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

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 114750e71e4c5cb127cf4b9407bd1841bb8aa622..296c95410df58f1aeabfbd5b3195b327a18fe170 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -44,7 +44,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                                it = parameters.find("fasta");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       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;            }
                                }
@@ -58,7 +58,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
                        //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      
+                               outputDir += m->hasPath(fasta); //if user entered a file with a path then preserve it   
                        }
 
                }
@@ -96,16 +96,16 @@ int ReverseSeqsCommand::execute(){
                if (abort == true) { return 0; }
                
                ifstream inFASTA;
-               openInputFile(fasta, inFASTA);
+               m->openInputFile(fasta, inFASTA);
                
                ofstream outFASTA;
-               string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
-               openOutputFile(reverseFile, outFASTA);
+               string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
+               m->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);
+                       Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                        if (currSeq.getName() != "") {
                                currSeq.reverseComplement();
                                currSeq.printSequence(outFASTA);