working on pam

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 363a7a88041ac97bfd207558fc4fa445af7d442b..1747b1480c732ae42f361940ff57dcbe151bbc7b 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -66,11 +66,9 @@ class MothurOut {
        
                vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
                vector<string> Treenames;
-               //map<string, string> names;
                vector<string> sharedBinLabelsInFile;
                vector<string> currentSharedBinLabels;
         vector<string> listBinLabelsInFile;
-        //vector<string> currentListBinLabels;
                string saveNextLabel, argv, sharedHeaderMode, groupMode;
                bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
                
@@ -84,6 +82,7 @@ class MothurOut {
                vector<unsigned long long> setFilePosFasta(string, int&);
                string sortFile(string, string);
                int appendFiles(string, string);
+        int appendBinaryFiles(string, string);
         int appendFilesWithoutHeaders(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
@@ -99,7 +98,11 @@ class MothurOut {
                int openOutputFileAppend(string, ofstream&);
         int openOutputFileBinaryAppend(string, ofstream&);
                int openInputFile(string, ifstream&);
-               int openInputFile(string, ifstream&, string); //no error given 
+        int openInputFileBinary(string, ifstream&);
+        int openInputFileBinary(string, ifstream&, string);
+               int openInputFile(string, ifstream&, string); //no error given
+    
+        bool checkLocations(string&, string);  //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location.  Returns false if cant be found. If found completes name with location
                string getline(ifstream&);
                string getline(istringstream&);
                void gobble(istream&);