added mantel command

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 32a9f7c2ebee2019ed3421eba21d42c4197087d0..b5214448cd2a5e8f8af0b70bfc700ee05465d4af 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -31,6 +31,24 @@
 #include "sharedbraycurtis.h"
 #include "sharedjackknife.h"
 #include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
 
 //**********************************************************************************************************************
 vector<string> SummarySharedCommand::getValidParameters(){     
@@ -47,8 +65,7 @@ vector<string> SummarySharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 SummarySharedCommand::SummarySharedCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;
        }
@@ -85,13 +102,13 @@ vector<string> SummarySharedCommand::getRequiredFiles(){
 SummarySharedCommand::SummarySharedCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                Estimators.clear();
                
                //allow user to run help
-               if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+               if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -210,6 +227,42 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                                                        sumCalculators.push_back(new BrayCurtis());
                                                }else if (Estimators[i] == "whittaker") { 
                                                        sumCalculators.push_back(new Whittaker());
+                                               }else if (Estimators[i] == "odum") { 
+                                                       sumCalculators.push_back(new Odum());
+                                               }else if (Estimators[i] == "canberra") { 
+                                                       sumCalculators.push_back(new Canberra());
+                                               }else if (Estimators[i] == "structeuclidean") { 
+                                                       sumCalculators.push_back(new StructEuclidean());
+                                               }else if (Estimators[i] == "structchord") { 
+                                                       sumCalculators.push_back(new StructChord());
+                                               }else if (Estimators[i] == "hellinger") { 
+                                                       sumCalculators.push_back(new Hellinger());
+                                               }else if (Estimators[i] == "manhattan") { 
+                                                       sumCalculators.push_back(new Manhattan());
+                                               }else if (Estimators[i] == "structpearson") { 
+                                                       sumCalculators.push_back(new StructPearson());
+                                               }else if (Estimators[i] == "soergel") { 
+                                                       sumCalculators.push_back(new Soergel());
+                                               }else if (Estimators[i] == "spearman") { 
+                                                       sumCalculators.push_back(new Spearman());
+                                               }else if (Estimators[i] == "structkulczynski") { 
+                                                       sumCalculators.push_back(new StructKulczynski());
+                                               }else if (Estimators[i] == "speciesprofile") { 
+                                                       sumCalculators.push_back(new SpeciesProfile());
+                                               }else if (Estimators[i] == "hamming") { 
+                                                       sumCalculators.push_back(new Hamming());
+                                               }else if (Estimators[i] == "structchi2") { 
+                                                       sumCalculators.push_back(new StructChi2());
+                                               }else if (Estimators[i] == "gower") { 
+                                                       sumCalculators.push_back(new Gower());
+                                               }else if (Estimators[i] == "memchi2") { 
+                                                       sumCalculators.push_back(new MemChi2());
+                                               }else if (Estimators[i] == "memchord") { 
+                                                       sumCalculators.push_back(new MemChord());
+                                               }else if (Estimators[i] == "memeuclidean") { 
+                                                       sumCalculators.push_back(new MemEuclidean());
+                                               }else if (Estimators[i] == "mempearson") { 
+                                                       sumCalculators.push_back(new MemPearson());
                                                }
                                        }
                                }
@@ -263,7 +316,7 @@ SummarySharedCommand::~SummarySharedCommand(){
 int SummarySharedCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ofstream outputFileHandle, outAll;
                string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
@@ -508,7 +561,11 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                                        }
                                                        
                                                        exit(0);
-                                               }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                                               }else { 
+                                                       m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                                                       for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                                                       exit(0);
+                                               }
                                        }
                                        
                                        //parent do your part
@@ -607,6 +664,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                                        outDist.close();
                                }
                        }
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "SummarySharedCommand", "process");
@@ -669,7 +727,15 @@ int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int sta
                                }
                                
                                for(int i=0;i<sumCalculators.size();i++) {
-
+                                       
+                                       //if this calc needs all groups to calculate the pair load all groups
+                                       if (sumCalculators[i]->getNeedsAll()) { 
+                                               //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+                                               for (int w = 0; w < thisLookup.size(); w++) {
+                                                       if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+                                               }
+                                       }
+                                       
                                        vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
                                        
                                        if (m->control_pressed) { outputFileHandle.close(); return 1; }
@@ -677,7 +743,7 @@ int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int sta
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
                                        
-                                       seqDist temp(l, k, tempdata[0]);
+                                       seqDist temp(l, k, (1.0 - tempdata[0]));
                                        calcDists[i].push_back(temp);
                                }
                                outputFileHandle << endl;