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

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index dc40611711062150b7046e1be665a34c87d87818..c08ee6ab2d512b56c6d39fa2a1290ab12da22bde 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -44,7 +44,7 @@ AlignCheckCommand::AlignCheckCommand(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 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                it = parameters.find("map");
                                //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["map"] = inputDir + it->second;              }
                                }
@@ -70,7 +70,7 @@ AlignCheckCommand::AlignCheckCommand(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       
                        }
 
                }
@@ -109,11 +109,11 @@ int AlignCheckCommand::execute(){
                readMap();
                
                ifstream in;
-               openInputFile(fastafile, in);
+               m->openInputFile(fastafile, in);
                
                ofstream out;
-               string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
-               openOutputFile(outfile, out);
+               string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+               m->openOutputFile(outfile, out);
                
                out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
                out << "loop" << '\t' << "tilde" << '\t' << "total" << endl;
@@ -122,7 +122,7 @@ int AlignCheckCommand::execute(){
                while(!in.eof()){
                        if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
                        
-                       Sequence seq(in);  gobble(in);
+                       Sequence seq(in);  m->gobble(in);
                        if (seq.getName() != "") {
                                statData data = getStats(seq.getAligned());
                                
@@ -158,13 +158,13 @@ void AlignCheckCommand::readMap(){
                structMap.resize(1, 0);
                ifstream in;
                
-               openInputFile(mapfile, in);
+               m->openInputFile(mapfile, in);
                
                while(!in.eof()){
                        int position;
                        in >> position;
                        structMap.push_back(position);  
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();