X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.cpp;h=42b531282c5f020664277a9e907699a3bf227658;hp=e89277b12078c089688c9c1cba7f9abe734ea8bc;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index e89277b..42b5312 100644
--- a/chimeracheckrdp.cpp
+++ b/chimeracheckrdp.cpp
@@ -20,7 +20,7 @@ ChimeraCheckRDP::ChimeraCheckRDP(string filename, string temp, string n, bool s,
 		kmerSize = k;
 		outputDir = o; 
 		
-		templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0);
+		templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
 		m->mothurOutEndLine();
 		
 		kmer = new Kmer(kmerSize);
@@ -47,7 +47,7 @@ ChimeraCheckRDP::~ChimeraCheckRDP() {
 	}
 }	
 //***************************************************************************************************************
-int ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
+Sequence ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 	try {
 		
 		m->mothurOut("Processing: " + querySeq->getName()); m->mothurOutEndLine();
@@ -72,7 +72,7 @@ int ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 			}
 		}
 		
-		return 0;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -81,7 +81,7 @@ int ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
+Sequence ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 	try {
 		
 		cout << "Processing: " << querySeq->getName() << endl; 
@@ -115,7 +115,7 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 			}
 		}
 		
-		return 0;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -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();
@@ -432,7 +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;