X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckrdp.cpp;h=1840c382627f8a65ff9849919b5f95de4cf60db0;hb=257eaa172451ede9d63a0715f6cdb7336a52996b;hp=4c93c1b97c5c7edd2a583cb449cf34440be2a324;hpb=a61980e36d61937acccadc41be260165a1e389f4;p=mothur.git

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index 4c93c1b..1840c38 100644
--- a/chimeracheckrdp.cpp
+++ b/chimeracheckrdp.cpp
@@ -283,7 +283,7 @@ void ChimeraCheckRDP::readName(string namefile) {
 		delete buffer;
 		
 		while(!iss.eof()) {
-			iss >> name; gobble(iss);
+			iss >> name; m->gobble(iss);
 			names[name] = name;
 		}
 	
@@ -292,10 +292,10 @@ void ChimeraCheckRDP::readName(string namefile) {
 	#else	
 	
 		ifstream in;
-		openInputFile(namefile, in);
+		m->openInputFile(namefile, in);
 				
 		while (!in.eof()) {
-			in >> name; gobble(in);
+			in >> name; m->gobble(in);
 			names[name] = name;
 		}
 		in.close();
@@ -315,25 +315,26 @@ int ChimeraCheckRDP::calcKmers(map<int, int> query, map<int, int> subject) {
 	try{
 		
 		int common = 0;
-		map<int, int>::iterator small;
-		map<int, int>::iterator large;
 		
+		map<int, int>::iterator smallone;
+		map<int, int>::iterator largeone;
+
 		if (query.size() < subject.size()) {
 		
-			for (small = query.begin(); small != query.end(); small++) {
-				large = subject.find(small->first);
+			for (smallone = query.begin(); smallone != query.end(); smallone++) {
+				largeone = subject.find(smallone->first);
 				
 				//if you found it they have that kmer in common
-				if (large != subject.end()) {	common++;	}
+				if (largeone != subject.end()) {	common++;	}
 			}
 			
 		}else { 
 		 
-			for (small = subject.begin(); small != subject.end(); small++) {
-				large = query.find(small->first);
+			for (smallone = subject.begin(); smallone != subject.end(); smallone++) {
+				largeone = query.find(smallone->first);
 				
 				//if you found it they have that kmer in common
-				if (large != query.end()) {		common++;	 }
+				if (largeone != query.end()) {		common++;	 }
 			}
 		}
 		
@@ -431,7 +432,7 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
 		
 		string file = outputDir + querySeq->getName() + ".chimeracheck.svg";
 		ofstream outsvg;
-		openOutputFile(file, outsvg);
+		m->openOutputFile(file, outsvg);
 		
 		int width = (info.size()*5) + 150;