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

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index c5b66a81eaa7ec7381af79c4170f1efaf41e91d1..0bd91328f0b6aab5a1f8f20cdaaefab2876cc15d 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -44,7 +44,7 @@ PreClusterCommand::PreClusterCommand(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;            }
                                }
@@ -52,7 +52,7 @@ PreClusterCommand::PreClusterCommand(string option) {
                                it = parameters.find("name");
                                //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["name"] = inputDir + it->second;             }
                                }
@@ -66,7 +66,7 @@ PreClusterCommand::PreClusterCommand(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(fastafile); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
                        }
 
                        //check for optional parameter and set defaults
@@ -125,14 +125,14 @@ int PreClusterCommand::execute(){
                if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
                if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
                
-               string fileroot = outputDir + getRootName(getSimpleName(fastafile));
-               string newFastaFile = fileroot + "precluster" + getExtension(fastafile);
+               string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+               string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
                string newNamesFile = fileroot + "precluster.names";
                ofstream outFasta;
                ofstream outNames;
                
-               openOutputFile(newFastaFile, outFasta);
-               openOutputFile(newNamesFile, outNames);
+               m->openOutputFile(newFastaFile, outFasta);
+               m->openOutputFile(newNamesFile, outNames);
 
                //sort seqs by number of identical seqs
                alignSeqs.sort(comparePriority);
@@ -215,8 +215,8 @@ int PreClusterCommand::readFASTA(){
                //ifstream inNames;
                ifstream inFasta;
                
-               //openInputFile(namefile, inNames);
-               openInputFile(fastafile, inFasta);
+               //m->openInputFile(namefile, inNames);
+               m->openInputFile(fastafile, inFasta);
                
                //string firstCol, secondCol, nameString;
                length = 0;
@@ -228,14 +228,14 @@ int PreClusterCommand::readFASTA(){
                        //inNames >> firstCol >> secondCol;
                        //nameString = secondCol;
                        
-                       //gobble(inNames);
+                       //m->gobble(inNames);
                        //int size = 1;
                        //while (secondCol.find_first_of(',') != -1) { 
                        //      size++;
                        //      secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
                        //}
                        
-                       Sequence seq(inFasta);  gobble(inFasta);
+                       Sequence seq(inFasta);  m->gobble(inFasta);
                        
                        if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
                                if (namefile != "") {
@@ -302,11 +302,11 @@ void PreClusterCommand::printData(ofstream& outFasta, ofstream& outNames, seqPNo
 void PreClusterCommand::readNameFile(){
        try {
                ifstream in;
-               openInputFile(namefile, in);
+               m->openInputFile(namefile, in);
                string firstCol, secondCol;
                                
                while (!in.eof()) {
-                       in >> firstCol >> secondCol; gobble(in);
+                       in >> firstCol >> secondCol; m->gobble(in);
                        names[firstCol] = secondCol;
                        int size = 1;