#include "rarefactsharedcommand.h"
#include "sharedsobs.h"
+#include "sharednseqs.h"
//**********************************************************************************************************************
fileNameRoot = getRootName(globaldata->inputFileName);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
-
- setGroups();
int i;
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
if (globaldata->Estimators[i] == "sharedobserved") {
rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+ }else if (globaldata->Estimators[i] == "sharednseqs") {
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
}
+
}
}
//**********************************************************************************************************************
RareFactSharedCommand::~RareFactSharedCommand(){
- delete order;
delete input;
delete rCurve;
delete read;
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
- if (format == "sharedfile") {
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ 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->read(&*globaldata);
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ 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]; }
+ return 0;
}
+
- while(order != NULL){
+ while(lookup[0] != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
//create collectors curve
- rCurve = new Rarefact(order, rDisplays);
+ rCurve = new Rarefact(lookup, rDisplays);
convert(globaldata->getFreq(), freq);
convert(globaldata->getIters(), nIters);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
- cout << order->getLabel() << '\t' << count << endl;
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
}
+ //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++;
}
//**********************************************************************************************************************
-
-void RareFactSharedCommand::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 RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/***********************************************************/
-