X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fastamap.cpp;h=bf55493faece21cbd6c0043ac89149826c83c166;hp=95d3f3cfe34397f603aecca3dc62bd65dc38c634;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6

diff --git a/fastamap.cpp b/fastamap.cpp
index 95d3f3c..bf55493 100644
--- 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.
@@ -59,11 +64,13 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
 	m->openInputFile(oldNameFileName, oldNameFile);
 	
 	map<string,string> oldNameMap;
+	map<string, string>::iterator itName;
 	string name, list;
 	while(!oldNameFile.eof()){
 		if (m->control_pressed) { break; }
 		
-		oldNameFile >> name >> list;
+		oldNameFile >> name; m->gobble(oldNameFile);
+		oldNameFile >> list;
 		oldNameMap[name] = list;
 		m->gobble(oldNameFile);
 	}
@@ -82,6 +89,10 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
 			if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
 			else						{	sequence = currSeq.getUnaligned();	}
 			
+			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(); }
+			
 			seqmap[name] = sequence;  
 			map<string,group>::iterator it = data.find(sequence);
 			if (it == data.end()) { 	//it's unique.