#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 {
+ int count = 1;
+
+ //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);
-
+
+ sabund = globaldata->sabund;
+ SAbundVector* lastSAbund = sabund;
+ 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 = globaldata->labels;
+ set<int> userLines = globaldata->lines;
+ while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->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(lastSAbund->getLabel()) != 1)) {
+
+ cout << lastSAbund->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lastSAbund->getLabel());
+ userLabels.erase(lastSAbund->getLabel());
+
+ outputFileHandle << lastSAbund->getLabel();
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }
+ outputFileHandle << endl;
+ }
+
+ if (count != 1) { delete lastSAbund; }
+ lastSAbund = 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(lastSAbund->getLabel()) != 1) {
+ cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastSAbund->getLabel() << '\t' << count << endl;
+ outputFileHandle << lastSAbund->getLabel();
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }
+ outputFileHandle << endl;
+ }
+
+ delete lastSAbund;
return 0;
}
catch(exception& e) {
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