created mothurOut class to handle logfiles

[mothur.git] / taxonomyequalizer.cpp

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index c84c439a9efbc3633372ffe3ff3461f127dae171..f3ccfe45852ba8065c454d4bf42a0ad83a75d088 100644 (file)
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -12,6 +12,7 @@
 /**************************************************************************************************/
 TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
        try {
+               m = MothurOut::getInstance();
                containsConfidence = false;
                
                ifstream inTax;
@@ -23,8 +24,8 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
                if ((cutoff != -1) && (cutoff < highestLevel)) { 
                        highestLevel = cutoff;
                }else if (cutoff > highestLevel) {
-                       mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
-                       mothurOutEndLine();
+                       m->mothurOut("The highest level taxonomy you have is " + toString(highestLevel) + " and your cutoff is " + toString(cutoff) + ". I will set the cutoff to " + toString(highestLevel));
+                       m->mothurOutEndLine();
                }
                
                inTax.close(); 
@@ -56,7 +57,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
                                        
        }
        catch(exception& e) {
-               errorOut(e, "TaxEqualizer", "TaxEqualizer");
+               m->errorOut(e, "TaxEqualizer", "TaxEqualizer");
                exit(1);
        }
 }
@@ -95,7 +96,7 @@ int TaxEqualizer::getHighestLevel(ifstream& in) {
                                        
        }
        catch(exception& e) {
-               errorOut(e, "TaxEqualizer", "getHighestLevel");
+               m->errorOut(e, "TaxEqualizer", "getHighestLevel");
                exit(1);
        }
 }
@@ -118,7 +119,7 @@ void TaxEqualizer::extendTaxonomy(string name, string& tax, int desiredLevel) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "TaxEqualizer", "extendTaxonomy");
+               m->errorOut(e, "TaxEqualizer", "extendTaxonomy");
                exit(1);
        }
 }
@@ -137,7 +138,7 @@ void TaxEqualizer::truncateTaxonomy(string name, string& tax, int desiredLevel)
                tax += ";";
        }
        catch(exception& e) {
-               errorOut(e, "TaxEqualizer", "truncateTaxonomy");
+               m->errorOut(e, "TaxEqualizer", "truncateTaxonomy");
                exit(1);
        }
 }
@@ -161,7 +162,7 @@ void TaxEqualizer::removeConfidences(string& tax) {
                tax = newTax;
        }
        catch(exception& e) {
-               errorOut(e, "TaxEqualizer", "removeConfidences");
+               m->errorOut(e, "TaxEqualizer", "removeConfidences");
                exit(1);
        }
 }