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

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 076c5ebd055259f81afa75c6953be2e13936d064..022b174a5c21f4de6f26c2dcd8232b0744da8120 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -164,22 +164,22 @@ SummaryCommand::SummaryCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
-                       else {  format = "sabund"; inputfile = sabundfile; }
+                       else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
-                       else {  format = "rabund"; inputfile = rabundfile; }
+                       else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else {  format = "sharedfile"; inputfile = sharedfile; }
+                       else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
                        
                        if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?
@@ -223,13 +223,18 @@ SummaryCommand::SummaryCommand(string option)  {
                                 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
                        }
                        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; } }
+                       }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
-                       convert(temp, size); 
+                       m->mothurConvert(temp, size); 
                        
                        temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
                        groupMode = m->isTrue(temp);
@@ -332,7 +337,7 @@ int SummaryCommand::execute(){
                        }
                        
                        //if the users entered no valid calculators don't execute command
-                       if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
+                       if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0; }
                        
                        ofstream outputFileHandle;
                        m->openOutputFile(fileNameRoot, outputFileHandle);
@@ -358,11 +363,11 @@ int SummaryCommand::execute(){
                        set<string> processedLabels;
                        set<string> userLabels = labels;
                        
-                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
                        
                        while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
                                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){                     
                                        
@@ -374,7 +379,7 @@ int SummaryCommand::execute(){
                                        for(int i=0;i<sumCalculators.size();i++){
                                                vector<double> data = sumCalculators[i]->getValues(sabund);
                                                
-                                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+                                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 
                                                outputFileHandle << '\t';
                                                sumCalculators[i]->print(outputFileHandle);
@@ -397,7 +402,7 @@ int SummaryCommand::execute(){
                                        for(int i=0;i<sumCalculators.size();i++){
                                                vector<double> data = sumCalculators[i]->getValues(sabund);
                                                
-                                               if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
+                                               if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
                                                
                                                outputFileHandle << '\t';
                                                sumCalculators[i]->print(outputFileHandle);
@@ -415,7 +420,7 @@ int SummaryCommand::execute(){
                                sabund = input->getSAbundVector();
                        }
                        
-                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -440,7 +445,7 @@ int SummaryCommand::execute(){
                                for(int i=0;i<sumCalculators.size();i++){
                                        vector<double> data = sumCalculators[i]->getValues(sabund);
                                        
-                                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
+                                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
 
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
@@ -452,19 +457,19 @@ int SummaryCommand::execute(){
                        
                        outputFileHandle.close();
                        
-                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 
                        
                        delete input;  
                        for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
                }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  return 0;  }
                
                //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
                if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0;  }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  return 0;  }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -493,7 +498,7 @@ vector<string> SummaryCommand::parseSharedFile(string filename) {
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
-                       remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+                       m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                        filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                }
                
@@ -587,7 +592,7 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                        files[outputNames[i]] = thisFilesLines;
                        
                        temp.close();
-                       remove(outputNames[i].c_str());
+                       m->mothurRemove(outputNames[i]);
                }
                
                //output label line to new file