#include "sharedthetayc.h"
#include "sharedthetan.h"
#include "sharedkstest.h"
-#include "sharedbdiversity.h"
+#include "whittaker.h"
#include "sharedochiai.h"
#include "sharedanderbergs.h"
#include "sharedkulczynski.h"
#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
//**********************************************************************************************************************
openOutputFile(outputFileName, outputFileHandle);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
- util = new SharedUtil();
+ mult = false;
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
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());
- }else if (globaldata->Estimators[i] == "sharedkstest") {
- sumCalculators.push_back(new SharedKSTest());
+ }else if (globaldata->Estimators[i] == "jabund") {
+ sumCalculators.push_back(new JAbund());
+ }else if (globaldata->Estimators[i] == "sorabund") {
+ sumCalculators.push_back(new SorAbund());
+ }else if (globaldata->Estimators[i] == "jclass") {
+ sumCalculators.push_back(new Jclass());
+ }else if (globaldata->Estimators[i] == "sorclass") {
+ sumCalculators.push_back(new SorClass());
+ }else if (globaldata->Estimators[i] == "jest") {
+ sumCalculators.push_back(new Jest());
+ }else if (globaldata->Estimators[i] == "sorest") {
+ sumCalculators.push_back(new SorEst());
+ }else if (globaldata->Estimators[i] == "thetayc") {
+ sumCalculators.push_back(new ThetaYC());
+ }else if (globaldata->Estimators[i] == "thetan") {
+ sumCalculators.push_back(new ThetaN());
+ }else if (globaldata->Estimators[i] == "kstest") {
+ sumCalculators.push_back(new KSTest());
}else if (globaldata->Estimators[i] == "sharednseqs") {
sumCalculators.push_back(new SharedNSeqs());
- }else if (globaldata->Estimators[i] == "sharedochiai") {
- sumCalculators.push_back(new SharedOchiai());
- }else if (globaldata->Estimators[i] == "sharedanderberg") {
- sumCalculators.push_back(new SharedAnderberg());
- }else if (globaldata->Estimators[i] == "sharedkulczynski") {
- sumCalculators.push_back(new SharedKulczynski());
- }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
- sumCalculators.push_back(new SharedKulczynskiCody());
- }else if (globaldata->Estimators[i] == "sharedlennon") {
- sumCalculators.push_back(new SharedLennon());
- }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
- sumCalculators.push_back(new SharedMorHorn());
- }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
- sumCalculators.push_back(new SharedBrayCurtis());
+ }else if (globaldata->Estimators[i] == "ochiai") {
+ sumCalculators.push_back(new Ochiai());
+ }else if (globaldata->Estimators[i] == "anderberg") {
+ sumCalculators.push_back(new Anderberg());
+ }else if (globaldata->Estimators[i] == "kulczynski") {
+ sumCalculators.push_back(new Kulczynski());
+ }else if (globaldata->Estimators[i] == "kulczynskicody") {
+ sumCalculators.push_back(new KulczynskiCody());
+ }else if (globaldata->Estimators[i] == "lennon") {
+ sumCalculators.push_back(new Lennon());
+ }else if (globaldata->Estimators[i] == "morisitahorn") {
+ sumCalculators.push_back(new MorHorn());
+ }else if (globaldata->Estimators[i] == "braycurtis") {
+ sumCalculators.push_back(new BrayCurtis());
+ }else if (globaldata->Estimators[i] == "whittaker") {
+ sumCalculators.push_back(new Whittaker());
}
- else if (globaldata->Estimators[i] == "sharedbdiversity") {
- sumCalculators.push_back(new SharedBDiversity());
- }
-
}
}
//reset calc for next command
SummarySharedCommand::~SummarySharedCommand(){
delete input;
delete read;
- delete util;
}
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
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();
+ //check if any calcs can do multiples
+ else{
+ for (int i = 0; i < sumCalculators.size(); i++) {
+ if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ }
}
- //set users groups
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
+ //read first line
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
}
outputFileHandle << endl;
- while(order != NULL){
+ //create file and put column headers for multiple groups file
+ if (mult == true) {
+ outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
+ openOutputFile(outAllFileName, outAll);
+
+ outAll << "label" <<'\t' << "comparison" << '\t';
+ for(int i=0;i<sumCalculators.size();i++){
+ if (sumCalculators[i]->getMultiple() == true) {
+ outAll << '\t' << sumCalculators[i]->getName();
+ }
+ }
+ outAll << endl;
+ }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if (lookup.size() < 2) {
+ cout << "I cannot run the command without at least 2 valid groups.";
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ //close files and clean up
+ outputFileHandle.close(); remove(outputFileName.c_str());
+ if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
+ return 0;
+ }
+
+
+ while(lookup[0] != NULL){
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
- util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. //fills group vectors from order vector.
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
- //randomize group order
- if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
-
+ //loop through calculators and add to file all for all calcs that can do mutiple groups
+ if (mult == true) {
+ //output label
+ outAll << lookup[0]->getLabel() << '\t';
+
+ //output groups names
+ string outNames = "";
+ for (int j = 0; j < lookup.size(); j++) {
+ outNames += lookup[j]->getGroup() + "-";
+ }
+ outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
+ outAll << outNames << '\t';
+
+ for(int i=0;i<sumCalculators.size();i++){
+ if (sumCalculators[i]->getMultiple() == true) {
+ sumCalculators[i]->getValues(lookup);
+ outAll << '\t';
+ sumCalculators[i]->print(outAll);
+ }
+ }
+ outAll << endl;
+ }
+
int n = 1;
+ vector<SharedRAbundVector*> subset;
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';
+ outputFileHandle << lookup[0]->getLabel() << '\t';
+
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(lookup[k]); subset.push_back(lookup[l]);
//sort groups to be alphanumeric
if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
}
- for(int i=0;i<sumCalculators.size();i++){
- sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
+ for(int i=0;i<sumCalculators.size();i++) {
+
+ sumCalculators[i]->getValues(subset); //saves the calculator outputs
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
}
}
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
//get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }else {
- //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;
- }
- }
+ lookup = input->getSharedRAbundVectors();
count++;
}
//reset groups parameter
globaldata->Groups.clear(); globaldata->setGroups("");
+
+ //close files
+ outputFileHandle.close();
+ if (mult == true) { outAll.close(); }
return 0;
}
projects / mothur.git / blobdiff