helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
- helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
- helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+ helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+ helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
else {
userGroups = "unique." + groups;
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
else {
userGroups = groups;
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
unique = false;
}
if (m->control_pressed) { delete groupMap; return 0; }
if (Groups.size() == 0) {
- Groups = groupMap->namesOfGroups;
+ Groups = groupMap->getNamesOfGroups();
//make string for outputfile name
userGroups = "unique.";
}else{
//sanity check for group names
SharedUtil util;
- util.setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesOfGroups);
+ groupMap->setNamesOfGroups(namesOfGroups);
}
//put groups in map to find easier
if (m->control_pressed) {
if (lastlist != NULL) { delete lastlist; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete groupMap; return 0;
}
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
if (lastlist != NULL) { delete lastlist; }
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; }
//set fasta file as new current fastafile
string current = "";
//go through each bin, find out if shared
for (int i = 0; i < shared->getNumBins(); i++) {
- if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+ if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
bool uniqueOTU = true;
outNames.close();
if (!wroteSomething) {
- remove(outputFileNames.c_str());
+ m->mothurRemove(outputFileNames);
string outputString = "\t" + toString(num) + " - No otus shared by groups";
string groupString = "";