exit(1);
}
}
-
+//**********************************************************************************************************************
+string ClearcutCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "tree") { outputFileName = "tre"; }
+ else if (type == "matrixout") { outputFileName = ""; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ClearcutCommand::ClearcutCommand(){
try {
//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();
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
- else { inputFile = fastafile; }
+ else { inputFile = fastafile; m->setFastaFile(fastafile); }
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputFile = phylipfile; }
+ else { inputFile = phylipfile; m->setPhylipFile(phylipfile); }
if ((phylipfile == "") && (fastafile == "")) {
//is there are current file available for either of these?
//give priority to phylip, then fasta
phylipfile = m->getPhylipFile();
- if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ if (phylipfile != "") { inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else {
fastafile = m->getFastaFile();
- if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ if (fastafile != "") { inputFile = fastafile; m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine();
abort = true;
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filename
- string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+ string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
vector<char*> cPara;