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

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 2eabbc1099c40cab04f6de929014b326fddab6d4..12e48f4ad34720a449a7dd7e2c197fe57faa4f64 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -46,7 +46,7 @@ ChopSeqsCommand::ChopSeqsCommand(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;            }
                                }
@@ -61,7 +61,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                        convert(temp, numbases);   
                        
                        temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; } 
-                       countGaps = isTrue(temp);   
+                       countGaps = m->isTrue(temp);   
                
                        keep = validParameter.validFile(parameters, "keep", false);             if (keep == "not found") { keep = "front"; } 
                                
@@ -100,17 +100,17 @@ int ChopSeqsCommand::execute(){
                
                if (abort == true) { return 0; }
                
-               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chop.fasta";
-               string outputFileNameAccnos = outputDir + getRootName(getSimpleName(fastafile)) + "chop.accnos";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
+               string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
                
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
                ofstream outAcc;
-               openOutputFile(outputFileNameAccnos, outAcc);
+               m->openOutputFile(outputFileNameAccnos, outAcc);
                
                ifstream in;
-               openInputFile(fastafile, in);
+               m->openInputFile(fastafile, in);
                
                bool wroteAccnos = false;