added boneh, efron, and solow calculators

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 189be88de11e4160b4e185727e324a581063727f..0928d2e6b439b9775e62b5abd8c91b4254216e67 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -9,28 +9,33 @@
 
 #include "rarefactsharedcommand.h"
 #include "sharedsobs.h"
+#include "sharednseqs.h"
 
 //**********************************************************************************************************************
 
 RareFactSharedCommand::RareFactSharedCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               string fileNameRoot, groups;
+               string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
-               groupmap = globaldata->gGroupmap;
-               
-               //initialize groups for label
-               groups = "";
-               for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
-                       groups = groups + groupmap->namesOfGroups[i];
-               }
-               
+               format = globaldata->getFormat();
+               validCalculator = new ValidCalculators();
+                               
                int i;
-               for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
-                       if (globaldata->sharedRareEstimators[i] == "sharedobserved") { 
-                               rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"r_shared.observed", groups)));
+               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", "")));
+                               }
+
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -46,7 +51,6 @@ RareFactSharedCommand::RareFactSharedCommand(){
 //**********************************************************************************************************************
 
 RareFactSharedCommand::~RareFactSharedCommand(){
-       delete order;
        delete input;
        delete rCurve;
        delete read;
@@ -57,38 +61,50 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 int RareFactSharedCommand::execute(){
        try {
                int count = 1;
-               read = new ReadPhilFile(globaldata->inputFileName);     
-               read->read(&*globaldata); 
                
+               //if the users entered no valid calculators don't execute command
+               if (rDisplays.size() == 0) { return 0; }
+
+               read = new ReadOTUFile(globaldata->inputFileName);      
+               read->read(&*globaldata); 
+                       
                input = globaldata->ginput;
-               SharedList = globaldata->gSharedList;
-               order = SharedList->getSharedOrderVector();
+               lookup = input->getSharedRAbundVectors();
+               
+               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;
                        }
                        
-                       SharedList = input->getSharedListVector(); //get new list vector to process
-                       if (SharedList != NULL) {
-                               order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               count++;
-                       }else {
-                               break;
-                       }
-               
+                       //prevent memory leak
+                       for (int i = 0; i < lookup.size(); i++) {       delete lookup[i];       }
+                               
+                       //get next line to process
+                       lookup = input->getSharedRAbundVectors();
+                       count++;
                }
        
                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }       
+               
+               //reset groups parameter
+               globaldata->Groups.clear();  globaldata->setGroups("");
+
                return 0;
        }
        catch(exception& e) {