added pipeline commands which involved change to command factory and command class...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index f1b9cd8103a2d5f9c8836f657411359b0845785c..1f880f38cdf5c48d4dd0418c1d9c68172af7b8b7 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -9,6 +9,54 @@
 
 #include "seqerrorcommand.h"
 
+//**********************************************************************************************************************
+vector<string> SeqErrorCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SeqErrorCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+SeqErrorCommand::SeqErrorCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["error"] = tempOutNames;
+               outputTypes["count"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SeqErrorCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"query","reference"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SeqErrorCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SeqErrorCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SeqErrorCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
 
 SeqErrorCommand::SeqErrorCommand(string option)  {
@@ -23,7 +71,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        string temp;
                        
                        //valid paramters for this command
-                       string AlignArray[] =  {"query", "reference", "name", "threshold"};
+                       string AlignArray[] =  {"query", "reference", "name", "threshold", "inputdir", "outputdir"};
                        
 //need to implement name file option
                        
@@ -40,6 +88,11 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["error"] = tempOutNames;
+                       outputTypes["count"] = tempOutNames;
+                       
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -97,6 +150,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                                
                        errorFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".errors";
                        m->openOutputFile(errorFileName, errorFile);
+                       outputNames.push_back(errorFileName); outputTypes["error"].push_back(errorFileName);
                        printErrorHeader();
                }
        }
@@ -195,6 +249,7 @@ int SeqErrorCommand::execute(){
                string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".count";
                ofstream errorCountFile;
                m->openOutputFile(errorCountFileName, errorCountFile);
+               outputNames.push_back(errorCountFileName);  outputTypes["count"].push_back(errorCountFileName);
                
                m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n\n");
                m->mothurOut("Errors\tSequences\n");