added pipeline commands which involved change to command factory and command class...

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 95d3f3cfe34397f603aecca3dc62bd65dc38c634..25860e1a7b22bb9f20fca7ff9aa77a884a09827a 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -19,7 +19,9 @@ void FastaMap::readFastaFile(string inFileName) {
                string name, sequence, line;
                sequence = "";
                string temp;
-
+               map<string, string>::iterator itName;
+               
+               
                while(!in.eof()){
                        if (m->control_pressed) { break; }
                        
@@ -30,7 +32,10 @@ void FastaMap::readFastaFile(string inFileName) {
                                if(currSeq.getIsAligned())      {       sequence = currSeq.getAligned();        }
                                else                                            {       sequence = currSeq.getUnaligned();      }
                                
-                               seqmap[name] = sequence;  
+                               itName = seqmap.find(name);
+                               if (itName == seqmap.end()) { seqmap[name] = sequence;  }
+                               else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+                               
                                map<string,group>::iterator it = data.find(sequence);
                                if (it == data.end()) {         //it's unique.
                                        data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.