working on pam

[mothur.git] / getcurrentcommand.cpp

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index bd7539a25a30a2c972dfa9157a1b25ceb3349c33..d74786ce1eaaa8767164a0fbd670d06843388b44 100644 (file)
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -9,48 +9,46 @@
 
 #include "getcurrentcommand.h"
 
-
 //**********************************************************************************************************************
-vector<string> GetCurrentCommand::getValidParameters(){        
+vector<string> GetCurrentCommand::setParameters(){     
        try {
-               string Array[] =  {"outputdir","inputdir","clear"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+               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);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "GetCurrentCommand", "getValidParameters");
+               m->errorOut(e, "GetCurrentCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-GetCurrentCommand::GetCurrentCommand(){        
+string GetCurrentCommand::getHelpString(){     
        try {
-               abort = true; calledHelp = true; 
+               string helpString = "";
+               helpString += "The get.current command outputs the current files saved by mothur.\n";
+               helpString += "The get.current command has one parameter: clear.\n";
+               helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+               helpString += "The get.current command should be in the following format: \n";
+               helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
+               m->errorOut(e, "GetCurrentCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> GetCurrentCommand::getRequiredParameters(){     
-       try {
-               vector<string> myArray;
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GetCurrentCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> GetCurrentCommand::getRequiredFiles(){  
+GetCurrentCommand::GetCurrentCommand(){        
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true;
+               setParameters();
        }
        catch(exception& e) {
-               m->errorOut(e, "GetCurrentCommand", "getRequiredFiles");
+               m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
                exit(1);
        }
 }
@@ -61,11 +59,10 @@ GetCurrentCommand::GetCurrentCommand(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 {
-                       //valid paramters for this command
-                       string Array[] =  {"outputdir","inputdir","clear"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -89,25 +86,6 @@ GetCurrentCommand::GetCurrentCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void GetCurrentCommand::help(){
-       try {
-               m->mothurOut("The get.current command outputs the current files saved by mothur.\n");
-               m->mothurOut("The get.current command has one parameter: clear.\n");
-               m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
-               m->mothurOut("The get.current command should be in the following format: \n");
-               m->mothurOut("get.current() or get.current(clear=fasta-name-accnos)\n");
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "GetCurrentCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-GetCurrentCommand::~GetCurrentCommand(){}
-//**********************************************************************************************************************
-
 int GetCurrentCommand::execute(){
        try {
                
@@ -157,7 +135,17 @@ int GetCurrentCommand::execute(){
                                }else if (types[i] == "accnos") {
                                        m->setAccnosFile("");
                                }else if (types[i] == "taxonomy") {
-                                               m->setTaxonomyFile("");
+                                       m->setTaxonomyFile("");
+                               }else if (types[i] == "flow") {
+                                       m->setFlowFile("");
+                }else if (types[i] == "biom") {
+                                       m->setBiomFile("");
+                }else if (types[i] == "count") {
+                                       m->setCountTableFile("");
+                }else if (types[i] == "summary") {
+                                       m->setSummaryFile("");
+                               }else if (types[i] == "processors") {
+                                       m->setProcessors("1");
                                }else if (types[i] == "all") {
                                        m->clearCurrentFiles();
                                }else {
@@ -166,8 +154,10 @@ int GetCurrentCommand::execute(){
                        }
                }
                
-               m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
-               m->printCurrentFiles();
+               if (m->hasCurrentFiles()) {
+                       m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+                       m->printCurrentFiles();
+               }
                
                return 0;       
        }