+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(it->second);
+ m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ container[parameter] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(it->second);
+ m->mothurOut("Unable to open " + it->second + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ container[parameter] = tryPath;
+ in2.close();
+ }
+ }
+
+
+
+ #ifdef USE_MPI
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+
+ int length = container[parameter].length();
+ MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&(container[parameter][0]), length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+
+ }
+ }else {
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+
+ int length;
+ MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ //recieve container
+ char* tempBuf = new char[length];
+ MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+
+ container[parameter] = tempBuf;
+ if (container[parameter].length() > length) { container[parameter] = container[parameter].substr(0, length); }
+ delete tempBuf;
+ }
+
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
+ return "not open";
+ }
+
+ //check phylip file to make sure its really phylip and not column
+ if ((it->first == "phylip") && (ableToOpen != 1)) {
+ ifstream inPhylip;
+ m->openInputFile(it->second, inPhylip);
+
+ string numTest, name;
+ inPhylip >> numTest >> name;
+ inPhylip.close();
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, aborting."); m->mothurOutEndLine(); return "not found"; }
+ }
+
+ //check for blank file
+ if (ableToOpen != 1) {
+ if (m->isBlank(container[parameter])) {
+ m->mothurOut("[ERROR]: " + container[parameter] + " is blank, aborting."); m->mothurOutEndLine(); return "not found";
+ }
+ }
+