sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 098da009eaeacfab076c9ad0f800f626158f4a15..643cf287bb9aded0847390aeea1091c12e95dd74 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -9,20 +9,63 @@
 
 #include "mergefilecommand.h"
 
+//**********************************************************************************************************************
+vector<string> MergeFileCommand::setParameters(){      
+       try {
+               CommandParameter pinput("input", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pinput);
+               CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+               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, "MergeFileCommand", "setParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+string MergeFileCommand::getHelpString(){      
+       try {
+               string helpString = "";
+               helpString += "The merge.file command takes a list of files separated by dashes and merges them into one file."; 
+               helpString += "The merge.file command parameters are input and output."; 
+               helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
+               helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
+               return helpString;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MergeFileCommand", "getHelpString");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+MergeFileCommand::MergeFileCommand(){  
+       try {
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["merge"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 MergeFileCommand::MergeFileCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                if(option == "help") {
                        help();
-                       abort = true; 
-               }
+                       abort = true; calledHelp = true;
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"input", "output","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -34,6 +77,10 @@ MergeFileCommand::MergeFileCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["merge"] = 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 = "";          }
@@ -67,7 +114,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
                        
                        outputFileName = validParameter.validFile(parameters, "output", false);                 
                        if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
-                       else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
+                       else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName);  }
                }
                        
        }
@@ -76,44 +123,20 @@ MergeFileCommand::MergeFileCommand(string option)  {
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-MergeFileCommand::~MergeFileCommand()  {       /*      do nothing      */      }
-
 //**********************************************************************************************************************
 
 int MergeFileCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
-               
-               ofstream outputFile;
-               m->openOutputFile(outputFileName, outputFile);
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               char c;
-               for(int i=0;i<numInputFiles;i++){
-                       ifstream inputFile; //declaration must be inside for loop of windows throws an error
-                       
-                       m->openInputFile(fileNames[i], inputFile);
-                       
-                       while(!inputFile.eof()){        
-                               if (m->control_pressed) { inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
-                       
-                               c = inputFile.get(); 
-                               //-1 is eof char
-                               if (int(c) != -1) { outputFile << c; }   
-                       }
-                       
-                       inputFile.close();
-               }
+               m->mothurRemove(outputFileName);
+               for(int i=0;i<numInputFiles;i++){  m->appendFiles(fileNames[i], outputFileName);  }
                
-               outputFile.close();
-               
-               if (m->control_pressed) { remove(outputFileName.c_str()); return 0;  }
+               if (m->control_pressed) {  m->mothurRemove(outputFileName); return 0;  }
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
                m->mothurOutEndLine();
 
                return 0;
@@ -123,17 +146,4 @@ int MergeFileCommand::execute(){
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-void MergeFileCommand::help(){
-       try {
-               m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MergeFileCommand", "help");
-               exit(1);
-       }
-}
-
 //**********************************************************************************************************************