#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(){
try {
globaldata = GlobalData::getInstance();
+ validCalculator = new ValidCalculators();
int i;
- for (i=0; i<globaldata->summaryEstimators.size(); i++) {
- if(globaldata->summaryEstimators[i] == "sobs"){
- sumCalculators.push_back(new Sobs());
- }else if(globaldata->summaryEstimators[i] == "chao"){
- sumCalculators.push_back(new Chao1());
- }else if(globaldata->summaryEstimators[i] == "ace"){
- sumCalculators.push_back(new Ace());
- }else if(globaldata->summaryEstimators[i] == "jack"){
- sumCalculators.push_back(new Jackknife());
- }else if(globaldata->summaryEstimators[i] == "shannon"){
- sumCalculators.push_back(new Shannon());
- }else if(globaldata->summaryEstimators[i] == "npshannon"){
- sumCalculators.push_back(new NPShannon());
- }else if(globaldata->summaryEstimators[i] == "simpson"){
- sumCalculators.push_back(new Simpson());
- }else if(globaldata->summaryEstimators[i] == "bootstrap"){
- sumCalculators.push_back(new Bootstrap());
+
+ 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] == "coverage"){
+ sumCalculators.push_back(new Coverage());
+ }else if(globaldata->Estimators[i] == "geometric"){
+ sumCalculators.push_back(new Geom());
+ }else if(globaldata->Estimators[i] == "logseries"){
+ sumCalculators.push_back(new LogSD());
+ }else if(globaldata->Estimators[i] == "qstat"){
+ sumCalculators.push_back(new QStat());
+ }else if(globaldata->Estimators[i] == "bergerparker"){
+ sumCalculators.push_back(new BergerParker());
+ }else if(globaldata->Estimators[i] == "bstick"){
+ sumCalculators.push_back(new BStick());
+ }else if(globaldata->Estimators[i] == "ace"){
+ convert(globaldata->getAbund(), abund);
+ if(abund < 5)
+ abund = 10;
+ sumCalculators.push_back(new Ace(abund));
+ }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());
+ }else if (globaldata->Estimators[i] == "nseqs") {
+ sumCalculators.push_back(new NSeqs());
+ }else if (globaldata->Estimators[i] == "goodscoverage") {
+ sumCalculators.push_back(new GoodsCoverage());
+ }else if (globaldata->Estimators[i] == "efron") {
+ convert(globaldata->getSize(), size);
+ sumCalculators.push_back(new Efron(size));
+ }else if (globaldata->Estimators[i] == "boneh") {
+ convert(globaldata->getSize(), size);
+ sumCalculators.push_back(new Boneh(size));
+ }else if (globaldata->Estimators[i] == "solow") {
+ convert(globaldata->getSize(), size);
+ sumCalculators.push_back(new Solow(size));
+ }else if (globaldata->Estimators[i] == "shen") {
+ convert(globaldata->getSize(), size);
+ sumCalculators.push_back(new Shen(size));
+ }
}
}
+
+ //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";
int SummaryCommand::execute(){
try {
+
+ //if the users entered no valid calculators don't execute command
+ if (sumCalculators.size() == 0) { return 0; }
+
outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
openOutputFile(outputFileName, outputFileHandle);
outputFileHandle << "label";
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
for(int i=0;i<sumCalculators.size();i++){
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
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;
}
-
sabund = input->getSAbundVector();
count++;
}