moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 9be29152445487dea77a36e62c01812aa617e1ea..296c95410df58f1aeabfbd5b3195b327a18fe170 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,19 +13,74 @@
 
 //***************************************************************************************************************
 
-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", "outputdir","inputdir"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
+                       map<string,string>::iterator it;
+                       
+                       //check to make sure all parameters are valid for command
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //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 = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("fasta");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
+                               }
+                       }
+
+                       //check for required parameters
+                       fasta = validParameter.validFile(parameters, "fasta", true);
+                       if (fasta == "not open") { abort = true; }
+                       else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true;  }       
+                       
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
+                               outputDir = ""; 
+                               outputDir += m->hasPath(fasta); //if user entered a file with a path then preserve it   
+                       }
+
+               }
        }
        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";
+               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
                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";
+}
+//**********************************************************************************************************************
+
+void ReverseSeqsCommand::help(){
+       try {
+               m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+               m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+               m->mothurOut("The reverse.seqs command should be in the following format: \n");
+               m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");   
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReverseSeqsCommand", "help");
                exit(1);
-       }       
+       }
 }
 
 //***************************************************************************************************************
@@ -38,30 +93,40 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){  /*      do nothing      */      }
 int ReverseSeqsCommand::execute(){
        try{
                
+               if (abort == true) { return 0; }
+               
                ifstream inFASTA;
-               openInputFile(globaldata->getFastaFile(), inFASTA);
+               m->openInputFile(fasta, inFASTA);
                
                ofstream outFASTA;
-               string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile());
-               openOutputFile(reverseFile, outFASTA);
+               string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
+               m->openOutputFile(reverseFile, outFASTA);
                
                while(!inFASTA.eof()){
-                       Sequence currSeq(inFASTA);
-                       currSeq.reverseComplement();
-                       currSeq.printSequence(outFASTA);
+                       if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(reverseFile.c_str()); return 0; }
+                        
+                       Sequence currSeq(inFASTA);  m->gobble(inFASTA);
+                       if (currSeq.getName() != "") {
+                               currSeq.reverseComplement();
+                               currSeq.printSequence(outFASTA);
+                       }
                }
                inFASTA.close();
                outFASTA.close();
                
+               if (m->control_pressed) {  remove(reverseFile.c_str()); return 0; }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(reverseFile); m->mothurOutEndLine();       
+               m->mothurOutEndLine();
+
+               
                return 0;
                
        }
        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";
-               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";
+               m->errorOut(e, "ReverseSeqsCommand", "execute");
                exit(1);
        }
 }