//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string PreClusterCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PreClusterCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //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 == "fasta") { outputFileName = "precluster" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "precluster.names"; }
- else if (type == "count") { outputFileName = "precluster.count_table"; }
- else if (type == "map") { outputFileName = "precluster.map"; }
- 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, "PreClusterCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],precluster,[extension]"; }
+ else if (type == "name") { pattern = "[filename],precluster.names"; }
+ else if (type == "count") { pattern = "[filename],precluster.count_table"; }
+ else if (type == "map") { pattern = "[filename],precluster.map"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
PreClusterCommand::PreClusterCommand(){
int start = time(NULL);
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
- string newNamesFile = fileroot + getOutputFileNameTag("name");
- string newCountFile = fileroot + getOutputFileNameTag("count");
- string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ string newNamesFile = getOutputFileName("name",variables);
+ string newCountFile = getOutputFileName("count",variables);
+ string newMapFile = getOutputFileName("map",variables); //add group name if by group
+ variables["[extension]"] = m->getExtension(fastafile);
+ string newFastaFile = getOutputFileName("fasta", variables);
outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
if (countfile == "") { outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); }
else { outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile); }