X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=1747b1480c732ae42f361940ff57dcbe151bbc7b;hp=363a7a88041ac97bfd207558fc4fa445af7d442b;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83

diff --git a/mothurout.h b/mothurout.h
index 363a7a8..1747b14 100644
--- 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&);