> RareFactCommand::getValidParameters(){
+ try {
+ string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RareFactCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RareFactCommand::getRequiredFiles(){
+ try {
+ string AlignArray[] = {"shared","list","rabund","sabund","or"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RareFactCommand::RareFactCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rarefaction"] = tempOutNames;
+ outputTypes["r_chao"] = tempOutNames;
+ outputTypes["r_ace"] = tempOutNames;
+ outputTypes["r_jack"] = tempOutNames;
+ outputTypes["r_shannon"] = tempOutNames;
+ outputTypes["r_shannoneven"] = tempOutNames;
+ outputTypes["r_heip"] = tempOutNames;
+ outputTypes["r_smithwilson"] = tempOutNames;
+ outputTypes["r_npshannon"] = tempOutNames;
+ outputTypes["r_simpson"] = tempOutNames;
+ outputTypes["r_simpsoneven"] = tempOutNames;
+ outputTypes["r_invsimpson"] = tempOutNames;
+ outputTypes["r_bootstrap"] = tempOutNames;
+ outputTypes["r_coverage"] = tempOutNames;
+ outputTypes["r_nseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "RareFactCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
RareFactCommand::RareFactCommand(string option) {
try {
globaldata = GlobalData::getInstance();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rarefaction"] = tempOutNames;
+ outputTypes["r_chao"] = tempOutNames;
+ outputTypes["r_ace"] = tempOutNames;
+ outputTypes["r_jack"] = tempOutNames;
+ outputTypes["r_shannon"] = tempOutNames;
+ outputTypes["r_shannoneven"] = tempOutNames;
+ outputTypes["r_heip"] = tempOutNames;
+ outputTypes["r_smithwilson"] = tempOutNames;
+ outputTypes["r_npshannon"] = tempOutNames;
+ outputTypes["r_simpson"] = tempOutNames;
+ outputTypes["r_simpsoneven"] = tempOutNames;
+ outputTypes["r_invsimpson"] = tempOutNames;
+ outputTypes["r_bootstrap"] = tempOutNames;
+ outputTypes["r_coverage"] = tempOutNames;
+ outputTypes["r_nseqs"] = tempOutNames;
+
//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 = "";
if (abort == true) { return 0; }
- vector<string> outputNames;
-
string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
- outputNames.push_back(fileNameRoot+"rarefaction");
+ outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
}else if (Estimators[i] == "chao") {
rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
- outputNames.push_back(fileNameRoot+"r_chao");
+ outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
- outputNames.push_back(fileNameRoot+"r_ace");
+ outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
}else if (Estimators[i] == "jack") {
rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
- outputNames.push_back(fileNameRoot+"r_jack");
+ outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
}else if (Estimators[i] == "shannon") {
rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
- outputNames.push_back(fileNameRoot+"r_shannon");
+ outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
}else if (Estimators[i] == "shannoneven") {
rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
- outputNames.push_back(fileNameRoot+"r_shannoneven");
+ outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
}else if (Estimators[i] == "heip") {
rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
- outputNames.push_back(fileNameRoot+"r_heip");
+ outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
}else if (Estimators[i] == "smithwilson") {
rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
- outputNames.push_back(fileNameRoot+"r_smithwilson");
+ outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
}else if (Estimators[i] == "npshannon") {
rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
- outputNames.push_back(fileNameRoot+"r_npshannon");
+ outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
}else if (Estimators[i] == "simpson") {
rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
- outputNames.push_back(fileNameRoot+"r_simpson");
+ outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
}else if (Estimators[i] == "simpsoneven") {
rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
- outputNames.push_back(fileNameRoot+"r_simpsoneven");
+ outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
}else if (Estimators[i] == "invsimpson") {
rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
- outputNames.push_back(fileNameRoot+"r_invsimpson");
+ outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
}else if (Estimators[i] == "bootstrap") {
rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
- outputNames.push_back(fileNameRoot+"r_bootstrap");
+ outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
}else if (Estimators[i] == "coverage") {
rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
- outputNames.push_back(fileNameRoot+"r_coverage");
+ outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
}else if (Estimators[i] == "nseqs") {
rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
- outputNames.push_back(fileNameRoot+"r_nseqs");
+ outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
}
}
}
projects / mothur.git / blobdiff