X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.cpp;h=42b531282c5f020664277a9e907699a3bf227658;hp=51a3d9bbac0eaea545e1626682049db382a973ac;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index 51a3d9b..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; 
@@ -97,11 +97,12 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 		
 		MPI_Status status;
 		int length = outString.length();
-		char buf[length];
-		strcpy(buf, outString.c_str()); 
+		char* buf = new char[length];
+		memcpy(buf, outString.c_str(), length);
 				
 		MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
-		
+		delete buf;
+
 		if (svg) {
 			if (name != "") { //if user has specific names
 				map<string, string>::iterator it = names.find(querySeq->getName());
@@ -114,7 +115,7 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 			}
 		}
 		
-		return 0;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -261,22 +262,28 @@ void ChimeraCheckRDP::readName(string namefile) {
 		MPI_File inMPI;
 		MPI_Offset size;
 		MPI_Status status;
+
+		//char* inFileName = new char[namefile.length()];
+		//memcpy(inFileName, namefile.c_str(), namefile.length());
 		
-		char inFileName[namefile.length()];
+		char inFileName[1024];
 		strcpy(inFileName, namefile.c_str());
 
 		MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
 		MPI_File_get_size(inMPI, &size);
 
-		char buffer[size];
+		//delete inFileName;
+
+		char* buffer = new char[size];
 		MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 
 		string tempBuf = buffer;
 		if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 		istringstream iss (tempBuf,istringstream::in);
+		delete buffer;
 		
 		while(!iss.eof()) {
-			iss >> name; gobble(iss);
+			iss >> name; m->gobble(iss);
 			names[name] = name;
 		}
 	
@@ -285,10 +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();
@@ -308,25 +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++;	 }
 			}
 		}
 		
@@ -347,12 +355,17 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
 		
 		MPI_File outSVG;
 		int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+		//char* FileName = new char[file.length()];
+		//memcpy(FileName, file.c_str(), file.length());
 		
-		char FileName[file.length()];
+		char FileName[1024];
 		strcpy(FileName, file.c_str());
-		
+
 		MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outSVG);  //comm, filename, mode, info, filepointer
 		
+		//delete FileName;
+
 		int width = (info.size()*5) + 150;
 		
 		string outString = "";
@@ -398,10 +411,11 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
 		
 		MPI_Status status;
 		int length = outString.length();
-		char buf2[length];
-		strcpy(buf2, outString.c_str()); 
+		char* buf2 = new char[length];
+		memcpy(buf2, outString.c_str(), length);
 				
 		MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);
+		delete buf2;
 		
 		MPI_File_close(&outSVG);
 
@@ -418,7 +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;