added concensus command and updated calcs

[mothur.git] / fileoutput.h

diff --git a/fileoutput.h b/fileoutput.h
index 3b73b148d88c7052421d48358c8ccdf0b39035ed..d7c4726e3f3d2b13786ebcf8bf6afa792b39fe52 100644 (file)
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -32,7 +32,7 @@ protected:
 class ThreeColumnFile : public FileOutput {
        
 public:
-       ThreeColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) { };
+       ThreeColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp") { };
        ~ThreeColumnFile();
        void initFile(string);
        void output(int, vector<double>);
@@ -56,7 +56,7 @@ class OneColumnFile : public FileOutput {
        
        
 public:
-       OneColumnFile(string n) : inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) {};
+       OneColumnFile(string n) : inName(n), counter(0), outName(getPathName(n) + ".temp") {};
        ~OneColumnFile();
        void output(int, vector<double>);
        void initFile(string);
@@ -80,7 +80,7 @@ class SharedOneColumnFile : public FileOutput {
        
        
 public:
-       SharedOneColumnFile(string n) : inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) {};
+       SharedOneColumnFile(string n) : inName(n), counter(0), outName(getPathName(n) + ".temp") {};
        ~SharedOneColumnFile();
        void output(int, vector<double>);
        void initFile(string);
@@ -105,7 +105,7 @@ private:
 class SharedThreeColumnFile : public FileOutput {
        
 public:
-       SharedThreeColumnFile(string n, string groups) : FileOutput(), groupLabel(groups), inName(n), counter(0), numGroup(1), outName(getPathName(n) + ".temp." + getSimpleName(n)) {  };
+       SharedThreeColumnFile(string n, string groups) : FileOutput(), groupLabel(groups), inName(n), counter(0), numGroup(1), outName(getPathName(n) + ".temp") {      };
        ~SharedThreeColumnFile();
        void initFile(string);
        void output(int, vector<double>);
@@ -125,11 +125,11 @@ private:
 };
 
 /***********************************************************************/
-
+//used by parsimony, unifrac.weighted and unifrac.unweighted
 class ColumnFile : public FileOutput {
        
 public:
-       ColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp." + getSimpleName(n)) { globaldata = GlobalData::getInstance(); };
+       ColumnFile(string n) : FileOutput(), inName(n), counter(0), outName(getPathName(n) + ".temp") { globaldata = GlobalData::getInstance(); };
        ~ColumnFile();
        
        //to make compatible with parent class