//**********************************************************************************************************************
vector<string> PhylotypeCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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 PhylotypeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PhylotypeCommand::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 == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- 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, "PhylotypeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[tag],list"; }
+ else if (type == "rabund") { pattern = "[filename],[tag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[tag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
PhylotypeCommand::PhylotypeCommand(){
if (m->control_pressed) { delete tree; return 0; }
string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
-
- ofstream outList;
- string outputListFile = fileroot + "tx." + getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = "tx";
+ ofstream outList;
+ string outputListFile = getOutputFileName("list",variables);
m->openOutputFile(outputListFile, outList);
ofstream outSabund;
- string outputSabundFile = fileroot + "tx." + getOutputFileNameTag("sabund");
+ string outputSabundFile = getOutputFileName("sabund",variables);
m->openOutputFile(outputSabundFile, outSabund);
ofstream outRabund;
- string outputRabundFile = fileroot + "tx." + getOutputFileNameTag("rabund");
+ string outputRabundFile = getOutputFileName("rabund",variables);
m->openOutputFile(outputRabundFile, outRabund);
outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
map<string, string>::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile
if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile
- else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1); }
+ else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
}else{ name += names[i] + ","; }
}
}
+
+ if (m->control_pressed) { break; }
+
name = name.substr(0, name.length()-1); //rip off extra ','
//add bin to list vector
if (name != "") { list.push_back(name); } //caused by unknown