single["jack"] = "jack";
single["shannon"] = "shannon";
single["npshannon"] = "npshannon";
+ single["shannoneven"] = "shannoneven";
+ single["smithwilson"] = "smithwilson";
+ single["heip"] = "heip";
single["simpson"] = "simpson";
+ single["simpsoneven"] = "simpsoneven";
+ single["invsimpson"] = "invsimpson";
single["bergerparker"] = "bergerparker";
single["bootstrap"] = "bootstrap";
single["geometric"] = "geometric";
- single["logseries"] = "logseries";
+ single["logseries"] = "logseries";
single["qstat"] = "qstat";
single["bstick"] = "bstick";
single["goodscoverage"] = "goodscoverage";
shared["lennon"] = "lennon";
shared["morisitahorn"] = "morisitahorn";
shared["braycurtis"] = "braycurtis";
+ shared["odum"] = "odum";
+ shared["canberra"] = "canberra";
+ shared["structeuclidean"] = "structeuclidean";
+ shared["structchord"] = "structchord";
+ shared["hellinger"] = "hellinger";
+ shared["manhattan"] = "manhattan";
+ shared["structpearson"] = "structpearson";
+ shared["soergel"] = "soergel";
+ shared["spearman"] = "spearman";
+ shared["structkulczynski"] = "structkulczynski";
+ shared["structchi2"] = "structchi2";
+ shared["speciesprofile"] = "speciesprofile";
+ shared["hamming"] = "hamming";
+ shared["gower"] = "gower";
+ shared["memchi2"] = "memchi2";
+ shared["memchord"] = "memchord";
+ shared["memeuclidean"] = "memeuclidean";
+ shared["mempearson"] = "mempearson";
shared["default"] = "default";
}
catch(exception& e) {
rarefaction["ace"] = "ace";
rarefaction["jack"] = "jack";
rarefaction["shannon"] = "shannon";
+ rarefaction["smithwilson"] = "smithwilson";
+ rarefaction["heip"] = "heip";
rarefaction["npshannon"] = "npshannon";
+ rarefaction["shannoneven"] = "shannoneven";
rarefaction["simpson"] = "simpson";
+ rarefaction["invsimpson"] = "invsimpson";
+ rarefaction["simpsoneven"] = "simpsoneven";
rarefaction["bootstrap"] = "bootstrap";
rarefaction["nseqs"] = "nseqs";
rarefaction["coverage"] = "coverage";
summary["ace"] = "ace";
summary["jack"] = "jack";
summary["shannon"] = "shannon";
+ summary["heip"] = "heip";
+ summary["shannoneven"] = "shannoneven";
+ summary["smithwilson"] = "smithwilson";
+ summary["invsimpson"] = "invsimpson";
summary["npshannon"] = "npshannon";
summary["simpson"] = "simpson";
+ summary["simpsoneven"] = "simpsoneven";
summary["bergerparker"] = "bergerparker";
summary["geometric"] = "geometric";
summary["bootstrap"] = "bootstrap";
sharedsummary["sharedchao"] = "sharedchao";
sharedsummary["sharedace"] = "sharedace";
sharedsummary["jabund"] = "jabund";
- sharedsummary["sorabund"] = "sorabund";
+ sharedsummary["sorabund"] = "sorabund";
sharedsummary["jclass"] = "jclass";
sharedsummary["sorclass"] = "sorclass";
sharedsummary["jest"] = "jest";
sharedsummary["lennon"] = "lennon";
sharedsummary["morisitahorn"] = "morisitahorn";
sharedsummary["braycurtis"] = "braycurtis";
+ sharedsummary["odum"] = "odum";
+ sharedsummary["canberra"] = "canberra";
+ sharedsummary["structeuclidean"] = "structeuclidean";
+ sharedsummary["structchord"] = "structchord";
+ sharedsummary["hellinger"] = "hellinger";
+ sharedsummary["manhattan"] = "manhattan";
+ sharedsummary["structpearson"] = "structpearson";
+ sharedsummary["structkulczynski"] = "structkulczynski";
+ sharedsummary["structchi2"] = "structchi2";
+ sharedsummary["soergel"] = "soergel";
+ sharedsummary["spearman"] = "spearman";
+ sharedsummary["speciesprofile"] = "speciesprofile";
+ sharedsummary["hamming"] = "hamming";
+ sharedsummary["gower"] = "gower";
+ sharedsummary["memchi2"] = "memchi2";
+ sharedsummary["memchord"] = "memchord";
+ sharedsummary["memeuclidean"] = "memeuclidean";
+ sharedsummary["mempearson"] = "mempearson";
sharedsummary["default"] = "default";
}
catch(exception& e) {
/********************************************************************/
void ValidCalculators::initialTreeGroups() {
try {
+ treegroup["sharedsobs"] = "sharedsobs";
+ treegroup["sharedchao"] = "sharedchao";
+ treegroup["sharedace"] = "sharedace";
treegroup["jabund"] = "jabund";
treegroup["sorabund"] = "sorabund";
treegroup["jclass"] = "jclass";
treegroup["sorest"] = "sorest";
treegroup["thetayc"] = "thetayc";
treegroup["thetan"] = "thetan";
+ treegroup["kstest"] = "kstest";
+ treegroup["whittaker"] = "whittaker";
+ treegroup["sharednseqs"] = "sharednseqs";
+ treegroup["ochiai"] = "ochiai";
+ treegroup["anderberg"] = "anderberg";
+ treegroup["kulczynski"] = "kulczynski";
+ treegroup["kulczynskicody"] = "kulczynskicody";
+ treegroup["lennon"] = "lennon";
treegroup["morisitahorn"] = "morisitahorn";
treegroup["braycurtis"] = "braycurtis";
+ treegroup["odum"] = "odum";
+ treegroup["canberra"] = "canberra";
+ treegroup["structeuclidean"] = "structeuclidean";
+ treegroup["structchord"] = "structchord";
+ treegroup["hellinger"] = "hellinger";
+ treegroup["manhattan"] = "manhattan";
+ treegroup["structpearson"] = "structpearson";
+ treegroup["structkulczynski"] = "structkulczynski";
+ treegroup["structchi2"] = "structchi2";
+ treegroup["soergel"] = "soergel";
+ treegroup["spearman"] = "spearman";
+ treegroup["speciesprofile"] = "speciesprofile";
+ treegroup["hamming"] = "hamming";
+ treegroup["gower"] = "gower";
+ treegroup["memchi2"] = "memchi2";
+ treegroup["memchord"] = "memchord";
+ treegroup["memeuclidean"] = "memeuclidean";
+ treegroup["mempearson"] = "mempearson";
+
}
catch(exception& e) {
m->errorOut(e, "ValidCalculator", "initialTreeGroups");
/********************************************************************/
void ValidCalculators::initialMatrix() {
try {
- matrix["jabund"] = "jabund";
+ matrix["sharedsobs"] = "sharedsobs";
+ matrix["sharedchao"] = "sharedchao";
+ matrix["sharedace"] = "sharedace";
+ matrix["jabund"] = "jabund";
matrix["sorabund"] = "sorabund";
- matrix["jclass"] = "jclass";
+ matrix["jclass"] = "jclass";
matrix["sorclass"] = "sorclass";
matrix["jest"] = "jest";
- matrix["sorest"] = "sorest";
+ matrix["sorest"] = "sorest";
matrix["thetayc"] = "thetayc";
- matrix["thetan"] = "thetan";
+ matrix["thetan"] = "thetan";
+ matrix["kstest"] = "kstest";
+ matrix["whittaker"] = "whittaker";
+ matrix["sharednseqs"] = "sharednseqs";
+ matrix["ochiai"] = "ochiai";
+ matrix["anderberg"] = "anderberg";
+ matrix["kulczynski"] = "kulczynski";
+ matrix["kulczynskicody"] = "kulczynskicody";
+ matrix["lennon"] = "lennon";
matrix["morisitahorn"] = "morisitahorn";
- matrix["braycurtis"] = "braycurtis";
+ matrix["braycurtis"] = "braycurtis";
+ matrix["odum"] = "odum";
+ matrix["canberra"] = "canberra";
+ matrix["structeuclidean"] = "structeuclidean";
+ matrix["structchord"] = "structchord";
+ matrix["hellinger"] = "hellinger";
+ matrix["manhattan"] = "manhattan";
+ matrix["structpearson"] = "structpearson";
+ matrix["structkulczynski"] = "structkulczynski";
+ matrix["structchi2"] = "structchi2";
+ matrix["soergel"] = "soergel";
+ matrix["spearman"] = "spearman";
+ matrix["speciesprofile"] = "speciesprofile";
+ matrix["hamming"] = "hamming";
+ matrix["gower"] = "gower";
+ matrix["memchi2"] = "memchi2";
+ matrix["memchord"] = "memchord";
+ matrix["memeuclidean"] = "memeuclidean";
+ matrix["mempearson"] = "mempearson";
+
}
catch(exception& e) {
m->errorOut(e, "ValidCalculator", "initialMatrix");