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

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index b4d601751630af81741d64ab605c95d5650838a5..fd95323e745bd0ce499368c5ea4cb7bd0ce21bf8 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -47,7 +47,7 @@ HClusterCommand::HClusterCommand(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;           }
                                }
@@ -55,7 +55,7 @@ HClusterCommand::HClusterCommand(string option)  {
                                it = parameters.find("column");
                                //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["column"] = inputDir + it->second;           }
                                }
@@ -63,7 +63,7 @@ HClusterCommand::HClusterCommand(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;             }
                                }
@@ -105,7 +105,7 @@ HClusterCommand::HClusterCommand(string option)  {
                        convert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
-                       hard = isTrue(temp);
+                       hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
@@ -123,7 +123,7 @@ HClusterCommand::HClusterCommand(string option)  {
                        
                        sort = validParameter.validFile(parameters, "sorted", false);
                        if (sort == "not found") { sort = "F"; }
-                       sorted = isTrue(sort);
+                       sorted = m->isTrue(sort);
 
                        timing = validParameter.validFile(parameters, "timing", false);
                        if (timing == "not found") { timing = "F"; }
@@ -131,16 +131,16 @@ HClusterCommand::HClusterCommand(string option)  {
                                
                        if (abort == false) {
                                
-                               if (outputDir == "") {  outputDir += hasPath(distfile); }
-                               fileroot = outputDir + getRootName(getSimpleName(distfile));
+                               if (outputDir == "") {  outputDir += m->hasPath(distfile); }
+                               fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
                                
                                if (method == "furthest")               { tag = "fn";  }
                                else if (method == "nearest")   { tag = "nn";  }
                                else                                                    { tag = "an";  }
                        
-                               openOutputFile(fileroot+ tag + ".sabund",       sabundFile);
-                               openOutputFile(fileroot+ tag + ".rabund",       rabundFile);
-                               openOutputFile(fileroot+ tag + ".list",         listFile);
+                               m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
+                               m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
+                               m->openOutputFile(fileroot+ tag + ".list",              listFile);
                                
                                outputNames.push_back(fileroot+ tag + ".sabund");
                                outputNames.push_back(fileroot+ tag + ".rabund");
@@ -282,9 +282,9 @@ int HClusterCommand::execute(){
                        
                                        float rndDist;
                                        if (hard) {
-                                               rndDist = ceilDist(seqs[i].dist, precision); 
+                                               rndDist = m->ceilDist(seqs[i].dist, precision); 
                                        }else{
-                                               rndDist = roundDist(seqs[i].dist, precision); 
+                                               rndDist = m->roundDist(seqs[i].dist, precision); 
                                        }
 
                                        
@@ -360,7 +360,7 @@ int HClusterCommand::execute(){
 
 void HClusterCommand::printData(string label){
        try {
-               if (isTrue(timing)) {
+               if (m->isTrue(timing)) {
                        m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) 
                     + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
                }
@@ -369,7 +369,7 @@ void HClusterCommand::printData(string label){
                start = time(NULL);
 
                oldRAbund.setLabel(label);
-               if (isTrue(showabund)) {
+               if (m->isTrue(showabund)) {
                        oldRAbund.getSAbundVector().print(cout);
                }
                oldRAbund.print(rabundFile);