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

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index b57f3a02670de0711b01bca5c52a711d4aa70292..1ca894fb391eae4e604736d0cb7102986ed3569d 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -40,7 +40,7 @@ HeatMapCommand::HeatMapCommand(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(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -53,7 +53,7 @@ HeatMapCommand::HeatMapCommand(string option) {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -66,7 +66,7 @@ HeatMapCommand::HeatMapCommand(string option) {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                        
@@ -178,7 +178,7 @@ int HeatMapCommand::execute(){
                                        userLabels.erase(lookup[0]->getLabel());
                                }
                                
-                               if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = lookup[0]->getLabel();
                                
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
@@ -252,7 +252,7 @@ int HeatMapCommand::execute(){
                                        userLabels.erase(rabund->getLabel());
                                }
                                
-                               if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = rabund->getLabel();
                                        
                                        delete rabund;