fixes while testing 1.33.0

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index e82d1f6600e0b83f79154634ddfbda43d7542d91..59c12a03dae958f4bb199a6aad94056264c0426a 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -17,7 +17,7 @@ vector<string> SummarySharedCommand::setParameters(){
                CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
         CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample);
                CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",false,false); parameters.push_back(pdistance);
-               CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+               CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
         CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
                CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
         CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
@@ -184,9 +184,6 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        string temp = validParameter.validFile(parameters, "all", false);                               if (temp == "not found") { temp = "false"; }
                        all = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "distance", false);                                 if (temp == "not found") { temp = "false"; }
-                       createPhylip = m->isTrue(temp);
-                       
             temp = validParameter.validFile(parameters, "iters", false);                       if (temp == "not found") { temp = "1000"; }
                        m->mothurConvert(temp, iters); 
             
@@ -204,6 +201,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
             
             if (subsample == false) { iters = 0; }
             
+            temp = validParameter.validFile(parameters, "distance", false);                                    if (temp == "not found") { temp = "false"; }
+                       createPhylip = m->isTrue(temp);
+            if (subsample) { createPhylip = true; }
+            
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors); 
@@ -293,6 +294,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                                        sumCalculators.push_back(new MemEuclidean());
                                                }else if (Estimators[i] == "mempearson") { 
                                                        sumCalculators.push_back(new MemPearson());
+                                               }else if (Estimators[i] == "jsd") {
+                                                       sumCalculators.push_back(new JSD());
+                                               }else if (Estimators[i] == "rjsd") {
+                                                       sumCalculators.push_back(new RJSD());
                                                }
                                        }
                                }
@@ -703,7 +708,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                 
                 vector<summarySharedData*> pDataArray; 
                 DWORD   dwThreadIdArray[processors-1];
-                HANDLE  hThreadArray[processors-1]; 
+                HANDLE  hThreadArray[processors-1];
                 
                 //Create processor worker threads.
                 for( int i=1; i<processors; i++ ){
@@ -716,6 +721,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                         temp->setGroup(thisLookup[k]->getGroup());
                         newLookup.push_back(temp);
                     }
+                
                     
                     //for each bin
                     for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {