X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.cpp;h=42b531282c5f020664277a9e907699a3bf227658;hp=cb101b6af9dd8d0c412a69067597d9a022f2e623;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=2bbb7273d4bf5209f098c764551c6e072d60df36

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index cb101b6..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; 
@@ -97,7 +97,7 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
 		
 		MPI_Status status;
 		int length = outString.length();
-		char* buf = new char[length];
+		char* buf = new char[length];
 		memcpy(buf, outString.c_str(), length);
 				
 		MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
@@ -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");
@@ -263,13 +263,16 @@ void ChimeraCheckRDP::readName(string namefile) {
 		MPI_Offset size;
 		MPI_Status status;
 
-		char* inFileName = new char[namefile.length()];
-		memcpy(inFileName, namefile.c_str(), namefile.length());
+		//char* inFileName = new char[namefile.length()];
+		//memcpy(inFileName, namefile.c_str(), 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);
 
-		delete inFileName;
+		//delete inFileName;
 
 		char* buffer = new char[size];
 		MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
@@ -280,7 +283,7 @@ void ChimeraCheckRDP::readName(string namefile) {
 		delete buffer;
 		
 		while(!iss.eof()) {
-			iss >> name; gobble(iss);
+			iss >> name; m->gobble(iss);
 			names[name] = name;
 		}
 	
@@ -289,10 +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();
@@ -312,25 +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++;	 }
 			}
 		}
 		
@@ -352,12 +356,15 @@ 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 = new char[file.length()];
+		//memcpy(FileName, file.c_str(), 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;
+		//delete FileName;
 
 		int width = (info.size()*5) + 150;
 		
@@ -404,7 +411,7 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
 		
 		MPI_Status status;
 		int length = outString.length();
-		char* buf2 = new char[length];
+		char* buf2 = new char[length];
 		memcpy(buf2, outString.c_str(), length);
 				
 		MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);
@@ -425,7 +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;