exit(1);
}
}
+//**********************************************************************************************************************
+string RareFactCommand::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 == "rarefaction") { outputFileName = "rarefaction"; }
+ else if (type == "r_chao") { outputFileName = "r_chao"; }
+ else if (type == "r_ace") { outputFileName = "r_ace"; }
+ else if (type == "r_jack") { outputFileName = "r_jack"; }
+ else if (type == "r_shannon") { outputFileName = "r_shannon"; }
+ else if (type == "r_shannoneven") { outputFileName = "r_shannoneven"; }
+ else if (type == "r_smithwilson") { outputFileName = "r_smithwilson"; }
+ else if (type == "r_npshannon") { outputFileName = "r_npshannon"; }
+ else if (type == "r_simpson") { outputFileName = "r_simpson"; }
+ else if (type == "r_simpsoneven") { outputFileName = "r_simpsoneven"; }
+ else if (type == "r_invsimpson") { outputFileName = "r_invsimpson"; }
+ else if (type == "r_bootstrap") { outputFileName = "r_bootstrap"; }
+ else if (type == "r_coverage") { outputFileName = "r_coverage"; }
+ else if (type == "r_nseqs") { outputFileName = "r_nseqs"; }
+ 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, "RareFactCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ map<string, set<int> > labelToEnds;
if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
- else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
-
- if (m->control_pressed) { return 0; }
+ else { inputFileNames = parseSharedFile(sharedfile, labelToEnds); format = "rabund"; }
+
+ if (m->control_pressed) { return 0; }
map<int, string> file2Group; //index in outputNames[i] -> group
for (int p = 0; p < inputFileNames.size(); p++) {
for (i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
- rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
- outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
+ rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("rarefaction"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("rarefaction")); outputTypes["rarefaction"].push_back(fileNameRoot+getOutputFileNameTag("rarefaction"));
}else if (Estimators[i] == "chao") {
- rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
- outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_chao"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_chao")); outputTypes["r_chao"].push_back(fileNameRoot+getOutputFileNameTag("r_chao"));
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
- rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
- outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
+ rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_ace"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_ace")); outputTypes["r_ace"].push_back(fileNameRoot+getOutputFileNameTag("r_ace"));
}else if (Estimators[i] == "jack") {
- rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
- outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_jack"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_jack")); outputTypes["r_jack"].push_back(fileNameRoot+getOutputFileNameTag("r_jack"));
}else if (Estimators[i] == "shannon") {
- rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
- outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
+ rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_shannon"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_shannon")); outputTypes["r_shannon"].push_back(fileNameRoot+getOutputFileNameTag("r_shannon"));
}else if (Estimators[i] == "shannoneven") {
- rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
- outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
+ rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_shannoneven"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_shannoneven")); outputTypes["r_shannoneven"].push_back(fileNameRoot+getOutputFileNameTag("r_shannoneven"));
}else if (Estimators[i] == "heip") {
- rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
- outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
+ rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_heip"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_heip")); outputTypes["r_heip"].push_back(fileNameRoot+getOutputFileNameTag("r_heip"));
}else if (Estimators[i] == "smithwilson") {
- rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
- outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
+ rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_smithwilson"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_smithwilson")); outputTypes["r_smithwilson"].push_back(fileNameRoot+getOutputFileNameTag("r_smithwilson"));
}else if (Estimators[i] == "npshannon") {
- rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
- outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_npshannon"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_npshannon")); outputTypes["r_npshannon"].push_back(fileNameRoot+getOutputFileNameTag("r_npshannon"));
}else if (Estimators[i] == "simpson") {
- rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
- outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
+ rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_simpson"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_simpson")); outputTypes["r_simpson"].push_back(fileNameRoot+getOutputFileNameTag("r_simpson"));
}else if (Estimators[i] == "simpsoneven") {
- rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
- outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
+ rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_simpsoneven"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_simpsoneven")); outputTypes["r_simpsoneven"].push_back(fileNameRoot+getOutputFileNameTag("r_simpsoneven"));
}else if (Estimators[i] == "invsimpson") {
- rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
- outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
+ rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_invsimpson"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_invsimpson")); outputTypes["r_invsimpson"].push_back(fileNameRoot+getOutputFileNameTag("r_invsimpson"));
}else if (Estimators[i] == "bootstrap") {
- rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
- outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_bootstrap"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_bootstrap")); outputTypes["r_bootstrap"].push_back(fileNameRoot+getOutputFileNameTag("r_bootstrap"));
}else if (Estimators[i] == "coverage") {
- rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
- outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
+ rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_coverage"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_coverage")); outputTypes["r_coverage"].push_back(fileNameRoot+getOutputFileNameTag("r_coverage"));
}else if (Estimators[i] == "nseqs") {
- rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
- outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
+ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_nseqs"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_nseqs")); outputTypes["r_nseqs"].push_back(fileNameRoot+getOutputFileNameTag("r_nseqs"));
}
if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
}
if(allLines == 1 || labels.count(order->getLabel()) == 1){
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- rCurve = new Rarefact(order, rDisplays, processors);
+ map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+ set<int> ends;
+ if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+ rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
order = (input->getOrderVector(lastLabel));
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- rCurve = new Rarefact(order, rDisplays, processors);
+ map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+ set<int> ends;
+ if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+ rCurve = new Rarefact(order, rDisplays, processors, ends);
+
rCurve->getCurve(freq, nIters);
delete rCurve;
order = (input->getOrderVector(lastLabel));
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- rCurve = new Rarefact(order, rDisplays, processors);
+ map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+ set<int> ends;
+ if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+ rCurve = new Rarefact(order, rDisplays, processors, ends);
+
rCurve->getCurve(freq, nIters);
delete rCurve;
}
}
//**********************************************************************************************************************
-vector<string> RareFactCommand::parseSharedFile(string filename) {
+vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
try {
vector<string> filenames;
m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
rav.print(*(filehandles[lookup[i]->getGroup()]));
(*(filehandles[lookup[i]->getGroup()])).close();
+ label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs());
}
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
projects / mothur.git / blobdiff