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

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 66f8193e647c94db5bc8ac815bb6eea9796cd138..2d46efc9efebcfbe7807292cb814cf58686f9ac4 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -126,8 +126,8 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        }
                        
                        m->runParse = true;
-                       m->Groups.clear();
-                       m->namesOfGroups.clear();
+                       m->clearGroups();
+                       m->clearAllGroups();
                        m->Treenames.clear();
                        m->names.clear();
                        
@@ -139,7 +139,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        if (randomtree == "")  {
                                //check for required parameters
                                treefile = validParameter.validFile(parameters, "tree", true);
-                               if (treefile == "not open") { abort = true; }
+                               if (treefile == "not open") { treefile = ""; abort = true; }
                                else if (treefile == "not found") {                             //if there is a current design file, use it
                                        treefile = m->getTreeFile(); 
                                        if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
@@ -153,7 +153,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                                else { m->setGroupFile(groupfile); }
                                
                                namefile = validParameter.validFile(parameters, "name", true);
-                               if (namefile == "not open") { abort = true; }
+                               if (namefile == "not open") { namefile = ""; abort = true; }
                                else if (namefile == "not found") { namefile = ""; }
                                else { m->setNameFile(namefile); }
                        }
@@ -164,18 +164,23 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        groups = validParameter.validFile(parameters, "groups", false);                 
-                       if (groups == "not found") { groups = ""; m->Groups.clear(); }
+                       if (groups == "not found") { groups = ""; m->clearGroups(); }
                        else { 
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                     if (itersString == "not found") { itersString = "1000"; }
-                       convert(itersString, iters); 
+                       m->mothurConvert(itersString, iters); 
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(treefile);
+                               parser.getNameFile(files);
+                       }
                        
                }
 
@@ -242,7 +247,7 @@ int ParsimonyCommand::execute() {
                                        if (m->control_pressed) { 
                                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                               m->Groups.clear();
+                                               m->clearGroups();
                                                return 0;
                                        }
                                        
@@ -280,8 +285,11 @@ int ParsimonyCommand::execute() {
                        
                //set users groups to analyze
                util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony");     //sets the groups the user wants to analyze
-               util->getCombos(groupComb, m->Groups, numComp);
+               vector<string> mGroups = m->getGroups();
+               vector<string> tGroups = tmap->getNamesOfGroups();
+               util->setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony");   //sets the groups the user wants to analyze
+               util->getCombos(groupComb, mGroups, numComp);
+               m->setGroups(mGroups);
                delete util;
                        
                if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
@@ -297,7 +305,7 @@ int ParsimonyCommand::execute() {
                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                        if (randomtree == "") {  outSum.close();  }
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                       m->Groups.clear();
+                       m->clearGroups();
                        return 0;
                }
                        
@@ -322,7 +330,7 @@ int ParsimonyCommand::execute() {
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                        if (randomtree == "") {  outSum.close();  }
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -361,7 +369,7 @@ int ParsimonyCommand::execute() {
                                        if (randomtree == "") {  outSum.close();  }
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                        
@@ -398,7 +406,7 @@ int ParsimonyCommand::execute() {
                                        delete reading; delete pars; delete output; delete randT;
                                        delete tmap; 
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -410,7 +418,7 @@ int ParsimonyCommand::execute() {
                                        delete reading; delete pars;  delete output; delete randT;
                                        delete tmap; 
                                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                        
@@ -467,7 +475,7 @@ int ParsimonyCommand::execute() {
                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                if (randomtree == "") {  outSum.close();  }
                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                }
                
@@ -480,7 +488,7 @@ int ParsimonyCommand::execute() {
                if (randomtree == "") { printUSummaryFile(); }
                
                //reset groups parameter
-               m->Groups.clear(); 
+               m->clearGroups(); 
                
                delete pars; delete output; 
                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
@@ -585,6 +593,7 @@ void ParsimonyCommand::getUserInput() {
                count = 1;
                numEachGroup.resize(numGroups, 0);  
                
+               
                for (int i = 1; i <= numGroups; i++) {
                        m->mothurOut("Please enter the number of sequences in group " + toString(i) +  ": ");
                        cin >> num;
@@ -592,7 +601,7 @@ void ParsimonyCommand::getUserInput() {
                                
                        //set tmaps seqsPerGroup
                        tmap->seqsPerGroup[toString(i)] = num;
-                       tmap->namesOfGroups.push_back(toString(i));
+                       tmap->addGroup(toString(i));
                        
                        //set tmaps namesOfSeqs
                        for (int j = 0; j < num; j++) {