added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 98bdcb2cba6cb726f9d793baca1c78f785a04c00..799d8dced192019f65a633e946262db92c1e615f 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -37,7 +37,7 @@ string GetSAbundCommand::getHelpString(){
                helpString += "Example get.sabund().\n";
                helpString += "The default value for label is all labels in your inputfile.\n";
                helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -67,6 +67,7 @@ GetSAbundCommand::GetSAbundCommand(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();
@@ -113,12 +114,12 @@ GetSAbundCommand::GetSAbundCommand(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); }
                        
                        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); }
                        
                
                                                //check for optional parameter and set defaults
@@ -186,7 +187,6 @@ int GetSAbundCommand::execute(){
                                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
                                        
                                        sabund->print(out);
-                                       delete sabund;
                                        
                                if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
 
@@ -202,7 +202,6 @@ int GetSAbundCommand::execute(){
                                        
                                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
                                        sabund->print(out);
-                                       delete sabund;
                                        
                                        if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }