added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 3a2875afb62b882e9e8654eecb19e2caab5c9673..f3a320b89e0695483a5124b6336d68cf89179293 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -57,7 +57,7 @@ vector<string> CollectSharedCommand::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 pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
-               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 pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -119,7 +119,7 @@ CollectSharedCommand::CollectSharedCommand(){
                outputTypes["sharednseqs"] = tempOutNames;
                outputTypes["ochiai"] = tempOutNames;
                outputTypes["anderberg"] = tempOutNames;
-               outputTypes["skulczynski"] = tempOutNames;
+               outputTypes["kulczynski"] = tempOutNames;
                outputTypes["kulczynskicody"] = tempOutNames;
                outputTypes["lennon"] = tempOutNames;
                outputTypes["morisitahorn"] = tempOutNames;
@@ -157,6 +157,7 @@ CollectSharedCommand::CollectSharedCommand(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();
@@ -190,7 +191,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                        outputTypes["sharednseqs"] = tempOutNames;
                        outputTypes["ochiai"] = tempOutNames;
                        outputTypes["anderberg"] = tempOutNames;
-                       outputTypes["skulczynski"] = tempOutNames;
+                       outputTypes["kulczynski"] = tempOutNames;
                        outputTypes["kulczynskicody"] = tempOutNames;
                        outputTypes["lennon"] = tempOutNames;
                        outputTypes["morisitahorn"] = tempOutNames;
@@ -237,7 +238,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -258,17 +259,22 @@ CollectSharedCommand::CollectSharedCommand(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 = ""; }
                        else { 
                                m->splitAtDash(groups, Groups);
                        }
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "all", false);                              if (temp == "not found") { temp = "false"; }
                        all = m->isTrue(temp);
@@ -329,7 +335,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
                                                }else if (Estimators[i] == "anderberg") { 
                                                        cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
                                                        outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg");
-                                               }else if (Estimators[i] == "skulczynski") { 
+                                               }else if (Estimators[i] == "kulczynski") { 
                                                        cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
                                                        outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
                                                }else if (Estimators[i] == "kulczynskicody") { 
@@ -434,15 +440,19 @@ int CollectSharedCommand::execute(){
                        
                //set users groups
                SharedUtil* util = new SharedUtil();
-               util->setGroups(m->Groups, m->namesOfGroups, "collect");
+               Groups = m->getGroups();
+               vector<string> allGroups = m->getAllGroups();
+               util->setGroups(Groups, allGroups, "collect");
+               m->setGroups(Groups);
+               m->setAllGroups(allGroups);
                delete util;
 
                while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        if (m->control_pressed) { 
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                        delete order; delete input;
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                        }
 
@@ -487,9 +497,9 @@ int CollectSharedCommand::execute(){
                }
                
                if (m->control_pressed) { 
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }   outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }   outputTypes.clear();
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        delete input;
                                        return 0;
                }
@@ -518,11 +528,11 @@ int CollectSharedCommand::execute(){
                        delete cCurve;
                        
                        if (m->control_pressed) { 
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  outputTypes.clear();
                                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
                                delete order; 
                                delete input;
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                        }
 
@@ -532,7 +542,7 @@ int CollectSharedCommand::execute(){
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
                
                //reset groups parameter
-               m->Groups.clear(); 
+               m->clearGroups(); 
                delete input;
                
                m->mothurOutEndLine();