#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;
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() {