X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.cpp;h=00cd3f1948e009a86456e32bbcde2a40c6f889ac;hp=c27644866c1f1d52c14a6f86b9f2002e9342d720;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=a61980e36d61937acccadc41be260165a1e389f4

diff --git a/ccode.cpp b/ccode.cpp
index c276448..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;
@@ -25,7 +26,7 @@ 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
 		
@@ -58,11 +59,16 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
 	#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() {
@@ -74,11 +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++) {
@@ -155,7 +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");
@@ -164,7 +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 = "";
@@ -263,7 +269,7 @@ int Ccode::print(MPI_File& out, MPI_File& 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");
@@ -280,6 +286,8 @@ int Ccode::printMapping(string& output) {
 				
 			MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
 			delete buf;
+			
+			return 0;
 
 	}
 	catch(exception& e) {