X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.cpp;h=2900c7ec4fc8e0df952163554f6fefb7e622cd64;hp=8892febb384cbb07233858f2c6b608f8153ca09f;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=a54ba6143022dc7294f4fdc468fc10b627c64b0e

diff --git a/mothurout.cpp b/mothurout.cpp
index 8892feb..2900c7e 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -348,6 +348,27 @@ void MothurOut::mothurOut(string output) {
 	}
 }
 /*********************************************************************************************/
+void MothurOut::mothurOutJustToScreen(string output) {
+	try {
+		
+#ifdef USE_MPI
+        int pid;
+        MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+        
+        if (pid == 0) { //only one process should output to screen
+#endif
+            logger() << output;
+            
+#ifdef USE_MPI
+        }
+#endif
+	}
+	catch(exception& e) {
+		errorOut(e, "MothurOut", "MothurOut");
+		exit(1);
+	}
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutEndLine() {
 	try {
 		#ifdef USE_MPI
@@ -1296,15 +1317,15 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
 				char c = inFASTA.get(); count++;
 				if (c == '>') {
 					positions.push_back(count-1);
-					//cout << count << endl;
+					if (debug) { mothurOut("[DEBUG]: numSeqs = " + toString(positions.size()) +  " count = " + toString(count) + ".\n"); }
 				}
 			}
 			inFASTA.close();
 		
 			num = positions.size();
-		
-			/*FILE * pFile;
-			long size;
+            if (debug) { mothurOut("[DEBUG]: num = " + toString(num) + ".\n"); }
+			FILE * pFile;
+			unsigned long long size;
 		
 			//get num bytes in file
 			pFile = fopen (filename.c_str(),"rb");
@@ -1313,9 +1334,9 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
 				fseek (pFile, 0, SEEK_END);
 				size=ftell (pFile);
 				fclose (pFile);
-			}*/
+			}
 			
-			unsigned long long size = positions[(positions.size()-1)];
+			/*unsigned long long size = positions[(positions.size()-1)];
 			ifstream in;
 			openInputFile(filename, in);
 			
@@ -1325,8 +1346,10 @@ vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num)
 				if(in.eof())		{	break;	}
 				else				{	size++;	}
 			}
-			in.close();
-		
+			in.close();*/
+        
+            if (debug) { mothurOut("[DEBUG]: size = " + toString(size) + ".\n"); }
+        
 			positions.push_back(size);
 			positions[0] = 0;
 		
@@ -2219,9 +2242,11 @@ map<string, int> MothurOut::readNames(string namefile, unsigned long int& numSeq
 /************************************************************/
 int MothurOut::checkName(string& name) {
     try {
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
-        }        
+        if (modifyNames) {
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
+            }
+        }
         return 0;
     }
 	catch(exception& e) {