#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
#include "npshannon.h"
#include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
#include "jackknife.h"
#include "geom.h"
#include "qstat.h"
#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 = ""; }
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 = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
if (abort == true) { return 0; }
- vector<string> outputNames;
-
+ string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
- else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+ 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(); 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 += hasPath(inputFileNames[p]); }
- string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
+ if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
globaldata->inputFileName = inputFileNames[p];
if (inputFileNames.size() > 1) {
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"); 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"); 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"); 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"); 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"); 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 the users entered no valid calculators don't execute command
- if (cDisplays.size() == 0) { return 0; }
+ if (cDisplays.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
read = new ReadOTUFile(inputFileNames[p]);
read->read(&*globaldata);
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;
delete validCalculator;
globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
return 0;
}
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;
delete validCalculator;
globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
return 0;
}
}
//you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = order->getLabel();
delete order;
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;
globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
return 0;
}
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;
delete validCalculator;
globaldata->Groups.clear();
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
return 0;
}
delete order;
delete validCalculator;
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ //return to shared mode if you changed above
+ if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
input = globaldata->ginput;
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
- string sharedFileRoot = getRootName(filename);
+ string sharedFileRoot = m->getRootName(filename);
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
for (int i = 0; i < lookup.size(); i++) {
RAbundVector rav = lookup[i]->getRAbundVector();
- openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+ m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
rav.print(*(filehandles[lookup[i]->getGroup()]));
(*(filehandles[lookup[i]->getGroup()])).close();
}
projects / mothur.git / blobdiff