//**********************************************************************************************************************
vector<string> ClassifyTreeCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptree);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptaxonomy);
- 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 pcutoff("cutoff", "Number", "", "51", "", "", "",false,true); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none","tree-summary",false,true,true); parameters.push_back(ptree);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none","",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff);
+ 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 ClassifyTreeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClassifyTreeCommand::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 == "tree") { outputFileName = "taxonomy.tre"; }
- else if (type == "summary") { outputFileName = "taxonomy.summary"; }
- 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, "ClassifyTreeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],taxonomy.summary"; } //makes file like: amazon.0.03.fasta
+ else if (type == "tree") { pattern = "[filename],taxonomy.tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClassifyTreeCommand::ClassifyTreeCommand(){
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(treefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
- string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
+ variables["[filename]"] = treeOutputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputTreeFileName = getOutputFileName("tree", variables);
//create a map from tree node index to names of descendants, save time later
map<int, map<string, set<string> > > nodeToDescendants; //node# -> (groupName -> groupMembers)