#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"
-
//**********************************************************************************************************************
-CollectCommand::CollectCommand(string option){
+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 {
+ 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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "CollectCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CollectCommand::CollectCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
else {
//valid paramters for this command
- string Array[] = {"freq","label","calc","abund","size"};
+ string Array[] = {"freq","label","calc","abund","size","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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 = ""; }
+
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the collect.single command."); mothurOutEndLine(); abort = true; }
+ if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
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"; }
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
convert(temp, size);
-
- if (abort == false) {
- string fileNameRoot = getRootName(globaldata->inputFileName);
- int i;
- validCalculator = new ValidCalculators();
-
- for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
- if (Estimators[i] == "sobs") {
- cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
- }else if (Estimators[i] == "chao") {
- cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
- }else if (Estimators[i] == "nseqs") {
- cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
- }else if (Estimators[i] == "coverage") {
- cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
- }else if (Estimators[i] == "ace") {
- cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
- }else if (Estimators[i] == "jack") {
- cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
- }else if (Estimators[i] == "shannon") {
- cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
- }else if (Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
- }else if (Estimators[i] == "simpson") {
- cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
- }else if (Estimators[i] == "bootstrap") {
- cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- }else if (Estimators[i] == "geometric") {
- cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
- }else if (Estimators[i] == "qstat") {
- cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
- }else if (Estimators[i] == "logseries") {
- cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
- }else if (Estimators[i] == "bergerparker") {
- cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
- }else if (Estimators[i] == "bstick") {
- cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
- }else if (Estimators[i] == "goodscoverage") {
- cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
- }else if (Estimators[i] == "efron") {
- cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
- }else if (Estimators[i] == "boneh") {
- cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
- }else if (Estimators[i] == "solow") {
- cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
- }else if (Estimators[i] == "shen") {
- cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
- }
- }
- }
- }
}
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "CollectCommand");
+ m->errorOut(e, "CollectCommand", "CollectCommand");
exit(1);
}
}
void CollectCommand::help(){
try {
- mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
- mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
- mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
- mothurOut("The collect.single command should be in the following format: \n");
- mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
- mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
- mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
+ m->mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
+ m->mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
+ m->mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
+ m->mothurOut("The collect.single command should be in the following format: \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
+ m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
+ m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
validCalculator->printCalc("single", cout);
- mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
+ m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "help");
+ m->errorOut(e, "CollectCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
-CollectCommand::~CollectCommand(){
- if (abort == false) {
- //delete order;
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- globaldata->gorder = NULL;
- }
-}
+CollectCommand::~CollectCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- //if the users entered no valid calculators don't execute command
- if (cDisplays.size() == 0) { return 0; }
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ 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) { 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]));
+ globaldata->inputFileName = inputFileNames[p];
- order = globaldata->gorder;
- string lastLabel = order->getLabel();
- input = globaldata->ginput;
+ if (inputFileNames.size() > 1) {
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+ }
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
+ validCalculator = new ValidCalculators();
+
+ for (int i=0; i<Estimators.size(); i++) {
+ 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); 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"); outputTypes["shen"].push_back(fileNameRoot+"shen");
+ }
+ }
+ }
- while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ //if the users entered no valid calculators don't execute command
+ if (cDisplays.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+
+ read = new ReadOTUFile(inputFileNames[p]);
+ read->read(&*globaldata);
- if(allLines == 1 || labels.count(order->getLabel()) == 1){
-
- cCurve = new Collect(order, cDisplays);
- cCurve->getCurve(freq);
- delete cCurve;
+ order = globaldata->gorder;
+ string lastLabel = order->getLabel();
+ input = globaldata->ginput;
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ 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()); } 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;
+ }
+
+
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- mothurOut(order->getLabel()); mothurOutEndLine();
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
+ 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()); } 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(allLines == 1 || labels.count(order->getLabel()) == 1){
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ cCurve = new Collect(order, cDisplays);
+ cCurve->getCurve(freq);
+ delete cCurve;
+
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+
+
+ }
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
+
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ cCurve = new Collect(order, cDisplays);
+ cCurve->getCurve(freq);
+ delete cCurve;
+
+
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+
+ //restore real lastlabel to save below
+ order->setLabel(saveLabel);
+ }
+
+ lastLabel = order->getLabel();
+
+ delete order;
+ order = (input->getOrderVector());
+ }
+ 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()); } outputTypes.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ 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)) {
- delete order;
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+
cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
-
- mothurOut(order->getLabel()); mothurOutEndLine();
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
+
+ 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()); } 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;
}
- lastLabel = order->getLabel();
-
- delete order;
- order = (input->getOrderVector());
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ cDisplays.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ globaldata->gorder = NULL;
+ delete validCalculator;
}
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
- needToRun = true;
- }else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
- }
- }
+ //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(); }
+ m->mothurOutEndLine();
+
- //run last label if you need to
- if (needToRun == true) {
- if (order != NULL) { delete order; }
- order = (input->getOrderVector(lastLabel));
-
- mothurOut(order->getLabel()); mothurOutEndLine();
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+vector<string> CollectCommand::parseSharedFile(string filename) {
+ try {
+ vector<string> filenames;
+
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+
+ //read first line
+ read = new ReadOTUFile(filename);
+ read->read(&*globaldata);
- cCurve = new Collect(order, cDisplays);
- cCurve->getCurve(freq);
- delete cCurve;
- delete order;
+ input = globaldata->ginput;
+ vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+
+ string sharedFileRoot = m->getRootName(filename);
+
+ //clears file before we start to write to it below
+ for (int i=0; i<lookup.size(); i++) {
+ remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+ filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
}
+ ofstream* temp;
+ for (int i=0; i<lookup.size(); i++) {
+ temp = new ofstream;
+ filehandles[lookup[i]->getGroup()] = temp;
+ groups.push_back(lookup[i]->getGroup());
+ }
+
+ while(lookup[0] != NULL) {
- for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- return 0;
+ for (int i = 0; i < lookup.size(); i++) {
+ RAbundVector rav = lookup[i]->getRAbundVector();
+ m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+ rav.print(*(filehandles[lookup[i]->getGroup()]));
+ (*(filehandles[lookup[i]->getGroup()])).close();
+ }
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ //free memory
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+ delete read;
+ delete input;
+ globaldata->ginput = NULL;
+
+ return filenames;
}
catch(exception& e) {
- errorOut(e, "CollectCommand", "execute");
+ m->errorOut(e, "CollectCommand", "parseSharedFile");
exit(1);
}
}
-
//**********************************************************************************************************************
+