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 (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
calc = validParameter.validFile(parameters, "calc", false);
string temp;
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
- convert(temp, precision);
+ m->mothurConvert(temp, precision);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
//if the user changes the output directory command factory will send this info to us in the output parameter
//create treemap class from groupmap for tree class to use
tmap = new TreeMap();
- tmap->makeSim(m->namesOfGroups);
+ tmap->makeSim(m->getAllGroups());
//clear globaldatas old tree names if any
m->Treenames.clear();
//fills globaldatas tree names
- m->Treenames = m->Groups;
+ m->Treenames = m->getGroups();
if (m->control_pressed) { return 0; }
//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;
tmap->makeSim(list);
- m->Groups = tmap->namesOfGroups;
+ vector<string> namesGroups = tmap->getNamesOfGroups();
+ m->setGroups(namesGroups);
//clear globaldatas old tree names if any
m->Treenames.clear();
//fills globaldatas tree names
- m->Treenames = m->Groups;
+ m->Treenames = m->getGroups();
//used in tree constructor
m->runParse = false;
}
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
//set tree file as new current treefile
string current = "";
//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;