CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
helpString += "The name parameter allows you to enter your name file and is required if your distance file is in column format. \n";
helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 10.0. \n";
helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
- helpString += "The method allows you to specify what clustering algorythm you want to use, default=furthest, option furthest, nearest, or average. \n";
+ helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list. \n";
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { distfile = phylipfile; format = "phylip"; }
+ else { distfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not open") { abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { distfile = columnfile; format = "column"; }
+ else { distfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
- else { distfile = fastafile; splitmethod = "fasta"; }
+ else { distfile = fastafile; splitmethod = "fasta"; m->setFastaFile(fastafile); }
taxFile = validParameter.validFile(parameters, "taxonomy", true);
if (taxFile == "not open") { abort = true; }
else if (taxFile == "not found") { taxFile = ""; }
+ else { m->setTaxonomyFile(taxFile); }
if ((phylipfile == "") && (columnfile == "") && (fastafile == "")) {
//is there are current file available for either of these?
length = temp.length();
convert(temp, precision);
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; }
+ temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
hard = m->isTrue(temp);
temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
temp = validParameter.validFile(parameters, "taxlevel", false); if (temp == "not found") { temp = "1"; }
convert(temp, taxLevelCutoff);
- method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "furthest"; }
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "average"; }
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }