added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index eacad376e1e91a519feff3c8e57727662042599b..64f0bc88713d2c3f56cfb6f98cc1cbc387ee7966 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1631,6 +1631,46 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool red
        }
 }
 /**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) { 
+       try {
+               
+               //open input file
+               ifstream in;
+               openInputFile(namefile, in);
+        
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        string firstCol, secondCol;
+        
+               while (!in.eof()) {
+                       if (control_pressed) { break; }
+                       
+            in.read(buffer, 4096);
+            vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    nameMap[secondCol] = firstCol;
+                    pairDone = false; 
+                }
+            }
+               }
+               in.close();
+               
+               return nameMap.size();
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "readNames");
+               exit(1);
+       }
+}
+/**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) { 
        try {
                nameMap.clear(); nameCount.clear();