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/*
* collectcommand.cpp
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "collectcommand.h"
#include "ace.h"
#include "sobs.h"
#include "nseqs.h"
#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 "logsd.h"
#include "bergerparker.h"
#include "bstick.h"
#include "goodscoverage.h"
#include "efron.h"
#include "boneh.h"
#include "solow.h"
#include "shen.h"
#include "coverage.h"
#include "shannonrange.h"
//**********************************************************************************************************************
vector<string> CollectCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(psabund);
CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson-shannonrange", "", "", "","",true,false,true); parameters.push_back(pcalc);
CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
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["shannonrange"] = tempOutNames;
outputTypes["npshannon"] = 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;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "CollectCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string CollectCommand::getHelpString(){
try {
string helpString = "";
ValidCalculators validCalculator;
helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc, alpha and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n";
helpString += "The collect.single command should be in the following format: \n";
helpString += "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";
helpString += "collect.single(label=yourLabel, freq=yourFreq, calc=yourEstimators).\n";
helpString += "Example collect(label=unique-.01-.03, freq=10, calc=sobs-chao-ace-jack).\n";
helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
helpString += validCalculator.printCalc("single");
helpString += "The label parameter is used to analyze specific labels in your input.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "CollectCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string CollectCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "sobs") { pattern = "[filename],sobs"; }
else if (type == "chao") { pattern = "[filename],chao"; }
else if (type == "nseqs") { pattern = "[filename],nseqs"; }
else if (type == "coverage") { pattern = "[filename],coverage"; }
else if (type == "ace") { pattern = "[filename],ace"; }
else if (type == "jack") { pattern = "[filename],jack"; }
else if (type == "shannon") { pattern = "[filename],shannon"; }
else if (type == "shannoneven") { pattern = "[filename],shannoneven"; }
else if (type == "shannonrange"){ pattern = "[filename],shannonrange"; }
else if (type == "npshannon") { pattern = "[filename],npshannon"; }
else if (type == "heip") { pattern = "[filename],heip"; }
else if (type == "smithwilson") { pattern = "[filename],smithwilson"; }
else if (type == "simpson") { pattern = "[filename],simpson"; }
else if (type == "simpsoneven") { pattern = "[filename],simpsoneven"; }
else if (type == "invsimpson") { pattern = "[filename],invsimpson"; }
else if (type == "bootstrap") { pattern = "[filename],bootstrap"; }
else if (type == "geometric") { pattern = "[filename],geometric"; }
else if (type == "qstat") { pattern = "[filename],qstat"; }
else if (type == "logseries") { pattern = "[filename],logseries"; }
else if (type == "bergerparker") { pattern = "[filename],bergerparker"; }
else if (type == "bstick") { pattern = "[filename],bstick"; }
else if (type == "goodscoverage") { pattern = "[filename],goodscoverage"; }
else if (type == "efron") { pattern = "[filename],efron"; }
else if (type == "boneh") { pattern = "[filename],boneh"; }
else if (type == "solow") { pattern = "[filename],solow"; }
else if (type == "shen") { pattern = "[filename],shen"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "CollectCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
CollectCommand::CollectCommand(string option) : Command() {
try {
allLines = true;
//allow user to run help
if(option == "help") { help(); calledHelp = true; abort = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { format = "list"; inputfile = listfile; current->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund");
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
else { format = "sabund"; inputfile = sabundfile; current->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund");
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { format = "rabund"; inputfile = rabundfile; current->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { format = "sharedfile"; inputfile = sharedfile; current->setSharedFile(sharedfile); }
if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
//is there are current file available for any of these?
//give priority to shared, then list, then rabund, then sabund
//if there is a current shared file, use it
sharedfile = current->getSharedFile();
if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else {
listfile = current->getListFile();
if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else {
rabundfile = current->getRabundFile();
if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter.\n"); }
else {
sabundfile = current->getSabundFile();
if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter.\n"); }
else {
m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command.\n"); abort = true;
}
}
}
}
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
//NOTE: if you add new calc options, don't forget to add them to the parameter initialize in setParameters or the gui won't be able to use them
calc = validParameter.valid(parameters, "calc");
if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
util.splitAtDash(calc, Estimators);
if (util.inUsersGroups("citation", Estimators)) {
ValidCalculators validCalc; validCalc.printCitations(Estimators);
//remove citation from list of calcs
for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
}
string temp;
temp = validParameter.valid(parameters, "freq"); if (temp == "not found") { temp = "100"; }
util.mothurConvert(temp, freq);
temp = validParameter.valid(parameters, "alpha"); if (temp == "not found") { temp = "1"; }
util.mothurConvert(temp, alpha);
if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2.\n"); abort=true; }
temp = validParameter.valid(parameters, "abund"); if (temp == "not found") { temp = "10"; }
util.mothurConvert(temp, abund);
temp = validParameter.valid(parameters, "size"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, size);
}
}
catch(exception& e) {
m->errorOut(e, "CollectCommand", "CollectCommand");
exit(1);
}
}
//**********************************************************************************************************************
int CollectCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
for (int p = 0; p < inputFileNames.size(); p++) {
if (m->getControl_pressed()) { break; }
if (outputdir == "") { outputdir += util.hasPath(inputFileNames[p]); }
string fileNameRoot = outputdir + util.getRootName(util.getSimpleName(inputFileNames[p]));
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
if (inputFileNames.size() > 1) { m->mothurOut("\nProcessing group " + groups[p] + "\n\n"); }
fillCDisplays(variables); //adds a display for each calc
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
InputData input(inputFileNames[p], format, nullVector);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
OrderVector* order = util.getNextOrder(input, allLines, userLabels, processedLabels, lastLabel);
while (order != nullptr) {
if (m->getControl_pressed()) { delete order; break; }
Collect cCurve(order, cDisplays);
cCurve.getCurve(freq); delete order;
order = util.getNextOrder(input, allLines, userLabels, processedLabels, lastLabel);
}
//delete displays
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; } cDisplays.clear();
}
if (inputFileNames.size() > 1) {
for (int p = 0; p < inputFileNames.size(); p++) { util.mothurRemove(inputFileNames[p]); }
}
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "CollectCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void CollectCommand::fillCDisplays(map<string, string> variables) {
try {
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("single", Estimators[i]) ) {
if (Estimators[i] == "sobs") {
cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(getOutputFileName("sobs", variables))));
outputNames.push_back(getOutputFileName("sobs", variables)); outputTypes["sobs"].push_back(getOutputFileName("sobs", variables));
}else if (Estimators[i] == "chao") {
cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("chao", variables))));
outputNames.push_back(getOutputFileName("chao", variables)); outputTypes["chao"].push_back(getOutputFileName("chao", variables));
}else if (Estimators[i] == "nseqs") {
cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(getOutputFileName("nseqs", variables))));
outputNames.push_back(getOutputFileName("nseqs", variables)); outputTypes["nseqs"].push_back(getOutputFileName("nseqs", variables));
}else if (Estimators[i] == "coverage") {
cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(getOutputFileName("coverage", variables))));
outputNames.push_back(getOutputFileName("coverage", variables)); outputTypes["coverage"].push_back(getOutputFileName("coverage", variables));
}else if (Estimators[i] == "ace") {
cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("ace", variables))));
outputNames.push_back(getOutputFileName("ace", variables)); outputTypes["ace"].push_back(getOutputFileName("ace", variables));
}else if (Estimators[i] == "jack") {
cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("jack", variables))));
outputNames.push_back(getOutputFileName("jack", variables)); outputTypes["jack"].push_back(getOutputFileName("jack", variables));
}else if (Estimators[i] == "shannon") {
cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("shannon", variables))));
outputNames.push_back(getOutputFileName("shannon", variables)); outputTypes["shannon"].push_back(getOutputFileName("shannon", variables));
}else if (Estimators[i] == "shannoneven") {
cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(getOutputFileName("shannoneven", variables))));
outputNames.push_back(getOutputFileName("shannoneven", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannoneven", variables));
}else if (Estimators[i] == "shannonrange") {
cDisplays.push_back(new CollectDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("shannonrange", variables))));
outputNames.push_back(getOutputFileName("shannonrange", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannonrange", variables));
}else if (Estimators[i] == "npshannon") {
cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(getOutputFileName("npshannon", variables))));
outputNames.push_back(getOutputFileName("npshannon", variables)); outputTypes["npshannon"].push_back(getOutputFileName("npshannon", variables));
}else if (Estimators[i] == "heip") {
cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(getOutputFileName("heip", variables))));
outputNames.push_back(getOutputFileName("heip", variables)); outputTypes["heip"].push_back(getOutputFileName("heip", variables));
}else if (Estimators[i] == "smithwilson") {
cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(getOutputFileName("smithwilson", variables))));
outputNames.push_back(getOutputFileName("smithwilson", variables)); outputTypes["smithwilson"].push_back(getOutputFileName("smithwilson", variables));
}else if (Estimators[i] == "simpson") {
cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("simpson", variables))));
outputNames.push_back(getOutputFileName("simpson", variables)); outputTypes["simpson"].push_back(getOutputFileName("simpson", variables));
}else if (Estimators[i] == "simpsoneven") {
cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(getOutputFileName("simpsoneven", variables))));
outputNames.push_back(getOutputFileName("simpsoneven", variables)); outputTypes["simpsoneven"].push_back(getOutputFileName("simpsoneven", variables));
}else if (Estimators[i] == "invsimpson") {
cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("invsimpson", variables))));
outputNames.push_back(getOutputFileName("invsimpson", variables)); outputTypes["invsimpson"].push_back(getOutputFileName("invsimpson", variables));
}else if (Estimators[i] == "bootstrap") {
cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(getOutputFileName("bootstrap", variables))));
outputNames.push_back(getOutputFileName("bootstrap", variables)); outputTypes["bootstrap"].push_back(getOutputFileName("bootstrap", variables));
}else if (Estimators[i] == "geometric") {
cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(getOutputFileName("geometric", variables))));
outputNames.push_back(getOutputFileName("geometric", variables)); outputTypes["geometric"].push_back(getOutputFileName("geometric", variables));
}else if (Estimators[i] == "qstat") {
cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(getOutputFileName("qstat", variables))));
outputNames.push_back(getOutputFileName("qstat", variables)); outputTypes["qstat"].push_back(getOutputFileName("qstat", variables));
}else if (Estimators[i] == "logseries") {
cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(getOutputFileName("logseries", variables))));
outputNames.push_back(getOutputFileName("logseries", variables)); outputTypes["logseries"].push_back(getOutputFileName("logseries", variables));
}else if (Estimators[i] == "bergerparker") {
cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(getOutputFileName("bergerparker", variables))));
outputNames.push_back(getOutputFileName("bergerparker", variables)); outputTypes["bergerparker"].push_back(getOutputFileName("bergerparker", variables));
}else if (Estimators[i] == "bstick") {
cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(getOutputFileName("bstick", variables))));
outputNames.push_back(getOutputFileName("bstick", variables)); outputTypes["bstick"].push_back(getOutputFileName("bstick", variables));
}else if (Estimators[i] == "goodscoverage") {
cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(getOutputFileName("goodscoverage", variables))));
outputNames.push_back(getOutputFileName("goodscoverage", variables)); outputTypes["goodscoverage"].push_back(getOutputFileName("goodscoverage", variables));
}else if (Estimators[i] == "efron") {
cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(getOutputFileName("efron", variables))));
outputNames.push_back(getOutputFileName("efron", variables)); outputTypes["efron"].push_back(getOutputFileName("efron", variables));
}else if (Estimators[i] == "boneh") {
cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(getOutputFileName("boneh", variables))));
outputNames.push_back(getOutputFileName("boneh", variables)); outputTypes["boneh"].push_back(getOutputFileName("boneh", variables));
}else if (Estimators[i] == "solow") {
cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(getOutputFileName("solow", variables))));
outputNames.push_back(getOutputFileName("solow", variables)); outputTypes["solow"].push_back(getOutputFileName("solow", variables));
}else if (Estimators[i] == "shen") {
cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(getOutputFileName("shen", variables))));
outputNames.push_back(getOutputFileName("shen", variables)); outputTypes["shen"].push_back(getOutputFileName("shen", variables));
}
}
}
}catch(exception& e) {
m->errorOut(e, "CollectCommand", "fillCDisplays");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> CollectCommand::parseSharedFile(string filename) {
try {
vector<string> filenames;
map<string, string> files;
map<string, string>::iterator it3;
InputData input(filename, "sharedfile", groups);
SharedRAbundVectors* shared = input.getSharedRAbundVectors();
string sharedFileRoot = util.getRootName(filename);
groups = shared->getNamesGroups();
//clears file before we start to write to it below
for (int i=0; i<groups.size(); i++) {
ofstream temp;
string group = groups[i];
util.openOutputFile((sharedFileRoot + group + ".rabund"), temp);
temp.close();
filenames.push_back((sharedFileRoot + group + ".rabund"));
files[group] = (sharedFileRoot + group + ".rabund");
}
while(shared != nullptr) {
vector<SharedRAbundVector*> lookup = shared->getSharedRAbundVectors();
for (int i = 0; i < lookup.size(); i++) {
ofstream temp;
string group = groups[i];
util.openOutputFileAppend(files[group], temp);
lookup[i]->getRAbundVector().print(temp);
temp.close();
}
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != nullptr) { delete lookup[i]; } lookup[i] = nullptr; }
shared = input.getSharedRAbundVectors();
}
return filenames;
}
catch(exception& e) {
m->errorOut(e, "CollectCommand", "parseSharedFile");
exit(1);
}
}
//**********************************************************************************************************************
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