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

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index b1f40e0a03f65e3dc04153cd554abdb8e8adb5aa..d6c284d68159b66255d3cdb29d57217e9dd73af6 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -42,7 +42,7 @@ ClearcutCommand::ClearcutCommand(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;            }
                                }
@@ -50,7 +50,7 @@ ClearcutCommand::ClearcutCommand(string option)  {
                                it = parameters.find("phylip");
                                //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["phylip"] = inputDir + it->second;           }
                                }
@@ -72,53 +72,53 @@ ClearcutCommand::ClearcutCommand(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 = hasPath(inputFile); }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputFile);      }
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "version", false);          if (temp == "not found"){       temp = "F";                     }
-                       version = isTrue(temp);
+                       version = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "verbose", false);          if (temp == "not found"){       temp = "F";                     }
-                       verbose = isTrue(temp); 
+                       verbose = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "quiet", false);            if (temp == "not found"){       temp = "F";                     }
-                       quiet = isTrue(temp); 
+                       quiet = m->isTrue(temp); 
                        
                        seed = validParameter.validFile(parameters, "seed", false);                     if (seed == "not found"){       seed = "*";                     }
                        
                        temp = validParameter.validFile(parameters, "norandom", false);         if (temp == "not found"){       temp = "F";                     }
-                       norandom = isTrue(temp); 
+                       norandom = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "shuffle", false);          if (temp == "not found"){       temp = "F";                     }
-                       shuffle = isTrue(temp); 
+                       shuffle = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "neighbor", false);         if (temp == "not found"){       temp = "T";                     }
-                       neighbor = isTrue(temp); 
+                       neighbor = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "DNA", false);                      if (temp == "not found"){       temp = "F";                     }
-                       DNA = isTrue(temp);
+                       DNA = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "protein", false);          if (temp == "not found"){       temp = "F";                     }
-                       protein = isTrue(temp);
+                       protein = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "jukes", false);            if (temp == "not found"){       temp = "F";                     }
-                       jukes = isTrue(temp);
+                       jukes = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "kimura", false);           if (temp == "not found"){       temp = "F";                     }
-                       kimura = isTrue(temp);
+                       kimura = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "stdout", false);           if (temp == "not found"){       temp = "F";                     }
-                       stdoutWanted = isTrue(temp); 
+                       stdoutWanted = m->isTrue(temp); 
                        
                        matrixout = validParameter.validFile(parameters, "matrixout", false);   if (matrixout == "not found"){  matrixout = "";         }
                        
                        ntrees = validParameter.validFile(parameters, "ntrees", false);         if (ntrees == "not found"){     ntrees = "1";           }
                        
                        temp = validParameter.validFile(parameters, "expblen", false);          if (temp == "not found"){       temp = "F";                     }
-                       expblen = isTrue(temp);
+                       expblen = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "expdist", false);          if (temp == "not found"){       temp = "F";                     }
-                       expdist = isTrue(temp);
+                       expdist = m->isTrue(temp);
                        
                        if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
                }
@@ -175,7 +175,7 @@ int ClearcutCommand::execute() {
                if (abort == true) { return 0; }
                                
                //prepare filename
-               string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
+               string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
                
                //get location of clearcut
                GlobalData* globaldata = GlobalData::getInstance();