#include "memchord.h"
#include "memeuclidean.h"
#include "mempearson.h"
+#include "sharedjsd.h"
+#include "sharedrjsd.h"
//**********************************************************************************************************************
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
- CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
else if (type == "memchord") { pattern = "[filename],memchord"; }
else if (type == "memeuclidean") { pattern = "[filename],memeuclidean"; }
else if (type == "mempearson") { pattern = "[filename],mempearson"; }
+ else if (type == "jsd") { pattern = "[filename],jsd"; }
+ else if (type == "rjsd") { pattern = "[filename],rjsd"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
outputTypes["memchord"] = tempOutNames;
outputTypes["memeuclidean"] = tempOutNames;
outputTypes["mempearson"] = tempOutNames;
+ outputTypes["jsd"] = tempOutNames;
+ outputTypes["rjsd"] = tempOutNames;
}
catch(exception& e) {
outputTypes["memchord"] = tempOutNames;
outputTypes["memeuclidean"] = tempOutNames;
outputTypes["mempearson"] = tempOutNames;
+ outputTypes["jsd"] = tempOutNames;
+ outputTypes["rjsd"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
}else if (Estimators[i] == "mempearson") {
cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(getOutputFileName("mempearson", variables))));
outputNames.push_back(getOutputFileName("mempearson", variables)); outputTypes["mempearson"].push_back(getOutputFileName("mempearson", variables));
+ }else if (Estimators[i] == "jsd") {
+ cDisplays.push_back(new CollectDisplay(new JSD(), new SharedOneColumnFile(getOutputFileName("jsd", variables))));
+ outputNames.push_back(getOutputFileName("jsd", variables)); outputTypes["jsd"].push_back(getOutputFileName("jsd", variables));
+ }else if (Estimators[i] == "rjsd") {
+ cDisplays.push_back(new CollectDisplay(new RJSD(), new SharedOneColumnFile(getOutputFileName("rjsd", variables))));
+ outputNames.push_back(getOutputFileName("rjsd", variables)); outputTypes["rjsd"].push_back(getOutputFileName("rjsd", variables));
}
+
}
}