added concensus command and updated calcs

[mothur.git] / venn.cpp

diff --git a/venn.cpp b/venn.cpp
index 7c33dd7a7bb1237480c4e5d95b28187832a7b71d..3c719ece9d3f68d886d4643fbd21f393b6673101 100644 (file)
--- a/venn.cpp
+++ b/venn.cpp
@@ -69,8 +69,7 @@ void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
 void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
        try {
                
-               //fills vector of sharedsabunds - lookup
-               //util->getSharedVectors(globaldata->Groups, lookup, sharedorder);  //fills group vectors from order vector.
+               vector<SharedRAbundVector*> subset;
                
                /******************* 1 Group **************************/
                if (lookup.size() == 1) {
@@ -125,13 +124,16 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
                        sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
                        
+                       subset.clear();
+                       subset.push_back(lookup[0]); subset.push_back(lookup[1]);
+                       
                        //make a file for each calculator
                        for(int i=0;i<vCalcs.size();i++){
                                string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
                                
                                //get estimates for sharedAB
-                               vector<double> shared = vCalcs[i]->getValues(lookup[0], lookup[1]);
+                               vector<double> shared = vCalcs[i]->getValues(subset);
                                
                                //in essence you want to run it like a single 
                                if (vCalcs[i]->getName() == "sharedsobs") {
@@ -199,11 +201,19 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                        for(int i=0;i<vCalcs.size();i++){
                                string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
                                openOutputFile(filenamesvg, outsvg);
-                               
+
                                //get estimates for sharedAB, sharedAC and sharedBC
-                               vector<double> sharedAB = vCalcs[i]->getValues(lookup[0], lookup[1]);
-                               vector<double> sharedAC = vCalcs[i]->getValues(lookup[0], lookup[2]);
-                               vector<double> sharedBC = vCalcs[i]->getValues(lookup[1], lookup[2]);
+                               subset.clear();
+                               subset.push_back(lookup[0]); subset.push_back(lookup[1]);
+                               vector<double> sharedAB = vCalcs[i]->getValues(subset);
+                               
+                               subset.clear();
+                               subset.push_back(lookup[0]); subset.push_back(lookup[2]);
+                               vector<double> sharedAC = vCalcs[i]->getValues(subset);
+                               
+                               subset.clear();
+                               subset.push_back(lookup[1]); subset.push_back(lookup[2]);
+                               vector<double> sharedBC = vCalcs[i]->getValues(subset);
                        
                                //merge BC and estimate with shared with A
                                SharedRAbundVector* merge = new SharedRAbundVector();
@@ -211,7 +221,9 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                        merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
                                }
                                
-                               vector<double> sharedAwithBC = vCalcs[i]->getValues(lookup[0], merge);
+                               subset.clear();
+                               subset.push_back(lookup[0]); subset.push_back(merge);
+                               vector<double> sharedAwithBC = vCalcs[i]->getValues(subset);
                        
                                delete merge;
                                //merge AC and estimate with shared with B
@@ -219,8 +231,10 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                for (int j = 0; j < lookup[0]->size(); j++) {
                                        merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
                                }
-               
-                               vector<double> sharedBwithAC = vCalcs[i]->getValues(lookup[1], merge);
+                               
+                               subset.clear();
+                               subset.push_back(merge); subset.push_back(lookup[1]);
+                               vector<double> sharedBwithAC = vCalcs[i]->getValues(subset);
                        
                                delete merge;
                                //merge AB and estimate with shared with C
@@ -229,7 +243,9 @@ void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs
                                        merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
                                }
                                
-                               vector<double> sharedCwithAB = vCalcs[i]->getValues(lookup[2], merge);
+                               subset.clear();
+                               subset.push_back(lookup[2]); subset.push_back(merge);
+                               vector<double> sharedCwithAB = vCalcs[i]->getValues(subset);
                                delete merge;
                                
                                //in essence you want to run it like a single