X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.cpp;h=00cd3f1948e009a86456e32bbcde2a40c6f889ac;hp=56856a9e4ac545627068eec2786dfdb4c476d1fb;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba

diff --git a/ccode.cpp b/ccode.cpp
index 56856a9..00cd3f1 100644
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -11,12 +11,13 @@
 #include "ignoregaps.h"
 #include "eachgapdist.h"
 
-
 //***************************************************************************************************************
 Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int numW, string o) : Chimera() {  
+ try {	
+	
 	fastafile = filename;  
 	outputDir = o; 
-	templateFileName = temp;  templateSeqs = readSeqs(temp);
+	templateFileName = temp;  templateSeqs = readSeqs(temp); 
 	setMask(mask);
 	filter = f;
 	window = win;
@@ -25,17 +26,22 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
 	distCalc = new eachGapDist();
 	decalc = new DeCalculator();
 	
-	mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
+	mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
 	
 	#ifdef USE_MPI
 		
-		char inFileName[mapInfo.length()];
+		//char* inFileName = new char[mapInfo.length()];
+		//memcpy(inFileName, mapInfo.c_str(), mapInfo.length());
+		
+		char inFileName[1024];
 		strcpy(inFileName, mapInfo.c_str());
 		
 		int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 
 		MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap);  //comm, filename, mode, info, filepointer
 		
+		//delete inFileName;
+
 		int pid;
 		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 		
@@ -44,19 +50,25 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
 			
 			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_shared(outMap, buf2, length, MPI_CHAR, &status);
+			delete buf2;
 		}
 	#else
 
 		ofstream out2;
-		openOutputFile(mapInfo, out2);
+		m->openOutputFile(mapInfo, out2);
 		
 		out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
 		out2.close();
 	#endif
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Ccode", "Ccode");
+		exit(1);
+	}
 }
 //***************************************************************************************************************
 Ccode::~Ccode() {
@@ -68,11 +80,11 @@ Ccode::~Ccode() {
 	#endif
 }	
 //***************************************************************************************************************
-int Ccode::print(ostream& out, ostream& outAcc) {
+Sequence Ccode::print(ostream& out, ostream& outAcc) {
 	try {
 		
 		ofstream out2;
-		openOutputFileAppend(mapInfo, out2);
+		m->openOutputFileAppend(mapInfo, out2);
 		
 		out2 << querySeq->getName() << endl;
 		for (it = spotMap.begin(); it!= spotMap.end(); it++) {
@@ -149,7 +161,7 @@ int Ccode::print(ostream& out, ostream& outAcc) {
 		//free memory
 		for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-		return results;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Ccode", "print");
@@ -158,7 +170,7 @@ int Ccode::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int Ccode::print(MPI_File& out, MPI_File& outAcc) {
+Sequence Ccode::print(MPI_File& out, MPI_File& outAcc) {
 	try {
 		
 		string outMapString = "";
@@ -235,27 +247,29 @@ int Ccode::print(MPI_File& out, MPI_File& outAcc) {
 		
 		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_shared(out, buf2, length, MPI_CHAR, &status);
-			
+		delete buf2;
+
 		if (results) {
 			m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
 			outAccString += querySeq->getName() + "\n";
 			
 			MPI_Status statusAcc;
 			length = outAccString.length();
-			char buf[length];
-			strcpy(buf, outAccString.c_str()); 
+			char* buf = new char[length];
+			memcpy(buf, outAccString.c_str(), length);
 				
 			MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
+			delete buf;
 		}
 
 		//free memory
 		for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-		return results;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Ccode", "print");
@@ -267,10 +281,13 @@ int Ccode::printMapping(string& output) {
 	try {
 			MPI_Status status;
 			int length = output.length();
-			char buf[length];
-			strcpy(buf, output.c_str()); 
+			char* buf = new char[length];
+			memcpy(buf, output.c_str(), length);
 				
 			MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
+			delete buf;
+			
+			return 0;
 
 	}
 	catch(exception& e) {