Sequence::Sequence(istringstream& fastaString){
try {
m = MothurOut::getInstance();
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid);
- cout << pid << " after mothur instance " << &name << endl;
+
initialize();
- cout << "after mothur initialize" << endl;
fastaString >> name;
- cout << pid << " after name " << name << endl;
name = name.substr(1);
-
string sequence;
-cout << pid << " name = " << name << endl;
+
//read comments
while ((name[0] == '#') && fastaString) {
while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
name = "";
break;
}
- cout << pid << "in while comment" << endl;
}
- cout << pid << "after mothur comment" << endl;
- while (!fastaString.eof()) { char c = fastaString.get(); cout << pid << " char = " << int(c) << endl; if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- cout << pid << " after mothur name" << endl;
+
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
sequence = getSequenceString(fastaString);
- cout << pid << " after mothur sequence" << endl;
setAligned(sequence);
//setUnaligned removes any gap characters for us
setUnaligned(sequence);
try {
char letter;
string sequence = "";
-int pid;
-MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
while(!fastaFile.eof()){
letter= fastaFile.get();
- cout << pid << '\t' << letter << endl;
+
if(letter == '>'){
fastaFile.putback(letter);
break;
aligned = temp;
}
-
+#ifdef USE_MPI
//********************************************************************************************************************
+int Sequence::MPISend(int receiver) {
+ try {
+
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "MPISend");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int Sequence::MPIRecv(int sender) {
+ try {
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "MPIRecv");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/