finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime...

[mothur.git] / taxonomyequalizer.cpp

diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index 1d2832d5fc3a3ba31861d75d93dd202caf82261e..2f6fc77c7c29f689c6283c68c76ae14d8eea2b79 100644 (file)
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -16,7 +16,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
                containsConfidence = false;
                
                ifstream inTax;
-               openInputFile(tfile, inTax);
+               m->openInputFile(tfile, inTax);
        
                highestLevel = getHighestLevel(inTax);
                
@@ -32,11 +32,11 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
                        
                        inTax.close(); 
                        ifstream in; 
-                       openInputFile(tfile, in);
+                       m->openInputFile(tfile, in);
                        
                        ofstream out;
-                       equalizedFile = outputDir + getRootName(getSimpleName(tfile)) + "equalized.taxonomy";
-                       openOutputFile(equalizedFile, out);
+                       equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
+                       m->openOutputFile(equalizedFile, out);
                        
        
                        string name, tax;
@@ -44,7 +44,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
                        
                                if (m->control_pressed) {  break; }
                                
-                               in >> name >> tax;   gobble(in);
+                               in >> name >> tax;   m->gobble(in);
                                
                                if (containsConfidence) {  removeConfidences(tax);      }
                                
@@ -61,7 +61,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
                        in.close();
                        out.close();
                        
-                       if (m->control_pressed) { remove(equalizedFile.c_str());  }
+                       if (m->control_pressed) { m->mothurRemove(equalizedFile);  }
                }else { inTax.close(); }
                
        }
@@ -78,7 +78,7 @@ int TaxEqualizer::getHighestLevel(ifstream& in) {
                string name, tax;
                
                while (in) {
-                       in >> name >> tax;   gobble(in);
+                       in >> name >> tax;   m->gobble(in);
                
                        //count levels in this taxonomy
                        int thisLevel = 0;