#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"
//**********************************************************************************************************************
-CollectCommand::CollectCommand(){
+vector<string> CollectCommand::setParameters(){
try {
- globaldata = GlobalData::getInstance();
- string fileNameRoot;
- fileNameRoot = getRootName(globaldata->inputFileName);
- convert(globaldata->getFreq(), freq);
- int i;
- validCalculator = new ValidCalculators();
-
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "sobs") {
- cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
- }else if (globaldata->Estimators[i] == "chao") {
- cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
- }else if (globaldata->Estimators[i] == "nseqs") {
- cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
- }else if (globaldata->Estimators[i] == "coverage") {
- cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
- }else if (globaldata->Estimators[i] == "ace") {
- convert(globaldata->getAbund(), abund);
- cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
- }else if (globaldata->Estimators[i] == "jack") {
- cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
- }else if (globaldata->Estimators[i] == "shannon") {
- cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
- }else if (globaldata->Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
- }else if (globaldata->Estimators[i] == "simpson") {
- cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
- }else if (globaldata->Estimators[i] == "bootstrap") {
- cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- }else if (globaldata->Estimators[i] == "geometric") {
- cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
- }else if (globaldata->Estimators[i] == "qstat") {
- cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
- }else if (globaldata->Estimators[i] == "logseries") {
- cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
- }else if (globaldata->Estimators[i] == "bergerparker") {
- cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
- }else if (globaldata->Estimators[i] == "bstick") {
- cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
- }else if (globaldata->Estimators[i] == "goodscoverage") {
- cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
- }else if (globaldata->Estimators[i] == "efron") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
- }else if (globaldata->Estimators[i] == "boneh") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
- }else if (globaldata->Estimators[i] == "solow") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
- }else if (globaldata->Estimators[i] == "shen") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Shen(size), new OneColumnFile(fileNameRoot+"shen")));
- }
- }
- }
+ 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", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
- //reset calc for next command
- globaldata->setCalc("");
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "CollectCommand", "setParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+string CollectCommand::getHelpString(){
+ try {
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc 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 += validCalculator.printCalc("single");
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "getHelpString");
exit(1);
- }
-
+ }
}
-
//**********************************************************************************************************************
-
-CollectCommand::~CollectCommand(){
- delete order;
- delete input;
- delete cCurve;
- delete read;
+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 == "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->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "getOutputPattern");
+ exit(1);
+ }
}
+//**********************************************************************************************************************
+CollectCommand::CollectCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ 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["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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "CollectCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CollectCommand::CollectCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); calledHelp = true; abort = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ 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["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;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { rabundfile = ""; abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
+
+
+ //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 ((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 = m->getSharedFile();
+ if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ listfile = m->getListFile();
+ if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ rabundfile = m->getRabundFile();
+ if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ 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."); 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") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //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.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ else {
+ if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ }
+ m->splitAtDash(calc, Estimators);
+ if (m->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.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, freq);
+
+ temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
+ m->mothurConvert(temp, abund);
+
+ temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, size);
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "CollectCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int CollectCommand::execute(){
try {
- int count = 1;
-
- //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);
- order = globaldata->gorder;
- lastOrder = order;
- input = globaldata->ginput;
+ if (abort == true) { 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->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
+
+ if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+ //globaldata->inputFileName = inputFileNames[p];
- //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 = globaldata->labels;
+ if (inputFileNames.size() > 1) {
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+ }
- while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+ ValidCalculators validCalculator;
+
+ 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(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] == "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));
+ }
+ }
+ }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ //if the users entered no valid calculators don't execute command
+ if (cDisplays.size() == 0) { return 0; }
+
+ input = new InputData(inputFileNames[p], format);
+ order = input->getOrderVector();
+ string lastLabel = order->getLabel();
+
+ //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++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete input;
+ delete order;
+ m->clearGroups();
+ return 0;
+ }
+
+
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete input;
+ delete order;
+ m->clearGroups();
+ return 0;
+ }
+
- cCurve = new Collect(order, cDisplays);
- cCurve->getCurve(freq);
- delete cCurve;
+ 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());
+ }
- cout << order->getLabel() << '\t' << count << endl;
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
- //you have a label the user want that is smaller than this line and the last line has not already been processed
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete input;
+ m->clearGroups();
+ return 0;
+ }
+
+ //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();
+ }
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- cCurve = new Collect(lastOrder, cDisplays);
+ //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;
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+
+ if (m->control_pressed) {
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete input;
+ delete order;
+ m->clearGroups();
+ return 0;
+ }
+ delete order;
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
- order = (input->getOrderVector());
- count++;
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ cDisplays.clear();
+ delete input;
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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();
+
+
+ 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;
+
+ input = new InputData(filename, "sharedfile");
+ 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++) {
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
+ 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) {
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
- needToRun = true;
- }else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ 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();
}
- //run last line if you need to
- if (needToRun == true) {
- cCurve = new Collect(lastOrder, cDisplays);
- cCurve->getCurve(freq);
- delete cCurve;
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ //free memory
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
}
- delete lastOrder;
- for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- return 0;
+ delete input;
+
+ return filenames;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "CollectCommand", "parseSharedFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
//**********************************************************************************************************************
+
projects / mothur.git / blobdiff