#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
#include "sharedochiai.h"
-#include "sharedanderberg.h"
+#include "sharedanderbergs.h"
#include "sharedkulczynski.h"
#include "sharedkulczynskicody.h"
#include "sharedlennon.h"
openOutputFile(outputFileName, outputFileHandle);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
+ util = new SharedUtil();
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] == "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());
}
+
}
}
-
//reset calc for next command
globaldata->setCalc("");
SummarySharedCommand::~SummarySharedCommand(){
delete input;
delete read;
+ delete util;
}
//**********************************************************************************************************************
if (sumCalculators.size() == 0) { return 0; }
if (format == "sharedfile") {
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(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 = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
}
//set users groups
- setGroups();
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
cout << order->getLabel() << '\t' << count << endl;
- getSharedVectors(); //fills group vectors from order vector.
+ util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. //fills group vectors from order vector.
//randomize group order
if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
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';
//sort groups to be alphanumeric
}
}
-//**********************************************************************************************************************
-
-void SummarySharedCommand::getSharedVectors(){
-try {
- lookup.clear();
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
- temp->setLabel(order->getLabel());
- temp->setGroup(globaldata->Groups[i]);
- lookup.push_back(temp);
- }
-
- int numSeqs = order->size();
- //sample all the members
- for(int i=0;i<numSeqs;i++){
- //get first sample
- individual chosen = order->get(i);
- int abundance;
-
- //set info for sharedvector in chosens group
- for (int j = 0; j < lookup.size(); j++) {
- if (chosen.group == lookup[j]->getGroup()) {
- abundance = lookup[j]->getAbundance(chosen.bin);
- lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
- }
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-
-//**********************************************************************************************************************
-void SummarySharedCommand::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase(globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
- }
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
/***********************************************************/
projects / mothur.git / blobdiff