- //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 == "sharedchao") { outputFileName = "shared.chao"; }
- else if (type == "sharedsobs") { outputFileName = "shared.sobs"; }
- else if (type == "sharedace") { outputFileName = "shared.ace"; }
- else if (type == "jabund") { outputFileName = "jabund"; }
- else if (type == "sorabund") { outputFileName = "sorabund"; }
- else if (type == "jclass") { outputFileName = "jclass"; }
- else if (type == "sorclass") { outputFileName = "sorclass"; }
- else if (type == "jest") { outputFileName = "jest"; }
- else if (type == "sorest") { outputFileName = "sorest"; }
- else if (type == "thetayc") { outputFileName = "thetayc"; }
- else if (type == "thetan") { outputFileName = "thetan"; }
- else if (type == "kstest") { outputFileName = "kstest"; }
- else if (type == "whittaker") { outputFileName = "whittaker"; }
- else if (type == "sharednseqs") { outputFileName = "shared.nseqs"; }
- else if (type == "ochiai") { outputFileName = "ochiai"; }
- else if (type == "anderberg") { outputFileName = "anderberg"; }
- else if (type == "kulczynski") { outputFileName = "kulczynski"; }
- else if (type == "kulczynskicody") { outputFileName = "kulczynskicody"; }
- else if (type == "lennon") { outputFileName = "lennon"; }
- else if (type == "morisitahorn") { outputFileName = "morisitahorn"; }
- else if (type == "braycurtis") { outputFileName = "braycurtis"; }
- else if (type == "odum") { outputFileName = "odum"; }
- else if (type == "canberra") { outputFileName = "canberra"; }
- else if (type == "structeuclidean") { outputFileName = "structeuclidean"; }
- else if (type == "structchord") { outputFileName = "structchord"; }
- else if (type == "hellinger") { outputFileName = "hellinger"; }
- else if (type == "manhattan") { outputFileName = "manhattan"; }
- else if (type == "structpearson") { outputFileName = "structpearson"; }
- else if (type == "soergel") { outputFileName = "soergel"; }
- else if (type == "spearman") { outputFileName = "spearman"; }
- else if (type == "structkulczynski") { outputFileName = "structkulczynski";}
- else if (type == "structchi2") { outputFileName = "structchi2"; }
- else if (type == "speciesprofile") { outputFileName = "speciesprofile"; }
- else if (type == "hamming") { outputFileName = "hamming"; }
- else if (type == "gower") { outputFileName = "gower"; }
- else if (type == "memchi2") { outputFileName = "memchi2"; }
- else if (type == "memchord") { outputFileName = "memchord"; }
- else if (type == "memeuclidean") { outputFileName = "memeuclidean"; }
- else if (type == "mempearson") { outputFileName = "mempearson"; }
- 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, "CollectSharedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "sharedchao") { pattern = "[filename],shared.chao"; }
+ else if (type == "sharedsobs") { pattern = "[filename],shared.sobs"; }
+ else if (type == "sharedace") { pattern = "[filename],shared.ace"; }
+ else if (type == "jabund") { pattern = "[filename],jabund"; }
+ else if (type == "sorabund") { pattern = "[filename],sorabund"; }
+ else if (type == "jclass") { pattern = "[filename],jclass"; }
+ else if (type == "sorclass") { pattern = "[filename],sorclass"; }
+ else if (type == "jest") { pattern = "[filename],jest"; }
+ else if (type == "sorest") { pattern = "[filename],sorest"; }
+ else if (type == "thetayc") { pattern = "[filename],thetayc"; }
+ else if (type == "thetan") { pattern = "[filename],thetan"; }
+ else if (type == "kstest") { pattern = "[filename],kstest"; }
+ else if (type == "whittaker") { pattern = "[filename],whittaker"; }
+ else if (type == "sharednseqs") { pattern = "[filename],shared.nseqs"; }
+ else if (type == "ochiai") { pattern = "[filename],ochiai"; }
+ else if (type == "anderberg") { pattern = "[filename],anderberg"; }
+ else if (type == "kulczynski") { pattern = "[filename],kulczynski"; }
+ else if (type == "kulczynskicody") { pattern = "[filename],kulczynskicody"; }
+ else if (type == "lennon") { pattern = "[filename],lennon"; }
+ else if (type == "morisitahorn") { pattern = "[filename],morisitahorn"; }
+ else if (type == "braycurtis") { pattern = "[filename],braycurtis"; }
+ else if (type == "odum") { pattern = "[filename],odum"; }
+ else if (type == "canberra") { pattern = "[filename],canberra"; }
+ else if (type == "structeuclidean") { pattern = "[filename],structeuclidean"; }
+ else if (type == "structchord") { pattern = "[filename],structchord"; }
+ else if (type == "hellinger") { pattern = "[filename],hellinger"; }
+ else if (type == "manhattan") { pattern = "[filename],manhattan"; }
+ else if (type == "structpearson") { pattern = "[filename],structpearson"; }
+ else if (type == "soergel") { pattern = "[filename],soergel"; }
+ else if (type == "spearman") { pattern = "[filename],spearman"; }
+ else if (type == "structkulczynski") { pattern = "[filename],structkulczynski";}
+ else if (type == "structchi2") { pattern = "[filename],structchi2"; }
+ else if (type == "speciesprofile") { pattern = "[filename],speciesprofile"; }
+ else if (type == "hamming") { pattern = "[filename],hamming"; }
+ else if (type == "gower") { pattern = "[filename],gower"; }
+ else if (type == "memchi2") { pattern = "[filename],memchi2"; }
+ else if (type == "memchord") { pattern = "[filename],memchord"; }
+ else if (type == "memeuclidean") { pattern = "[filename],memeuclidean"; }
+ else if (type == "mempearson") { pattern = "[filename],mempearson"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getOutputPattern");
+ exit(1);
+ }