//***************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(){
+ReverseSeqsCommand::ReverseSeqsCommand(string option){
try {
- globaldata = GlobalData::getInstance();
- if(globaldata->getFastaFile() == "") { cout << "you need to at least enter a fasta file name" << endl; }
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //check for required parameters
+ fasta = validParameter.validFile(parameters, "fasta", true);
+ if (fasta == "not open") { abort = true; }
+ else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true; }
+
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void ReverseSeqsCommand::help(){
+ try {
+ cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
+ cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
+ cout << "The reverse.seqs command should be in the following format: " << "\n";
+ cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
int ReverseSeqsCommand::execute(){
try{
+ if (abort == true) { return 0; }
+
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fasta, inFASTA);
ofstream outFASTA;
- string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile());
+ string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
openOutputFile(reverseFile, outFASTA);
while(!inFASTA.eof()){
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}