phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputfile = phylipfile; format = "phylip"; }
+ else { inputfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not open") { columnfile = ""; abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { inputfile = columnfile; format = "column"; }
+ else { inputfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { inputfile = sharedfile; format = "sharedfile"; }
+ else { inputfile = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
//is there are current file available for either of these?
if (calc == "default") { calc = "jclass-thetayc"; }
}
m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
string temp;
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
//create tree file
makeSimsShared();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}else{
//read in dist file
filename = inputfile;
//delete tree
delete t;
- if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
+ if (m->control_pressed) { m->mothurRemove(outputFile); outputNames.pop_back(); return 1; }
return 0;
if (m->control_pressed) { return 1; }
//save values in similarity matrix
- simMatrix[k][l] = data[0];
- simMatrix[l][k] = data[0];
+ simMatrix[k][l] = -(data[0]-1.0);
+ simMatrix[l][k] = -(data[0]-1.0);
}
}
}