fixed some bugs and added scriptengine

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 9be29152445487dea77a36e62c01812aa617e1ea..9e2a08b2a493fec7ed717505d7d02112a8530b49 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,17 +13,59 @@
 
 //***************************************************************************************************************
 
-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);
        }       
 }
@@ -38,11 +80,13 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){  /*      do nothing      */      }
 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()){
@@ -57,11 +101,11 @@ int ReverseSeqsCommand::execute(){
                
        }
        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);
        }
 }