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

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 1e89cdcca0d5230867356d37f8c6404a98639da6..857f68431c54b8a0076577ae74b70ecfba6e9773 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -72,6 +72,7 @@ CatchAllCommand::CatchAllCommand(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();
@@ -118,10 +119,12 @@ CatchAllCommand::CatchAllCommand(string option)  {
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }
                        else if (sabundfile == "not found") { sabundfile = "";  }
+                       else { m->setSabundFile(sabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }
                        else if (sharedfile == "not found") { sharedfile = "";   }
+                       else { m->setSharedFile(sharedfile); }
                        
                        string label = validParameter.validFile(parameters, "label", false);                    
                        if (label == "not found") { label = ""; }
@@ -210,7 +213,7 @@ int CatchAllCommand::execute() {
                        
                        //for each label the user selected
                        while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
+                               
                                                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
                                                m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
@@ -218,7 +221,7 @@ int CatchAllCommand::execute() {
                                                //create catchall input file from mothur's inputfile
                                                string filename = process(sabund, inputFileNames[p]);
                                                string outputPath = m->getPathName(filename);
-                                       
+                                                                                       
                                                //create system command
                                                string catchAllCommand = "";
                                                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -233,7 +236,7 @@ int CatchAllCommand::execute() {
                                                //run catchall
                                                system(catchAllCommand.c_str());
                                        
-                                               remove(filename.c_str());
+                                               m->mothurRemove(filename);
                                        
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
@@ -245,7 +248,7 @@ int CatchAllCommand::execute() {
                                        
                                                createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
                                                                                        
-                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str());    }  delete input;  delete sabund;  return 0; }
+                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }  delete input;  delete sabund;  return 0; }
 
                                                processedLabels.insert(sabund->getLabel());
                                                userLabels.erase(sabund->getLabel());
@@ -263,7 +266,7 @@ int CatchAllCommand::execute() {
                                                //create catchall input file from mothur's inputfile
                                                string filename = process(sabund, inputFileNames[p]);
                                                string outputPath = m->getPathName(filename);
-                                               
+                                                                                       
                                                //create system command
                                                string catchAllCommand = "";
                                                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -277,7 +280,7 @@ int CatchAllCommand::execute() {
                                                //run catchall
                                                system(catchAllCommand.c_str());
                                        
-                                               remove(filename.c_str());
+                                               m->mothurRemove(filename);
                                        
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
@@ -289,7 +292,7 @@ int CatchAllCommand::execute() {
                                        
                                                createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
                                        
-                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str());    }  delete input;  delete sabund;  return 0; }
+                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }  delete input;  delete sabund;  return 0; }
 
                                                processedLabels.insert(sabund->getLabel());
                                                userLabels.erase(sabund->getLabel());
@@ -342,7 +345,7 @@ int CatchAllCommand::execute() {
                                //run catchall
                                system(catchAllCommand.c_str());
                                
-                               remove(filename.c_str());
+                               m->mothurRemove(filename);
                                
                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
@@ -360,7 +363,7 @@ int CatchAllCommand::execute() {
                        out.close();
                        delete input; 
                        
-                       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; }
                                
                }
                
@@ -468,7 +471,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
                        numLines = thisFilesLines.size();
                        
                        temp.close();
-                       remove(outputNames[i].c_str());
+                       m->mothurRemove(outputNames[i]);
                }
                
                //for each label
@@ -576,7 +579,7 @@ vector<string> CatchAllCommand::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() + ".sabund").c_str());
+                       m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
                        filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
                        groups.push_back(lookup[i]->getGroup());
                }