X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=d5b7e5f806b54bdd2b9c8283cd6d781d5fe2abe1;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=f58f4e874a7f72961489d7e2651bda651e3d2bb4;hpb=a935b75dd890da5ae7f09e5e6179f90ab2955348;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index f58f4e8..d5b7e5f 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -66,11 +66,11 @@ class MothurOut {
 	
 		vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
 		vector<string> Treenames;
-		//map<string, string> names;
-		vector<string> binLabelsInFile;
-		vector<string> currentBinLabels;
+		vector<string> sharedBinLabelsInFile;
+		vector<string> currentSharedBinLabels;
+        vector<string> listBinLabelsInFile;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+		bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
 		
 		//functions from mothur.h
 		//file operations
@@ -82,6 +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);
@@ -97,7 +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&);
@@ -141,6 +146,7 @@ class MothurOut {
         bool isLabelEquivalent(string, string);
         string getSimpleLabel(string);
         string findEdianness();
+        string mothurGetpid(int);
 	
 		
 		//string manipulation
@@ -270,7 +276,8 @@ class MothurOut {
             counttablefile = "";
             summaryfile = "";
 			gui = false;
-			printedHeaders = false;
+			printedSharedHeaders = false;
+            printedListHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;