X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=a56a6217a8c136e1fcb9f3f3078c5418547220fa;hb=f06fdb807822f8e06db003ed809c87250905cfc8;hp=3205ae794165a5b8c045c473403d8a66b1b54f90;hpb=a150db3c2bfd7b76420048a1e94ebe397f2c6045;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 3205ae7..a56a621 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -247,6 +247,53 @@ void MothurOut::mothurOutEndLine() {
 	}
 }
 /*********************************************************************************************/
+void MothurOut::mothurOut(string output, ofstream& outputFile) {
+	try {
+		
+#ifdef USE_MPI
+		int pid;
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+		
+		if (pid == 0) { //only one process should output to screen
+#endif
+			
+			cout << output;
+			out << output;
+			outputFile << output;
+			
+#ifdef USE_MPI
+		}
+#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
+void MothurOut::mothurOutEndLine(ofstream& outputFile) {
+	try {
+#ifdef USE_MPI
+		int pid;
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+		
+		if (pid == 0) { //only one process should output to screen
+#endif
+			
+			cout << endl;
+			out << endl;
+			outputFile << endl;
+			
+#ifdef USE_MPI
+		}
+#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOutEndLine");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutJustToLog(string output) {
 	try {
 		#ifdef USE_MPI
@@ -1229,6 +1276,33 @@ float MothurOut::ceilDist(float dist, int precision){
 		exit(1);
 	}
 }
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
+	try {
+		
+		//open input file
+		ifstream in;
+		openInputFile(namefile, in);
+		
+		while (!in.eof()) {
+			if (control_pressed) { break; }
+			
+			string firstCol, secondCol;
+			in >> firstCol >> secondCol; gobble(in);
+			
+			nameMap[firstCol] = secondCol;
+		}
+		in.close();
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "readNames");
+		exit(1);
+	}
+}
+
 /**********************************************************************************************************************/
 map<string, int> MothurOut::readNames(string namefile) { 
 	try {