added concensus command and updated calcs

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index eca2033ed6b0f675374e4e855933a8142a6435c5..b3e665085e701b51db3873f7e5f503112c4fc91e 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -41,6 +41,7 @@ SummarySharedCommand::SummarySharedCommand(){
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
                util = new SharedUtil();
+               mult = false;
                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -88,7 +89,6 @@ SummarySharedCommand::SummarySharedCommand(){
                                }else if (globaldata->Estimators[i] == "whittaker") { 
                                        sumCalculators.push_back(new Whittaker());
                                }
-                               
                        }
                }
                //reset calc for next command
@@ -120,7 +120,13 @@ int SummarySharedCommand::execute(){
                
                //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); 
@@ -147,6 +153,20 @@ int SummarySharedCommand::execute(){
                }
                outputFileHandle << endl;
                
+               //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;
+               }
+               
                while(order != NULL){
                
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
@@ -154,15 +174,40 @@ int SummarySharedCommand::execute(){
                                cout << order->getLabel() << '\t' << count << endl;
                                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';
                                                
+                                               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
@@ -170,8 +215,8 @@ int SummarySharedCommand::execute(){
                                                        outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
                                                }
                                                
-                                               for(int i=0;i<sumCalculators.size();i++){
-                                                       sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
+                                               for(int i=0;i<sumCalculators.size();i++) {
+                                                       sumCalculators[i]->getValues(subset); //saves the calculator outputs
                                                        outputFileHandle << '\t';
                                                        sumCalculators[i]->print(outputFileHandle);
                                                }