X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=468c063cb5c7e74a8d5901a1a38203f47409e2d5;hb=4542a79d20176ff0ee830b0f9d4f4c92637439d9;hp=124fbb876b38def3d61f1bf425ef15f36237fa5f;hpb=006601d68abe8d0061f77e8d28323b160750e343;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index 124fbb8..468c063 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1608,8 +1608,17 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
                 if (pairDone) { 
                     //are there confidence scores, if so remove them
                     if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);	}
-                    taxMap[firstCol] = secondCol;
-                    if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
+                    map<string, string>::iterator itTax = taxMap.find(firstCol);
+                    
+                    if(itTax == taxMap.end()) {
+                        bool ignore = false;
+                        if (secondCol != "") { if (secondCol[secondCol.length()-1] != ';') { mothurOut("[ERROR]: " + firstCol + " is missing the final ';', ignoring.\n"); ignore=true; }
+                        }
+                        if (!ignore) { taxMap[firstCol] = secondCol; }
+                        if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
+                    }else {
+                        mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); control_pressed = true;
+                    }
                     pairDone = false; 
                 }
             }
@@ -1626,8 +1635,18 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
                 if (pairDone) { 
                     //are there confidence scores, if so remove them
                     if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);	}
-                    taxMap[firstCol] = secondCol;
-                    if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
+                    map<string, string>::iterator itTax = taxMap.find(firstCol);
+                    
+                    if(itTax == taxMap.end()) {
+                        bool ignore = false;
+                        if (secondCol != "") { if (secondCol[secondCol.length()-1] != ';') { mothurOut("[ERROR]: " + firstCol + " is missing the final ';', ignoring.\n"); ignore=true; }
+                        }
+                        if (!ignore) { taxMap[firstCol] = secondCol; }
+                        if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
+                    }else {
+                        mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); control_pressed = true;
+                    }
+
                     pairDone = false; 
                 }
             }