Adds numSeqs to return values in sequenceParser classes

mothur · d10ca55a160321874e2c273ee7918ee8eefcfbce · mothur-westcott committed Jan 10, 2017 · Jan 10, 2017 · d10ca55
1 parent 719e77e
commit d10ca55a160321874e2c273ee7918ee8eefcfbce
Unified Split

Showing with 11 additions and 6 deletions.

+4 −2 source/datastructures/sequencecountparser.cpp

+1 −1 source/datastructures/sequencecountparser.h

+5 −2 source/datastructures/sequenceparser.cpp

+1 −1 source/datastructures/sequenceparser.h
diff --git a/source/datastructures/sequencecountparser.cpp b/source/datastructures/sequencecountparser.cpp
@@ -204,7 +204,7 @@ vector<Sequence> SequenceCountParser::getSeqs(string g){
 	}
 }
 /************************************************************/
-int SequenceCountParser::getSeqs(string g, string filename, string tag, string tag2, bool uchimeFormat=false){
+int SequenceCountParser::getSeqs(string g, string filename, string tag, string tag2, long long& numSeqs, bool uchimeFormat=false){
 	try {
 		map<string, vector<Sequence> >::iterator it;
 		vector<Sequence> seqForThisGroup;
@@ -214,11 +214,13 @@ int SequenceCountParser::getSeqs(string g, string filename, string tag, string t
 		if(it == seqs.end()) {
 			m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 		}else {
-			
+
 			ofstream out;
 			m->openOutputFile(filename, out);
 			
 			seqForThisGroup = it->second;
+            
+            numSeqs = seqForThisGroup.size();
 			
 			if (uchimeFormat) {
 				// format should look like 
diff --git a/source/datastructures/sequencecountparser.h b/source/datastructures/sequencecountparser.h
@@ -38,7 +38,7 @@ class SequenceCountParser {
     vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
     map<string, int> getCountTable(string); //returns seqName -> numberOfRedundantSeqs for a specific group - the count file format, but each line is parsed by group.
     
-    int getSeqs(string, string, string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag (/ab= or ;size=), tag2(/ or ;)
+    int getSeqs(string, string, string, string, long long&, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag (/ab= or ;size=), tag2(/ or ;)
     int getCountTable(string, string); //print seqName -> numberRedundantSeqs for a specific group - group, filename
     
     map<string, string> getAllSeqsMap(); //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
diff --git a/source/datastructures/sequenceparser.cpp b/source/datastructures/sequenceparser.cpp
@@ -219,7 +219,7 @@ vector<Sequence> SequenceParser::getSeqs(string g){
 	}
 }
 /************************************************************/
-int SequenceParser::getSeqs(string g, string filename, string tag, string tag2, bool uchimeFormat=false){
+int SequenceParser::getSeqs(string g, string filename, string tag, string tag2, long long& numSeqs, bool uchimeFormat=false){
 	try {
 		map<string, vector<Sequence> >::iterator it;
 		vector<Sequence> seqForThisGroup;
@@ -229,11 +229,14 @@ int SequenceParser::getSeqs(string g, string filename, string tag, string tag2,
 		if(it == seqs.end()) {
 			m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
 		}else {
-			
+
 			ofstream out;
 			m->openOutputFile(filename, out);
 			
 			seqForThisGroup = it->second;
+            
+            numSeqs = seqForThisGroup.size();
+
 			
 			if (uchimeFormat) {
 				// format should look like 
diff --git a/source/datastructures/sequenceparser.h b/source/datastructures/sequenceparser.h
@@ -41,7 +41,7 @@ class SequenceParser {
 		vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
 		map<string, string> getNameMap(string); //returns seqName -> namesOfRedundantSeqs separated by commas for a specific group - the name file format, but each line is parsed by group.
 		
-		int getSeqs(string, string, string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag(/ab= or ;size=), tag2(/ or ;)
+		int getSeqs(string, string, string, string, long long&, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag(/ab= or ;size=), tag2(/ or ;)
 		int getNameMap(string, string); //print seqName -> namesOfRedundantSeqs separated by commas for a specific group - group, filename
 		
 		map<string, string> getAllSeqsMap(){ return allSeqsMap; }  //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing