*/
#include "summarysharedcommand.h"
+#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
+#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
//**********************************************************************************************************************
SummarySharedCommand::SummarySharedCommand(){
try {
globaldata = GlobalData::getInstance();
+ outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ openOutputFile(outputFileName, outputFileHandle);
+ format = globaldata->getFormat();
+ validCalculator = new ValidCalculators();
+ util = new SharedUtil();
+ mult = false;
int i;
- for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
- 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] == "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] == "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("");
+
}
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";
SummarySharedCommand::~SummarySharedCommand(){
delete input;
delete read;
+ delete util;
}
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
- outputFileName = ((getRootName(globaldata->inputFileName)) + "sharedSummary");
- 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; }
+ //check if any calcs can do multiples
+ else{
+ for (int i = 0; i < sumCalculators.size(); i++) {
+ if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ }
+ }
+
+ if (format == "sharedfile") {
+ 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 ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ SharedList = globaldata->gSharedList;
+ order = SharedList->getSharedOrderVector();
+ }
+
+ //set users groups
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
- outputFileHandle << '\t' << '\t' << '\t' << '\t'; //pads file for labels and groupnames
+ //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;
- list = globaldata->glist;
- input = globaldata->ginput;
- order = list->getSharedOrderVector();
- getGroupComb();
+ //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;
+ }
- int count = 1;
while(order != NULL){
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()); }
+ //loop through calculators and add to file all for all calcs that can do mutiple groups
+ if (mult = true) {
+ //output label
+ outAll << order->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' << groupComb[n-1] << '\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 << order->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[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
+ }else{
+ outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
+ }
+
+ for(int i=0;i<sumCalculators.size();i++) {
+ sumCalculators[i]->getValues(subset); //saves the calculator outputs
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
}
}
- list = input->getListVector(); //get new list vector to process
- if (list != NULL) {
- order = list->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++;
}
-
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
return 0;
}
catch(exception& e) {
}
}
-//**********************************************************************************************************************
-
-void SummarySharedCommand::getSharedVectors(){
-try {
- lookup.clear();
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
- temp->setLabel(order->getLabel());
- temp->setGroup(globaldata->gGroupmap->namesOfGroups[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::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