if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); }
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
+ if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
if (taxonomyfile != "") { return true; }
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
+ if (biomfile != "") { return true; }
if (processors != "1") { return true; }
return hasCurrent;
accnosfile = "";
taxonomyfile = "";
flowfile = "";
+ biomfile = "";
processors = "1";
}
catch(exception& e) {
int numLines = 0;
if (ableToOpen == 0) { //you opened it
- while(char c = input.get()){
+ while(!input.eof()){
+ char c = input.get();
if(input.eof()) { break; }
else { output << c; if (c == '\n') {numLines++;} }
}
if (control_pressed) { break; }
string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
+ in >> firstCol; gobble(in);
+ in >> secondCol; gobble(in);
int num = getNumNames(secondCol);
exit(1);
}
}
+/***********************************************************************/
+string MothurOut::makeList(vector<string>& names) {
+ try {
+ string list = "";
+
+ if (names.size() == 0) { return list; }
+
+ for (int i = 0; i < names.size()-1; i++) { list += names[i] + ","; }
+
+ //get last name
+ list += names[names.size()-1];
+
+ return list;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "makeList");
+ exit(1);
+ }
+}
+
/***********************************************************************/
//This function parses the a string and puts peices in a vector
void MothurOut::splitAtComma(string& estim, vector<string>& container) {
exit(1);
}
}
+/***********************************************************************/
+//This function splits up the various option parameters
+void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
+ try {
+ prefix = suffix.substr(0,suffix.find_first_of(c));
+ if ((suffix.find_first_of(c)+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
+ suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
+ string space = " ";
+ while(suffix.at(0) == ' ')
+ suffix = suffix.substr(1, suffix.length());
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtComma");
+ exit(1);
+ }
+}
+
/***********************************************************************/
//This function splits up the various option parameters