#include "summarycommand.h"
#include "ace.h"
#include "sobs.h"
+#include "nseqs.h"
#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
#include "npshannon.h"
#include "shannon.h"
#include "jackknife.h"
+#include "geom.h"
+#include "logsd.h"
+#include "qstat.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "goodscoverage.h"
+#include "coverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
//**********************************************************************************************************************
-SummaryCommand::SummaryCommand(){
+SummaryCommand::SummaryCommand(string option){
try {
globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
- int i;
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Estimators.clear();
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
- if(globaldata->Estimators[i] == "sobs"){
- sumCalculators.push_back(new Sobs());
- }else if(globaldata->Estimators[i] == "chao"){
- sumCalculators.push_back(new Chao1());
- }else if(globaldata->Estimators[i] == "ace"){
- sumCalculators.push_back(new Ace());
- }else if(globaldata->Estimators[i] == "jack"){
- sumCalculators.push_back(new Jackknife());
- }else if(globaldata->Estimators[i] == "shannon"){
- sumCalculators.push_back(new Shannon());
- }else if(globaldata->Estimators[i] == "npshannon"){
- sumCalculators.push_back(new NPShannon());
- }else if(globaldata->Estimators[i] == "simpson"){
- sumCalculators.push_back(new Simpson());
- }else if(globaldata->Estimators[i] == "bootstrap"){
- sumCalculators.push_back(new Bootstrap());
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"line","label","calc","abund","size"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the summary.single command." << endl; abort = true; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter.validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ 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"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, abund);
+
+ temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, size);
+
+ if (abort == false) {
+
+ validCalculator = new ValidCalculators();
+ int i;
+
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
+ if(Estimators[i] == "sobs"){
+ sumCalculators.push_back(new Sobs());
+ }else if(Estimators[i] == "chao"){
+ sumCalculators.push_back(new Chao1());
+ }else if(Estimators[i] == "coverage"){
+ sumCalculators.push_back(new Coverage());
+ }else if(Estimators[i] == "geometric"){
+ sumCalculators.push_back(new Geom());
+ }else if(Estimators[i] == "logseries"){
+ sumCalculators.push_back(new LogSD());
+ }else if(Estimators[i] == "qstat"){
+ sumCalculators.push_back(new QStat());
+ }else if(Estimators[i] == "bergerparker"){
+ sumCalculators.push_back(new BergerParker());
+ }else if(Estimators[i] == "bstick"){
+ sumCalculators.push_back(new BStick());
+ }else if(Estimators[i] == "ace"){
+ if(abund < 5)
+ abund = 10;
+ sumCalculators.push_back(new Ace(abund));
+ }else if(Estimators[i] == "jack"){
+ sumCalculators.push_back(new Jackknife());
+ }else if(Estimators[i] == "shannon"){
+ sumCalculators.push_back(new Shannon());
+ }else if(Estimators[i] == "npshannon"){
+ sumCalculators.push_back(new NPShannon());
+ }else if(Estimators[i] == "simpson"){
+ sumCalculators.push_back(new Simpson());
+ }else if(Estimators[i] == "bootstrap"){
+ sumCalculators.push_back(new Bootstrap());
+ }else if (Estimators[i] == "nseqs") {
+ sumCalculators.push_back(new NSeqs());
+ }else if (Estimators[i] == "goodscoverage") {
+ sumCalculators.push_back(new GoodsCoverage());
+ }else if (Estimators[i] == "efron") {
+ sumCalculators.push_back(new Efron(size));
+ }else if (Estimators[i] == "boneh") {
+ sumCalculators.push_back(new Boneh(size));
+ }else if (Estimators[i] == "solow") {
+ sumCalculators.push_back(new Solow(size));
+ }else if (Estimators[i] == "shen") {
+ sumCalculators.push_back(new Shen(size, abund));
+ }
+ }
}
}
}
-
- //reset calc for next command
- globaldata->setCalc("");
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
//**********************************************************************************************************************
+void SummaryCommand::help(){
+ try {
+ cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
+ cout << "The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
+ cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
+ cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
+ cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
+ cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
+ validCalculator->printCalc("summary", cout);
+ cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\n";
+ cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SummaryCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
SummaryCommand::~SummaryCommand(){
- delete sabund;
- delete input;
- delete read;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->sabund = NULL;
+ }
}
//**********************************************************************************************************************
int SummaryCommand::execute(){
try {
+ if (abort == true) { return 0; }
+
+ int count = 1;
+
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
openOutputFile(outputFileName, outputFileHandle);
outputFileHandle << "label";
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
-
+
+ sabund = globaldata->sabund;
+ string lastLabel = sabund->getLabel();
+ input = globaldata->ginput;
+
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
outputFileHandle << '\t' << sumCalculators[i]->getName();
}
outputFileHandle << endl;
- sabund = globaldata->sabund;
- input = globaldata->ginput;
- int count = 1;
- while(sabund != NULL){
+ //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;
+ set<int> userLines = lines;
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
cout << sabund->getLabel() << '\t' << count << endl;
-
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+ userLines.erase(count);
+
+
outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
vector<double> data = sumCalculators[i]->getValues(sabund);
}
outputFileHandle << endl;
}
-
+
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ cout << sabund->getLabel() << '\t' << count << endl;
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+
+ outputFileHandle << sabund->getLabel();
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(sabund);
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }
+ outputFileHandle << endl;
+ }
+
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
sabund = input->getSAbundVector();
count++;
}
-
+
+ //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(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLabel << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ cout << sabund->getLabel() << '\t' << count << endl;
+ outputFileHandle << sabund->getLabel();
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(sabund);
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }
+ outputFileHandle << endl;
+ delete sabund;
+ }
+
+ outputFileHandle.close();
+
return 0;
}
catch(exception& e) {
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