*
*/
-#include "sequenceParser.h"
+#include "sequenceparser.h"
/************************************************************/
string first, second;
int countName = 0;
+ set<string> thisnames1;
+
while(!inName.eof()) {
if (m->control_pressed) { break; }
it = splitMap.find(group);
if (it != splitMap.end()) { //adding seqs to this group
(it->second) += "," + names[i];
+ thisnames1.insert(names[i]);
countName++;
}else { //first sighting of this group
splitMap[group] = names[i];
countName++;
+ thisnames1.insert(names[i]);
//is this seq in the fasta file?
if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
if (error == 1) { m->control_pressed = true; }
if (countName != (groupMap->getNumSeqs())) {
+ vector<string> groupseqsnames = groupMap->getNamesSeqs();
+
+ for (int i = 0; i < groupseqsnames.size(); i++) {
+ set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
+ if (itnamesfile == thisnames1.end()){
+ cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
+ }
+ }
+
m->mothurOutEndLine();
m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
m->mothurOutEndLine();