paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 13a77ed31b19ae8b87006ea36ba5a53839365ebe..4363eaa9523570cd56146a75805b9dfc8e65e3d7 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -56,7 +56,7 @@ vector<string> SummarySharedCommand::setParameters(){
                CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "",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-skulczynski-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); 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", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
                CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
@@ -119,6 +119,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -183,6 +184,11 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
                        }
                        m->splitAtDash(calc, Estimators);
+                       if (m->inUsersGroups("citation", Estimators)) { 
+                               ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+                               //remove citation from list of calcs
+                               for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+                       }
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
@@ -574,7 +580,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                        ifstream intemp;
                                                        m->openInputFile(tempdistFileName, intemp);
                                                        
-                                                       for (int i = 0; i < calcDists.size(); i++) {
+                                                       for (int k = 0; k < calcDists.size(); k++) {
                                                                int size = 0;
                                                                intemp >> size; m->gobble(intemp);
                                                                        
@@ -586,7 +592,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                                        intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
                                                                        
                                                                        seqDist tempDist(seq1, seq2, dist);
-                                                                       calcDists[i].push_back(tempDist);
+                                                                       calcDists[k].push_back(tempDist);
                                                                }
                                                        }
                                                        intemp.close();