types.insert("tree");
types.insert("flow");
types.insert("biom");
+ types.insert("counttable");
types.insert("processors");
return types;
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
+ if (counttablefile != "") { mothurOut("counttable=" + counttablefile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
if (biomfile != "") { return true; }
+ if (counttablefile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
taxonomyfile = "";
flowfile = "";
biomfile = "";
+ counttablefile = "";
processors = "1";
}
catch(exception& e) {
positions.push_back(0);
while(!in.eof()){
- //unsigned long long lastpos = in.tellg();
- //input = getline(in);
- //if (input.length() != 0) {
- //unsigned long long pos = in.tellg();
- //if (pos != -1) { positions.push_back(pos - input.length() - 1); }
- //else { positions.push_back(lastpos); }
- //}
- //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
-
-
//getline counting reads
char d = in.get(); count++;
while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) {
for (int i = 0; i < size; i++) {
if (!isspace(buffer[i])) { rest += buffer[i]; }
else {
- pieces.push_back(rest); rest = "";
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
while (i < size) { //gobble white space
if (isspace(buffer[i])) { i++; }
else { rest = buffer[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
for (int i = 0; i < input.length(); i++) {
if (!isspace(input[i])) { rest += input[i]; }
else {
- pieces.push_back(rest); rest = "";
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
while (i < input.length()) { //gobble white space
if (isspace(input[i])) { i++; }
else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;