bug fixes

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index a3f88cf74d2c1eaa5c88fd792f678a7e5a7b4bf3..406085728838262b79100a70133600639e6c47a2 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -11,14 +11,61 @@
 #include "sequence.hpp"
 #include "listvector.hpp"
 
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ListSeqsCommand::ListSeqsCommand(){    
+       try {
+               abort = true; calledHelp = true; 
+               vector<string> tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ListSeqsCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 ListSeqsCommand::ListSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -36,6 +83,10 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["accnos"] = tempOutNames;
+                       
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
                        
@@ -154,7 +205,7 @@ void ListSeqsCommand::help(){
 int ListSeqsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read functions fill names vector
                if (fastafile != "")            {       inputFileName = fastafile;      readFasta();    }
@@ -164,7 +215,7 @@ int ListSeqsCommand::execute(){
                else if (listfile != "")        {       inputFileName = listfile;       readList();             }
                else if (taxfile != "")         {       inputFileName = taxfile;        readTax();              }
                
-               if (m->control_pressed) { return 0; }
+               if (m->control_pressed) { outputTypes.clear();  return 0; }
                
                //sort in alphabetical order
                sort(names.begin(), names.end());
@@ -179,17 +230,17 @@ int ListSeqsCommand::execute(){
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
                        
-                       if (m->control_pressed) { out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
                        
                        out << names[i] << endl;
                }
                out.close();
                
-               if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
 
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
                m->mothurOutEndLine();
                
                return 0;               
@@ -315,7 +366,7 @@ int ListSeqsCommand::readGroup(){
                        
                        if (m->control_pressed) { in.close(); return 0; }
                        
-                       in >> name;                             //read from first column
+                       in >> name;     m->gobble(in);                  //read from first column
                        in >> group;                    //read from second column
                        
                        names.push_back(name);
@@ -393,6 +444,7 @@ int ListSeqsCommand::readTax(){
                        names.push_back(firstCol);
                        
                        m->gobble(in);
+                       
                }
                in.close();