X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequenceparser.cpp;h=fd94b246a43217cc9cbfa131bfe4cd672955e001;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=76c90c3f9eb7f2802276526c8491dee1d1ba3883;hpb=96f25c3c0f3ba2a1634094de146630dbc9ee0d03;p=mothur.git

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index 76c90c3..fd94b24 100644
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -7,7 +7,7 @@
  *
  */
 
-#include "sequenceParser.h"
+#include "sequenceparser.h"
 
 
 /************************************************************/
@@ -64,6 +64,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 		string first, second;
 		int countName = 0;
 		set<string> thisnames1;
+		
 		while(!inName.eof()) {
 			
 			if (m->control_pressed) { break; }
@@ -135,12 +136,14 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 		
 		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();
@@ -313,6 +316,7 @@ int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
 				}
 				
 			}else { 
+                //m->mothurOut("Group " + g +  " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
 				for (int i = 0; i < seqForThisGroup.size(); i++) {
 					
 					if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }