#include "shen.h"
#include "coverage.h"
-
+//**********************************************************************************************************************
+vector<string> CollectCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"freq","label","calc","abund","size","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CollectCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CollectCommand::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, "CollectCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CollectCommand::CollectCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sobs"] = tempOutNames;
+ outputTypes["chao"] = tempOutNames;
+ outputTypes["nseqs"] = tempOutNames;
+ outputTypes["coverage"] = tempOutNames;
+ outputTypes["ace"] = tempOutNames;
+ outputTypes["jack"] = tempOutNames;
+ outputTypes["shannon"] = tempOutNames;
+ outputTypes["shannoneven"] = tempOutNames;
+ outputTypes["np_shannon"] = tempOutNames;
+ outputTypes["heip"] = tempOutNames;
+ outputTypes["smithwilson"] = tempOutNames;
+ outputTypes["simpson"] = tempOutNames;
+ outputTypes["simpsoneven"] = tempOutNames;
+ outputTypes["invsimpson"] = tempOutNames;
+ outputTypes["bootstrap"] = tempOutNames;
+ outputTypes["geometric"] = tempOutNames;
+ outputTypes["qstat"] = tempOutNames;
+ outputTypes["logseries"] = tempOutNames;
+ outputTypes["bergerparker"] = tempOutNames;
+ outputTypes["bstick"] = tempOutNames;
+ outputTypes["goodscoverage"] = tempOutNames;
+ outputTypes["efron"] = tempOutNames;
+ outputTypes["boneh"] = tempOutNames;
+ outputTypes["solow"] = tempOutNames;
+ outputTypes["shen"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "CollectCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
CollectCommand::CollectCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sobs"] = tempOutNames;
+ outputTypes["chao"] = tempOutNames;
+ outputTypes["nseqs"] = tempOutNames;
+ outputTypes["coverage"] = tempOutNames;
+ outputTypes["ace"] = tempOutNames;
+ outputTypes["jack"] = tempOutNames;
+ outputTypes["shannon"] = tempOutNames;
+ outputTypes["shannoneven"] = tempOutNames;
+ outputTypes["np_shannon"] = tempOutNames;
+ outputTypes["heip"] = tempOutNames;
+ outputTypes["smithwilson"] = tempOutNames;
+ outputTypes["simpson"] = tempOutNames;
+ outputTypes["simpsoneven"] = tempOutNames;
+ outputTypes["invsimpson"] = tempOutNames;
+ outputTypes["bootstrap"] = tempOutNames;
+ outputTypes["geometric"] = tempOutNames;
+ outputTypes["qstat"] = tempOutNames;
+ outputTypes["logseries"] = tempOutNames;
+ outputTypes["bergerparker"] = tempOutNames;
+ outputTypes["bstick"] = tempOutNames;
+ outputTypes["goodscoverage"] = tempOutNames;
+ outputTypes["efron"] = tempOutNames;
+ outputTypes["boneh"] = tempOutNames;
+ outputTypes["solow"] = tempOutNames;
+ outputTypes["shen"] = 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"); }
for (int p = 0; p < inputFileNames.size(); p++) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
- outputNames.push_back(fileNameRoot+"sobs");
+ outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
}else if (Estimators[i] == "chao") {
cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
- outputNames.push_back(fileNameRoot+"chao");
+ outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
}else if (Estimators[i] == "nseqs") {
cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
- outputNames.push_back(fileNameRoot+"nseqs");
+ outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
}else if (Estimators[i] == "coverage") {
cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
- outputNames.push_back(fileNameRoot+"coverage");
+ outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
}else if (Estimators[i] == "ace") {
cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
- outputNames.push_back(fileNameRoot+"ace");
+ outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
}else if (Estimators[i] == "jack") {
cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
- outputNames.push_back(fileNameRoot+"jack");
+ outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
}else if (Estimators[i] == "shannon") {
cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
- outputNames.push_back(fileNameRoot+"shannon");
+ outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
}else if (Estimators[i] == "shannoneven") {
cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
- outputNames.push_back(fileNameRoot+"shannoneven");
+ outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
}else if (Estimators[i] == "npshannon") {
cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
- outputNames.push_back(fileNameRoot+"np_shannon");
+ outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
}else if (Estimators[i] == "heip") {
cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
- outputNames.push_back(fileNameRoot+"heip");
+ outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
}else if (Estimators[i] == "smithwilson") {
cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
- outputNames.push_back(fileNameRoot+"smithwilson");
+ outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
}else if (Estimators[i] == "simpson") {
cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
- outputNames.push_back(fileNameRoot+"simpson");
+ outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
}else if (Estimators[i] == "simpsoneven") {
cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
- outputNames.push_back(fileNameRoot+"simpsoneven");
+ outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
}else if (Estimators[i] == "invsimpson") {
cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
- outputNames.push_back(fileNameRoot+"invsimpson");
+ outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
}else if (Estimators[i] == "bootstrap") {
cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- outputNames.push_back(fileNameRoot+"bootstrap");
+ outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
}else if (Estimators[i] == "geometric") {
cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
- outputNames.push_back(fileNameRoot+"geometric");
+ outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
}else if (Estimators[i] == "qstat") {
cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
- outputNames.push_back(fileNameRoot+"qstat");
+ outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
}else if (Estimators[i] == "logseries") {
cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
- outputNames.push_back(fileNameRoot+"logseries");
+ outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
}else if (Estimators[i] == "bergerparker") {
cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
- outputNames.push_back(fileNameRoot+"bergerparker");
+ outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
}else if (Estimators[i] == "bstick") {
cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
- outputNames.push_back(fileNameRoot+"bstick");
+ outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
}else if (Estimators[i] == "goodscoverage") {
cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
- outputNames.push_back(fileNameRoot+"goodscoverage");
+ outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
}else if (Estimators[i] == "efron") {
cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
- outputNames.push_back(fileNameRoot+"efron");
+ outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
}else if (Estimators[i] == "boneh") {
cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
- outputNames.push_back(fileNameRoot+"boneh");
+ outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
}else if (Estimators[i] == "solow") {
cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
- outputNames.push_back(fileNameRoot+"solow");
+ outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
}else if (Estimators[i] == "shen") {
cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
- outputNames.push_back(fileNameRoot+"shen");
+ outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
}
}
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
delete input; globaldata->ginput = NULL;
delete read;
delete order; globaldata->gorder = NULL;
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
delete input; globaldata->ginput = NULL;
delete read;
delete order; globaldata->gorder = NULL;
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
delete input; globaldata->ginput = NULL;
delete read;
delete validCalculator;
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
delete input; globaldata->ginput = NULL;
delete read;
delete order; globaldata->gorder = NULL;
projects / mothur.git / blobdiff