changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 37e95685430184760cd0919c18a1cfeea2ec4c42..114750e71e4c5cb127cf4b9407bd1841bb8aa622 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,7 +13,7 @@
 
 //***************************************************************************************************************
 
-ReverseSeqsCommand::ReverseSeqsCommand(string option){
+ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
        try {
                abort = false;
                
@@ -22,28 +22,49 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta"};
+                       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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       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 = 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 = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); 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 += hasPath(fasta); //if user entered a file with a path then preserve it      
+                       }
+
                }
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
                exit(1);
        }
 }
@@ -51,13 +72,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
 
 void ReverseSeqsCommand::help(){
        try {
-               mothurOut("The reverse.seqs command reads a fastafile and ....\n");
-               mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
-               mothurOut("The reverse.seqs command should be in the following format: \n");
-               mothurOut("reverse.seqs(fasta=yourFastaFile) \n");      
+               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) {
-               errorOut(e, "ReverseSeqsCommand", "help");
+               m->errorOut(e, "ReverseSeqsCommand", "help");
                exit(1);
        }
 }
@@ -78,10 +99,12 @@ int ReverseSeqsCommand::execute(){
                openInputFile(fasta, inFASTA);
                
                ofstream outFASTA;
-               string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
+               string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
                openOutputFile(reverseFile, outFASTA);
                
                while(!inFASTA.eof()){
+                       if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(reverseFile.c_str()); return 0; }
+                        
                        Sequence currSeq(inFASTA);  gobble(inFASTA);
                        if (currSeq.getName() != "") {
                                currSeq.reverseComplement();
@@ -91,11 +114,19 @@ int ReverseSeqsCommand::execute(){
                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) {
-               errorOut(e, "ReverseSeqsCommand", "execute");
+               m->errorOut(e, "ReverseSeqsCommand", "execute");
                exit(1);
        }
 }