fixes while testing 1.33.0

[mothur.git] / ccode.cpp

diff --git a/ccode.cpp b/ccode.cpp
index e82018409013f59bc4ce9f80474e99d22e111f21..00cd3f1948e009a86456e32bbcde2a40c6f889ac 100644 (file)
--- 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;
@@ -63,6 +64,11 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
                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() {
@@ -74,7 +80,7 @@ Ccode::~Ccode() {
        #endif
 }      
 //***************************************************************************************************************
-Sequence* Ccode::print(ostream& out, ostream& outAcc) {
+Sequence Ccode::print(ostream& out, ostream& outAcc) {
        try {
                
                ofstream out2;
@@ -155,7 +161,7 @@ Sequence* Ccode::print(ostream& out, ostream& outAcc) {
                //free memory
                for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-               return NULL;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "Ccode", "print");
@@ -164,7 +170,7 @@ Sequence* Ccode::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-Sequence* Ccode::print(MPI_File& out, MPI_File& outAcc) {
+Sequence Ccode::print(MPI_File& out, MPI_File& outAcc) {
        try {
                
                string outMapString = "";
@@ -263,7 +269,7 @@ Sequence* Ccode::print(MPI_File& out, MPI_File& outAcc) {
                //free memory
                for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
 
-               return NULL;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "Ccode", "print");