*/
#include "summarysharedcommand.h"
-#include "sharedsobs.h"
+#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
#include "sharedjabund.h"
SummarySharedCommand::SummarySharedCommand(){
try {
globaldata = GlobalData::getInstance();
+ outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ openOutputFile(outputFileName, outputFileHandle);
+ format = globaldata->getFormat();
+ validCalculator = new ValidCalculators();
int i;
- for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
- if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") {
- sumCalculators.push_back(new SharedSobs());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedChao") {
- sumCalculators.push_back(new SharedChao1());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") {
- sumCalculators.push_back(new SharedAce());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedJabund") {
- sumCalculators.push_back(new SharedJAbund());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorensonAbund") {
- sumCalculators.push_back(new SharedSorAbund());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedJclass") {
- sumCalculators.push_back(new SharedJclass());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorClass") {
- sumCalculators.push_back(new SharedSorClass());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedJest") {
- sumCalculators.push_back(new SharedJest());
- }else if (globaldata->sharedSummaryEstimators[i] == "sharedSorEst") {
- sumCalculators.push_back(new SharedSorEst());
- }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaYC") {
- sumCalculators.push_back(new SharedThetaYC());
- }else if (globaldata->sharedSummaryEstimators[i] == "SharedThetaN") {
- sumCalculators.push_back(new SharedThetaN());
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "sharedsobs") {
+ sumCalculators.push_back(new SharedSobsCS());
+ }else if (globaldata->Estimators[i] == "sharedchao") {
+ sumCalculators.push_back(new SharedChao1());
+ }else if (globaldata->Estimators[i] == "sharedace") {
+ sumCalculators.push_back(new SharedAce());
+ }else if (globaldata->Estimators[i] == "sharedjabund") {
+ sumCalculators.push_back(new SharedJAbund());
+ }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
+ sumCalculators.push_back(new SharedSorAbund());
+ }else if (globaldata->Estimators[i] == "sharedjclass") {
+ sumCalculators.push_back(new SharedJclass());
+ }else if (globaldata->Estimators[i] == "sharedsorclass") {
+ sumCalculators.push_back(new SharedSorClass());
+ }else if (globaldata->Estimators[i] == "sharedjest") {
+ sumCalculators.push_back(new SharedJest());
+ }else if (globaldata->Estimators[i] == "sharedsorest") {
+ sumCalculators.push_back(new SharedSorEst());
+ }else if (globaldata->Estimators[i] == "sharedthetayc") {
+ sumCalculators.push_back(new SharedThetaYC());
+ }else if (globaldata->Estimators[i] == "sharedthetan") {
+ sumCalculators.push_back(new SharedThetaN());
+ }
}
}
+
+ //reset calc for next command
+ globaldata->setCalc("");
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
int SummarySharedCommand::execute(){
try {
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
- openOutputFile(outputFileName, outputFileHandle);
-
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ int count = 1;
+ //if the users entered no valid calculators don't execute command
+ if (sumCalculators.size() == 0) { return 0; }
+
+ if (format == "sharedfile") {
+ read = new ReadPhilFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ order = input->getSharedOrderVector();
+ }else {
+ //you are using a list and a groupfile
+ read = new ReadPhilFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ SharedList = globaldata->gSharedList;
+ order = SharedList->getSharedOrderVector();
+ }
+
+ //output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
outputFileHandle << '\t' << sumCalculators[i]->getName();
}
outputFileHandle << endl;
-
- SharedList = globaldata->gSharedList;
- input = globaldata->ginput;
- order = SharedList->getSharedOrderVector();
- getGroupComb();
-
- int count = 1;
+
while(order != NULL){
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
int n = 1;
for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
for (int l = n; l < lookup.size(); l++) {
- outputFileHandle << order->getLabel() << '\t' << groupComb[n-1] << '\t' << '\t'; //print out label and group
+ outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
for(int i=0;i<sumCalculators.size();i++){
sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
outputFileHandle << '\t';
}
}
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- count++;
+ //get next line to process
+ if (format == "sharedfile") {
+ order = input->getSharedOrderVector();
}else {
- break;
+ //you are using a list and a groupfile
+ SharedList = input->getSharedListVector(); //get new list vector to process
+ if (SharedList != NULL) {
+ order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
+ }else {
+ break;
+ }
}
+ count++;
}
return 0;
}
-/**************************************************************************************/
-void SummarySharedCommand::getGroupComb() {
- try {
- string group;
-
- int n = 1;
- for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
- for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
- group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
- groupComb.push_back(group);
- }
- n++;
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function getGroupComb. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-
+//**********************************************************************************************************************
projects / mothur.git / blobdiff