#include "mergefilecommand.h"
//**********************************************************************************************************************
-vector<string> MergeFileCommand::getValidParameters(){
+vector<string> MergeFileCommand::setParameters(){
try {
- string Array[] = {"input", "output","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-MergeFileCommand::MergeFileCommand(){
- try {
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["merge"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
+ m->errorOut(e, "MergeFileCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MergeFileCommand::getRequiredParameters(){
+string MergeFileCommand::getHelpString(){
try {
- string Array[] = {"input","output"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ 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", "getRequiredParameters");
+ m->errorOut(e, "MergeFileCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MergeFileCommand::getRequiredFiles(){
+MergeFileCommand::MergeFileCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["merge"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "getRequiredFiles");
+ 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();
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-MergeFileCommand::~MergeFileCommand() { /* do nothing */ }
-
//**********************************************************************************************************************
int MergeFileCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- ofstream outputFile;
- m->openOutputFile(outputFileName, outputFile);
-
- 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) { outputTypes.clear(); 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();
- }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- outputFile.close();
+ m->mothurRemove(outputFileName);
+ for(int i=0;i<numInputFiles;i++){ m->appendFiles(fileNames[i], outputFileName); }
- if (m->control_pressed) { outputTypes.clear(); 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("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
m->mothurOutEndLine();
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void MergeFileCommand::help(){
- try {
- m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
- }
- catch(exception& e) {
- m->errorOut(e, "MergeFileCommand", "help");
- exit(1);
- }
-}
-
//**********************************************************************************************************************