*/
#include "matrixoutputcommand.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
-
+#include "sharedjackknife.h"
+#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
//**********************************************************************************************************************
vector<string> MatrixOutputCommand::getValidParameters(){
try {
//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
}
MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Groups.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
int i;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
- if (Estimators[i] == "jabund") {
+ if (Estimators[i] == "sharedsobs") {
+ matrixCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ matrixCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ matrixCalculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
matrixCalculators.push_back(new JAbund());
}else if (Estimators[i] == "sorabund") {
matrixCalculators.push_back(new SorAbund());
matrixCalculators.push_back(new ThetaYC());
}else if (Estimators[i] == "thetan") {
matrixCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ matrixCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ matrixCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ matrixCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ matrixCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ matrixCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ matrixCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ matrixCalculators.push_back(new Lennon());
}else if (Estimators[i] == "morisitahorn") {
matrixCalculators.push_back(new MorHorn());
}else if (Estimators[i] == "braycurtis") {
matrixCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ matrixCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ matrixCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ matrixCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ matrixCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ matrixCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ matrixCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ matrixCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ matrixCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ matrixCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ matrixCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ matrixCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ matrixCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ matrixCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ matrixCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ matrixCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ matrixCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ matrixCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ matrixCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ matrixCalculators.push_back(new MemPearson());
}
}
}
int MatrixOutputCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the users entered no valid calculators don't execute command
if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
//reset groups parameter
globaldata->Groups.clear();
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
//add new pair of sharedrabunds
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+ //if this calc needs all groups to calculate the pair load all groups
+ if (matrixCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+ }
+ }
+
data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
projects / mothur.git / blobdiff