paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 3205ae794165a5b8c045c473403d8a66b1b54f90..a56a6217a8c136e1fcb9f3f3078c5418547220fa 100644 (file)
--- 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 {