added *.count.summary file to count.groups command. added deltaq and insert parameter...

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 570d64e34166cafcf734181a370dd9fc854e64a3..d5f5a8b8b8450deef538f564d59885b57647c430 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> GetRAbundCommand::setParameters(){      
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-               CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);            
-               CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psorted);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist);
+               CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund);             
+               CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -39,7 +39,7 @@ string GetRAbundCommand::getHelpString(){
                helpString += "Example get.rabund(sorted=F).\n";
                helpString += "The default value for label is all labels in your inputfile.\n";
                helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -47,6 +47,21 @@ string GetRAbundCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string GetRAbundCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "rabund")      {   pattern = "[filename],rabund";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 
 //**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(){  
@@ -69,6 +84,7 @@ GetRAbundCommand::GetRAbundCommand(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();
@@ -115,12 +131,12 @@ GetRAbundCommand::GetRAbundCommand(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); }
                        
                        
                        //check for optional parameter and set defaults
@@ -172,7 +188,9 @@ int GetRAbundCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "rabund";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+               filename = getOutputFileName("rabund", variables);
                m->openOutputFile(filename, out);
                
                input = new InputData(inputfile, format);
@@ -183,19 +201,17 @@ int GetRAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+               if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
                
                while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
                        if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
-                                       
-                                       delete rabund;
                                                                                                                        
                                        processedLabels.insert(rabund->getLabel());
                                        userLabels.erase(rabund->getLabel());
@@ -209,13 +225,11 @@ int GetRAbundCommand::execute(){
                                        
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
 
-                                       delete rabund;
-
                                        processedLabels.insert(rabund->getLabel());
                                        userLabels.erase(rabund->getLabel());
                                        
@@ -249,7 +263,7 @@ int GetRAbundCommand::execute(){
                        
                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
                        
                        if(sorted)      {   rabund->print(out);                         }
                        else            {       rabund->nonSortedPrint(out);    }
@@ -258,7 +272,7 @@ int GetRAbundCommand::execute(){
                }
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
                m->mothurOutEndLine();