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A7DA2059113FECD400BF472F /* geom.h */,
A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
A7DA206D113FECD400BF472F /* goodscoverage.h */,
+ A7BB565F12BBB0480041F26F /* gower.h */,
+ A7BB566012BBB0480041F26F /* gower.cpp */,
A7460B7812B9444800866BB6 /* hamming.h */,
A7460B7912B9444800866BB6 /* hamming.cpp */,
7E5B2917121FF53C0005339C /* heip.h */,
A7DA2094113FECD400BF472F /* logsd.h */,
A7460A9812B9061B00866BB6 /* manhattan.h */,
A7460A9912B9061B00866BB6 /* manhattan.cpp */,
+ A7BB56B812BBB5690041F26F /* memchi2.h */,
+ A7BB56B912BBB5690041F26F /* memchi2.cpp */,
+ A7BB56EB12BBBFDF0041F26F /* memchord.h */,
+ A7BB56EC12BBBFDF0041F26F /* memchord.cpp */,
+ A7BB570B12BBC2880041F26F /* memeuclidean.h */,
+ A7BB570C12BBC2880041F26F /* memeuclidean.cpp */,
+ A7BB573712BBC43B0041F26F /* mempearson.h */,
+ A7BB573812BBC43B0041F26F /* mempearson.cpp */,
A7DA20AE113FECD400BF472F /* npshannon.cpp */,
A7DA20AF113FECD400BF472F /* npshannon.h */,
A7DA20B0113FECD400BF472F /* nseqs.h */,
A7460B5A12B93F1F00866BB6 /* speciesprofile.cpp */,
A7460AF712B9218400866BB6 /* spearman.h */,
A7460AF812B9218400866BB6 /* spearman.cpp */,
- A7BB555212BB87F30041F26F /* strictchi2.h */,
- A7BB555312BB87F30041F26F /* strictchi2.cpp */,
- A7460A3F12B8EF1C00866BB6 /* strictchord.h */,
- A7460A4012B8EF1C00866BB6 /* strictchord.cpp */,
- A7F0C10112B80EEC0048BC64 /* stricteuclidean.h */,
- A7F0C10212B80EEC0048BC64 /* stricteuclidean.cpp */,
- A7460B3612B9377400866BB6 /* strictkulczynski.h */,
- A7460B3712B9377400866BB6 /* strictkulczynski.cpp */,
- A7460AC912B90C5600866BB6 /* strictpearson.h */,
- A7460ACA12B90C5600866BB6 /* strictpearson.cpp */,
+ A7BB555212BB87F30041F26F /* structchi2.h */,
+ A7BB555312BB87F30041F26F /* structchi2.cpp */,
+ A7460A3F12B8EF1C00866BB6 /* structchord.h */,
+ A7460A4012B8EF1C00866BB6 /* structchord.cpp */,
+ A7F0C10112B80EEC0048BC64 /* structeuclidean.h */,
+ A7F0C10212B80EEC0048BC64 /* structeuclidean.cpp */,
+ A7460B3612B9377400866BB6 /* structkulczynski.h */,
+ A7460B3712B9377400866BB6 /* structkulczynski.cpp */,
+ A7460AC912B90C5600866BB6 /* structpearson.h */,
+ A7460ACA12B90C5600866BB6 /* structpearson.cpp */,
A7DA2160113FECD400BF472F /* treecalculator.h */,
A7DA216D113FECD400BF472F /* unweighted.cpp */,
A7DA216E113FECD400BF472F /* unweighted.h */,
#include "whittaker.h"
#include "odum.h"
#include "canberra.h"
-#include "stricteuclidean.h"
-#include "strictchord.h"
+#include "structeuclidean.h"
+#include "structchord.h"
#include "hellinger.h"
#include "manhattan.h"
-#include "strictpearson.h"
+#include "structpearson.h"
#include "soergel.h"
#include "spearman.h"
-#include "strictkulczynski.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> CollectSharedCommand::getValidParameters(){
outputTypes["braycurtis"] = tempOutNames;
outputTypes["odum"] = tempOutNames;
outputTypes["canberra"] = tempOutNames;
- outputTypes["stricteuclidean"] = tempOutNames;
- outputTypes["strictchord"] = tempOutNames;
+ outputTypes["structeuclidean"] = tempOutNames;
+ outputTypes["structchord"] = tempOutNames;
outputTypes["hellinger"] = tempOutNames;
outputTypes["manhattan"] = tempOutNames;
- outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["structpearson"] = tempOutNames;
outputTypes["soergel"] = tempOutNames;
outputTypes["spearman"] = tempOutNames;
- outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["structkulczynski"] = tempOutNames;
+ outputTypes["structchi2"] = tempOutNames;
outputTypes["speciesprofile"] = tempOutNames;
outputTypes["hamming"] = tempOutNames;
+ outputTypes["gower"] = tempOutNames;
+ outputTypes["memchi2"] = tempOutNames;
+ outputTypes["memchord"] = tempOutNames;
+ outputTypes["memeuclidean"] = tempOutNames;
+ outputTypes["mempearson"] = tempOutNames;
}
catch(exception& e) {
outputTypes["braycurtis"] = tempOutNames;
outputTypes["odum"] = tempOutNames;
outputTypes["canberra"] = tempOutNames;
- outputTypes["stricteuclidean"] = tempOutNames;
- outputTypes["strictchord"] = tempOutNames;
+ outputTypes["structeuclidean"] = tempOutNames;
+ outputTypes["structchord"] = tempOutNames;
outputTypes["hellinger"] = tempOutNames;
outputTypes["manhattan"] = tempOutNames;
- outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["structpearson"] = tempOutNames;
outputTypes["soergel"] = tempOutNames;
outputTypes["spearman"] = tempOutNames;
- outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["structkulczynski"] = tempOutNames;
outputTypes["speciesprofile"] = tempOutNames;
+ outputTypes["structchi2"] = tempOutNames;
outputTypes["hamming"] = tempOutNames;
-
+ outputTypes["gower"] = tempOutNames;
+ outputTypes["memchi2"] = tempOutNames;
+ outputTypes["memchord"] = tempOutNames;
+ outputTypes["memeuclidean"] = tempOutNames;
+ outputTypes["mempearson"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
}else if (Estimators[i] == "canberra") {
cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+"canberra")));
outputNames.push_back(fileNameRoot+"canberra"); outputTypes["canberra"].push_back(fileNameRoot+"canberra");
- }else if (Estimators[i] == "stricteuclidean") {
- cDisplays.push_back(new CollectDisplay(new StrictEuclidean(), new SharedOneColumnFile(fileNameRoot+"stricteuclidean")));
- outputNames.push_back(fileNameRoot+"stricteuclidean"); outputTypes["stricteuclidean"].push_back(fileNameRoot+"stricteuclidean");
- }else if (Estimators[i] == "strictchord") {
- cDisplays.push_back(new CollectDisplay(new StrictChord(), new SharedOneColumnFile(fileNameRoot+"strictchord")));
- outputNames.push_back(fileNameRoot+"strictchord"); outputTypes["strictchord"].push_back(fileNameRoot+"strictchord");
+ }else if (Estimators[i] == "structeuclidean") {
+ cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(fileNameRoot+"structeuclidean")));
+ outputNames.push_back(fileNameRoot+"structeuclidean"); outputTypes["structeuclidean"].push_back(fileNameRoot+"structeuclidean");
+ }else if (Estimators[i] == "structchord") {
+ cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(fileNameRoot+"structchord")));
+ outputNames.push_back(fileNameRoot+"structchord"); outputTypes["structchord"].push_back(fileNameRoot+"structchord");
}else if (Estimators[i] == "hellinger") {
cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+"hellinger")));
outputNames.push_back(fileNameRoot+"hellinger"); outputTypes["hellinger"].push_back(fileNameRoot+"hellinger");
}else if (Estimators[i] == "manhattan") {
cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+"manhattan")));
outputNames.push_back(fileNameRoot+"manhattan"); outputTypes["manhattan"].push_back(fileNameRoot+"manhattan");
- }else if (Estimators[i] == "strictpearson") {
- cDisplays.push_back(new CollectDisplay(new StrictPearson(), new SharedOneColumnFile(fileNameRoot+"strictpearson")));
- outputNames.push_back(fileNameRoot+"strictpearson"); outputTypes["strictpearson"].push_back(fileNameRoot+"strictpearson");
+ }else if (Estimators[i] == "structpearson") {
+ cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(fileNameRoot+"structpearson")));
+ outputNames.push_back(fileNameRoot+"structpearson"); outputTypes["structpearson"].push_back(fileNameRoot+"structpearson");
}else if (Estimators[i] == "soergel") {
cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+"soergel")));
outputNames.push_back(fileNameRoot+"soergel"); outputTypes["soergel"].push_back(fileNameRoot+"soergel");
}else if (Estimators[i] == "spearman") {
cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+"spearman")));
outputNames.push_back(fileNameRoot+"spearman"); outputTypes["spearman"].push_back(fileNameRoot+"spearman");
- }else if (Estimators[i] == "strictkulczynski") {
- cDisplays.push_back(new CollectDisplay(new StrictKulczynski(), new SharedOneColumnFile(fileNameRoot+"strictkulczynski")));
- outputNames.push_back(fileNameRoot+"strictkulczynski"); outputTypes["strictkulczynski"].push_back(fileNameRoot+"strictkulczynski");
+ }else if (Estimators[i] == "structkulczynski") {
+ cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+"structkulczynski")));
+ outputNames.push_back(fileNameRoot+"structkulczynski"); outputTypes["structkulczynski"].push_back(fileNameRoot+"structkulczynski");
}else if (Estimators[i] == "speciesprofile") {
cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+"speciesprofile")));
outputNames.push_back(fileNameRoot+"speciesprofile"); outputTypes["speciesprofile"].push_back(fileNameRoot+"speciesprofile");
}else if (Estimators[i] == "hamming") {
cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+"hamming")));
outputNames.push_back(fileNameRoot+"hamming"); outputTypes["hamming"].push_back(fileNameRoot+"hamming");
+ }else if (Estimators[i] == "structchi2") {
+ cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(fileNameRoot+"structchi2")));
+ outputNames.push_back(fileNameRoot+"structchi2"); outputTypes["structchi2"].push_back(fileNameRoot+"structchi2");
+ }else if (Estimators[i] == "gower") {
+ cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(fileNameRoot+"gower")));
+ outputNames.push_back(fileNameRoot+"gower"); outputTypes["gower"].push_back(fileNameRoot+"gower");
+ }else if (Estimators[i] == "memchi2") {
+ cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(fileNameRoot+"memchi2")));
+ outputNames.push_back(fileNameRoot+"memchi2"); outputTypes["memchi2"].push_back(fileNameRoot+"memchi2");
+ }else if (Estimators[i] == "memchord") {
+ cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(fileNameRoot+"memchord")));
+ outputNames.push_back(fileNameRoot+"memchord"); outputTypes["memchord"].push_back(fileNameRoot+"memchord");
+ }else if (Estimators[i] == "memeuclidean") {
+ cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(fileNameRoot+"memeuclidean")));
+ outputNames.push_back(fileNameRoot+"memeuclidean"); outputTypes["memeuclidean"].push_back(fileNameRoot+"memeuclidean");
+ }else if (Estimators[i] == "mempearson") {
+ cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(fileNameRoot+"mempearson")));
+ outputNames.push_back(fileNameRoot+"mempearson"); outputTypes["mempearson"].push_back(fileNameRoot+"mempearson");
}
}
--- /dev/null
+/*
+ * gower.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "gower.h"
+
+/***********************************************************************/
+EstOutput Gower::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ vector<int> maxOtus; maxOtus.resize(shared[0]->getNumBins());
+ vector<int> minOtus; minOtus.resize(shared[0]->getNumBins());
+ //for each otu
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+
+ //set otus min and max to first one
+ minOtus[i] = shared[0]->getAbundance(i);
+ maxOtus[i] = shared[0]->getAbundance(i);
+
+ //for each group
+ for (int j = 1; j < shared.size(); j++) {
+ maxOtus[i] = max(shared[j]->getAbundance(i), maxOtus[i]);
+ minOtus[i] = min(shared[j]->getAbundance(i), minOtus[i]);
+ }
+ }
+
+ double sum = 0.0;
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ double numerator = abs(A - B);
+ double denominator = maxOtus[i] - minOtus[i];
+
+ if (denominator != 0) { sum += (numerator / denominator); }
+ }
+
+ data[0] = sum;
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Gower", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef GOWER_H
+#define GOWER_H
+
+/*
+ * gower.h
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Gower : public Calculator {
+
+public:
+ Gower() : Calculator("gower", 1, false, true) {}; //the true means this calculator needs all groups to calculate the pair value
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
--- /dev/null
+/*
+ * memchi2.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "memchi2.h"
+
+/***********************************************************************/
+EstOutput MemChi2::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ int nonZeroA = 0;
+ int nonZeroB = 0;
+ int totalOtus = shared[0]->getNumBins();
+ int totalGroups = shared.size();
+
+ //for each otu
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
+ if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
+ }
+
+ double totalTerm = 1 / (float) totalGroups;
+ double sum = 0.0;
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ if (A > 0) { A = 1; }
+ if (B > 0) { B = 1; }
+
+ double Aterm = A / (float) nonZeroA;
+ double Bterm = B / (float) nonZeroB;
+
+ sum += (totalTerm * ((Aterm-Bterm)*(Aterm-Bterm)));
+ }
+
+ data[0] = sqrt((totalOtus * sum));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MemChi2", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef MEMCHI2_H
+#define MEMCHI2_H
+
+/*
+ * memchi2.h
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class MemChi2 : public Calculator {
+
+public:
+ MemChi2() : Calculator("memchi2", 1, false, true) {}; //the true means this calculator needs all groups to calculate the pair value
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
--- /dev/null
+/*
+ * memchord.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "memchord.h"
+
+/***********************************************************************/
+EstOutput MemChord::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double nonZeroA = 0;
+ double nonZeroB = 0;
+
+ //for each otu
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
+ if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
+ }
+
+ nonZeroA = sqrt(nonZeroA);
+ nonZeroB = sqrt(nonZeroB);
+
+ double sum = 0.0;
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ if (A > 0) { A = 1; }
+ if (B > 0) { B = 1; }
+
+ double Aterm = A / nonZeroA;
+ double Bterm = B / nonZeroB;
+
+ sum += ((Aterm-Bterm)*(Aterm-Bterm));
+ }
+
+ data[0] = sqrt(sum);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MemChord", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef MEMCHORD_H
+#define MEMCHORD_H
+
+/*
+ * memchord.h
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class MemChord : public Calculator {
+
+public:
+ MemChord() : Calculator("memchord", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
--- /dev/null
+/*
+ * memeuclidean.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "memeuclidean.h"
+
+/***********************************************************************/
+EstOutput MemEuclidean::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sum = 0.0;
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ if (A > 0) { A = 1; }
+ if (B > 0) { B = 1; }
+
+ sum += ((A-B)*(A-B));
+ }
+
+ data[0] = sqrt(sum);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MemEuclidean", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef MEMEUCLIDEAN_H
+#define MEMEUCLIDEAN_H
+
+/*
+ * memeuclidean.h
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class MemEuclidean : public Calculator {
+
+public:
+ MemEuclidean() : Calculator("memeuclidean", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
--- /dev/null
+/*
+ * mempearson.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mempearson.h"
+
+/***********************************************************************/
+EstOutput MemPearson::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ int nonZeroA = 0;
+ int nonZeroB = 0;
+ int numOTUS = shared[0]->getNumBins();
+
+ //for each otu
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ if (shared[0]->getAbundance(i) != 0) { nonZeroA++; }
+ if (shared[1]->getAbundance(i) != 0) { nonZeroB++; }
+ }
+
+ double numTerm1 = 0.0;
+ double numTerm2 = 0.0;
+ double denomTerm1 = 0.0;
+ double denomTerm2 = 0.0;
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int Aij = shared[0]->getAbundance(i);
+ int Bij = shared[1]->getAbundance(i);
+
+ if (Aij > 0) { Aij = 1; }
+ if (Bij > 0) { Bij = 1; }
+
+ numTerm1 += (Aij - (nonZeroA / (float) numOTUS));
+ numTerm2 += (Bij - (nonZeroB / (float) numOTUS));
+
+ denomTerm1 += ((Aij - (nonZeroA / (float) numOTUS)) * (Aij - (nonZeroA / (float) numOTUS)));
+ denomTerm2 += ((Bij - (nonZeroB / (float) numOTUS)) * (Bij - (nonZeroB / (float) numOTUS)));
+ }
+
+ denomTerm1 = sqrt(denomTerm1);
+ denomTerm2 = sqrt(denomTerm2);
+
+ double denom = denomTerm1 * denomTerm2;
+ double numerator = numTerm1 * numTerm2;
+
+ if (denom != 0) {
+ data[0] = 1.0 - (numerator / denom);
+ }else {
+ data[0] = 1.0;
+ }
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MemPearson", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef MEMPEARSON_H
+#define MEMPEARSON_H
+
+/*
+ * mempearson.h
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class MemPearson : public Calculator {
+
+public:
+ MemPearson() : Calculator("mempearson", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+++ /dev/null
-/*
- * strictchi2.cpp
- * Mothur
- *
- * Created by westcott on 12/17/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "strictchi2.h"
-
-/***********************************************************************/
-EstOutput StrictChi2::getValues(vector<SharedRAbundVector*> shared) {
- try {
- data.resize(1,0);
-
- double sumA = shared[0]->getNumSeqs();
- double sumB = shared[1]->getNumSeqs();
- double totalSum = 0.0;
-
- for (int i = 0; i < shared.size(); i++) { totalSum += shared[i]->getNumSeqs(); }
-
- vector<int> sumOtus; sumOtus.resize(shared[0]->getNumBins(), 0);
- //for each otu
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
- //for each group
- for (int j = 0; j < shared.size(); j++) {
-
- }
- }
-
-
-
- //data[0] = sqrt(sum);
-
- if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "StrictChi2", "getValues");
- exit(1);
- }
-}
-/***********************************************************************/
+++ /dev/null
-#ifndef STRICTCHI2_H
-#define STRICTCHI2_H
-
-/*
- * strictchi2.h
- * Mothur
- *
- * Created by westcott on 12/17/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "calculator.h"
-
-/***********************************************************************/
-
-class StrictChi2 : public Calculator {
-
-public:
- StrictChi2() : Calculator("strictchi2", 1, false, true) {}; //the true means this calculator needs all groups to calculate the pair value
- EstOutput getValues(SAbundVector*) {return data;};
- EstOutput getValues(vector<SharedRAbundVector*>);
-private:
-
-};
-
-/***********************************************************************/
-
-#endif
\ No newline at end of file
+++ /dev/null
-/*
- * strictchord.cpp
- * Mothur
- *
- * Created by westcott on 12/15/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "strictchord.h"
-
-/***********************************************************************/
-EstOutput StrictChord::getValues(vector<SharedRAbundVector*> shared) {
- try {
- data.resize(1,0);
-
- double sumAj2 = 0.0;
- double sumBj2 = 0.0;
-
- //calc the 2 denominators
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
-
- int Aij = shared[0]->getAbundance(i);
- int Bij = shared[1]->getAbundance(i);
-
- //(Aij) ^ 2
- sumAj2 += (Aij * Aij);
- sumBj2 += (Bij * Bij);
- }
-
- sumAj2 = sqrt(sumAj2);
- sumBj2 = sqrt(sumBj2);
-
- //calc sum
- double sum = 0.0;
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
-
- int Aij = shared[0]->getAbundance(i);
- int Bij = shared[1]->getAbundance(i);
-
- sum += (((Aij / sumAj2) - (Bij / sumBj2)) * ((Aij / sumAj2) - (Bij / sumBj2)));
- }
-
- data[0] = sqrt(sum);
-
- if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "StrictChord", "getValues");
- exit(1);
- }
-}
-/***********************************************************************/
+++ /dev/null
-#ifndef STRICTCHORD_H
-#define STRICTCHORD_H
-
-/*
- * strictchord.h
- * Mothur
- *
- * Created by westcott on 12/15/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "calculator.h"
-
-/***********************************************************************/
-
-class StrictChord : public Calculator {
-
-public:
- StrictChord() : Calculator("strictchord", 1, false) {};
- EstOutput getValues(SAbundVector*) {return data;};
- EstOutput getValues(vector<SharedRAbundVector*>);
-private:
-
-};
-
-/***********************************************************************/
-
-#endif
-
-
-
+++ /dev/null
-/*
- * stricteuclidean.cpp
- * Mothur
- *
- * Created by westcott on 12/14/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "stricteuclidean.h"
-
-/***********************************************************************/
-EstOutput StrictEuclidean::getValues(vector<SharedRAbundVector*> shared) {
- try {
- data.resize(1,0);
-
- double sum = 0.0;
-
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
-
- int Aij = shared[0]->getAbundance(i);
- int Bij = shared[1]->getAbundance(i);
-
- //(Aij - Bij) ^ 2
- sum += ((Aij - Bij) * (Aij - Bij));
- }
-
- data[0] = sqrt(sum);
-
- if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "StrictEuclidean", "getValues");
- exit(1);
- }
-}
-/***********************************************************************/
-
+++ /dev/null
-#ifndef STRICTEUCLIDEAN_H
-#define STRICTEUCLIDEAN_H
-
-/*
- * stricteuclidean.h
- * Mothur
- *
- * Created by westcott on 12/14/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-
-#include "calculator.h"
-
-/***********************************************************************/
-
-class StrictEuclidean : public Calculator {
-
-public:
- StrictEuclidean() : Calculator("stricteuclidean", 1, false) {};
- EstOutput getValues(SAbundVector*) {return data;};
- EstOutput getValues(vector<SharedRAbundVector*>);
-private:
-
-};
-
-/***********************************************************************/
-
-#endif
-
-
+++ /dev/null
-/*
- * strictkulczynski.cpp
- * Mothur
- *
- * Created by westcott on 12/15/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "strictkulczynski.h"
-
-/***********************************************************************/
-EstOutput StrictKulczynski::getValues(vector<SharedRAbundVector*> shared) {
- try {
- data.resize(1,0);
-
- double sumA = 0.0;
- double sumB = 0.0;
- double sumMin = 0.0;
-
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
-
- int A = shared[0]->getAbundance(i);
- int B = shared[1]->getAbundance(i);
-
- sumA += A;
- sumB += B;
- sumMin += min(A, B);
- }
-
- data[0] = 1.0 - (0.5 * ((sumMin / sumA) + (sumMin / sumB)));
-
- if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "StrictKulczynski", "getValues");
- exit(1);
- }
-}
-/***********************************************************************/
-
-
+++ /dev/null
-#ifndef STRICTKULCZYNSKI_H
-#define STRICTKULCZYNSKI_H
-
-/*
- * strictkulczynski.h
- * Mothur
- *
- * Created by westcott on 12/15/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "calculator.h"
-
-/***********************************************************************/
-
-class StrictKulczynski : public Calculator {
-
-public:
- StrictKulczynski() : Calculator("strictkulczynski", 1, false) {};
- EstOutput getValues(SAbundVector*) {return data;};
- EstOutput getValues(vector<SharedRAbundVector*>);
-private:
-
-};
-
-/***********************************************************************/
-
-#endif
-
-
-
+++ /dev/null
-/*
- * strictpearson.cpp
- * Mothur
- *
- * Created by westcott on 12/15/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "strictpearson.h"
-
-/***********************************************************************/
-EstOutput StrictPearson::getValues(vector<SharedRAbundVector*> shared) {
- try {
- data.resize(1,0);
-
- double sumA = 0.0;
- double sumB = 0.0;
- int numOTUS = shared[0]->getNumBins();
-
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
- sumA += shared[0]->getAbundance(i);
- sumB += shared[1]->getAbundance(i);
- }
-
- double numTerm1 = 0.0;
- double numTerm2 = 0.0;
- double denomTerm1 = 0.0;
- double denomTerm2 = 0.0;
-
- for (int i = 0; i < shared[0]->getNumBins(); i++) {
- int Aij = shared[0]->getAbundance(i);
- int Bij = shared[1]->getAbundance(i);
-
- numTerm1 += (Aij - (sumA / (float) numOTUS));
- numTerm2 += (Bij - (sumB / (float) numOTUS));
-
- denomTerm1 += ((Aij - (sumA / (float) numOTUS)) * (Aij - (sumA / (float) numOTUS)));
- denomTerm2 += ((Bij - (sumB / (float) numOTUS)) * (Bij - (sumB / (float) numOTUS)));
- }
-
- denomTerm1 = sqrt(denomTerm1);
- denomTerm2 = sqrt(denomTerm2);
-
- double denom = denomTerm1 * denomTerm2;
- double numerator = numTerm1 * numTerm2;
-
- data[0] = 1.0 - (numerator / denom);
-
- if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "StrictPearson", "getValues");
- exit(1);
- }
-}
-/***********************************************************************/
+++ /dev/null
-#ifndef STRICTPEARSON_H
-#define STRICTPEARSON_H
-
-/*
- * strictpearson.h
- * Mothur
- *
- * Created by westcott on 12/15/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-
-#include "calculator.h"
-
-/***********************************************************************/
-
-class StrictPearson : public Calculator {
-
-public:
- StrictPearson() : Calculator("strictpearson", 1, false) {};
- EstOutput getValues(SAbundVector*) {return data;};
- EstOutput getValues(vector<SharedRAbundVector*>);
-private:
-
-};
-
-/***********************************************************************/
-
-#endif
-
-
--- /dev/null
+/*
+ * structchi2.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structchi2.h"
+
+/***********************************************************************/
+EstOutput StructChi2::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumA = shared[0]->getNumSeqs();
+ double sumB = shared[1]->getNumSeqs();
+ double totalSum = 0.0;
+
+ for (int i = 0; i < shared.size(); i++) { totalSum += shared[i]->getNumSeqs(); }
+
+ vector<int> sumOtus; sumOtus.resize(shared[0]->getNumBins(), 0);
+ //for each otu
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ //for each group
+ for (int j = 0; j < shared.size(); j++) {
+ sumOtus[i] += shared[j]->getAbundance(i);
+ }
+ }
+
+ double sum = 0.0;
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ double totalTerm = 1 / (float) sumOtus[i];
+ double Aterm = A / sumA;
+ double Bterm = B / sumB;
+
+ sum += (totalTerm * ((Aterm-Bterm)*(Aterm-Bterm)));
+ }
+
+ data[0] = sqrt((totalSum * sum));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "StructChi2", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef STRUCTCHI2_H
+#define STRUCTCHI2_H
+
+/*
+ * structchi2.h
+ * Mothur
+ *
+ * Created by westcott on 12/17/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class StructChi2 : public Calculator {
+
+public:
+ StructChi2() : Calculator("structchi2", 1, false, true) {}; //the true means this calculator needs all groups to calculate the pair value
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * structchord.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structchord.h"
+
+/***********************************************************************/
+EstOutput StructChord::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumAj2 = 0.0;
+ double sumBj2 = 0.0;
+
+ //calc the 2 denominators
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+
+ int Aij = shared[0]->getAbundance(i);
+ int Bij = shared[1]->getAbundance(i);
+
+ //(Aij) ^ 2
+ sumAj2 += (Aij * Aij);
+ sumBj2 += (Bij * Bij);
+ }
+
+ sumAj2 = sqrt(sumAj2);
+ sumBj2 = sqrt(sumBj2);
+
+ //calc sum
+ double sum = 0.0;
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+
+ int Aij = shared[0]->getAbundance(i);
+ int Bij = shared[1]->getAbundance(i);
+
+ sum += (((Aij / sumAj2) - (Bij / sumBj2)) * ((Aij / sumAj2) - (Bij / sumBj2)));
+ }
+
+ data[0] = sqrt(sum);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "StructChord", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
--- /dev/null
+#ifndef STRUCTCHORD_H
+#define STRUCTCHORD_H
+
+/*
+ * structchord.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class StructChord : public Calculator {
+
+public:
+ StructChord() : Calculator("structchord", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
+
+
--- /dev/null
+/*
+ * structeuclidean.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/14/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structeuclidean.h"
+
+/***********************************************************************/
+EstOutput StructEuclidean::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sum = 0.0;
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+
+ int Aij = shared[0]->getAbundance(i);
+ int Bij = shared[1]->getAbundance(i);
+
+ //(Aij - Bij) ^ 2
+ sum += ((Aij - Bij) * (Aij - Bij));
+ }
+
+ data[0] = sqrt(sum);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "StructEuclidean", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef STRUCTEUCLIDEAN_H
+#define STRUCTEUCLIDEAN_H
+
+/*
+ * structeuclidean.h
+ * Mothur
+ *
+ * Created by westcott on 12/14/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class StructEuclidean : public Calculator {
+
+public:
+ StructEuclidean() : Calculator("structeuclidean", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
+
--- /dev/null
+/*
+ * structkulczynski.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structkulczynski.h"
+
+/***********************************************************************/
+EstOutput StructKulczynski::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumA = 0.0;
+ double sumB = 0.0;
+ double sumMin = 0.0;
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ sumA += A;
+ sumB += B;
+ sumMin += min(A, B);
+ }
+
+ data[0] = 1.0 - (0.5 * ((sumMin / sumA) + (sumMin / sumB)));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "StructKulczynski", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+
--- /dev/null
+#ifndef STRUCTKULCZYNSKI_H
+#define STRUCTKULCZYNSKI_H
+
+/*
+ * structkulczynski.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class StructKulczynski : public Calculator {
+
+public:
+ StructKulczynski() : Calculator("structkulczynski", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
+
+
--- /dev/null
+/*
+ * structpearson.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "structpearson.h"
+
+/***********************************************************************/
+EstOutput StructPearson::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumA = 0.0;
+ double sumB = 0.0;
+ int numOTUS = shared[0]->getNumBins();
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ sumA += shared[0]->getAbundance(i);
+ sumB += shared[1]->getAbundance(i);
+ }
+
+ double numTerm1 = 0.0;
+ double numTerm2 = 0.0;
+ double denomTerm1 = 0.0;
+ double denomTerm2 = 0.0;
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int Aij = shared[0]->getAbundance(i);
+ int Bij = shared[1]->getAbundance(i);
+
+ numTerm1 += (Aij - (sumA / (float) numOTUS));
+ numTerm2 += (Bij - (sumB / (float) numOTUS));
+
+ denomTerm1 += ((Aij - (sumA / (float) numOTUS)) * (Aij - (sumA / (float) numOTUS)));
+ denomTerm2 += ((Bij - (sumB / (float) numOTUS)) * (Bij - (sumB / (float) numOTUS)));
+ }
+
+ denomTerm1 = sqrt(denomTerm1);
+ denomTerm2 = sqrt(denomTerm2);
+
+ double denom = denomTerm1 * denomTerm2;
+ double numerator = numTerm1 * numTerm2;
+
+ data[0] = 1.0 - (numerator / denom);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "StructPearson", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
--- /dev/null
+#ifndef STRUCTPEARSON_H
+#define STRUCTPEARSON_H
+
+/*
+ * structpearson.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class StructPearson : public Calculator {
+
+public:
+ StructPearson() : Calculator("structpearson", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
+
#include "whittaker.h"
#include "odum.h"
#include "canberra.h"
-#include "stricteuclidean.h"
-#include "strictchord.h"
+#include "structeuclidean.h"
+#include "structchord.h"
#include "hellinger.h"
#include "manhattan.h"
-#include "strictpearson.h"
+#include "structpearson.h"
#include "soergel.h"
#include "spearman.h"
-#include "strictkulczynski.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> SummarySharedCommand::getValidParameters(){
sumCalculators.push_back(new Odum());
}else if (Estimators[i] == "canberra") {
sumCalculators.push_back(new Canberra());
- }else if (Estimators[i] == "stricteuclidean") {
- sumCalculators.push_back(new StrictEuclidean());
- }else if (Estimators[i] == "strictchord") {
- sumCalculators.push_back(new StrictChord());
+ }else if (Estimators[i] == "structeuclidean") {
+ sumCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ sumCalculators.push_back(new StructChord());
}else if (Estimators[i] == "hellinger") {
sumCalculators.push_back(new Hellinger());
}else if (Estimators[i] == "manhattan") {
sumCalculators.push_back(new Manhattan());
- }else if (Estimators[i] == "strictpearson") {
- sumCalculators.push_back(new StrictPearson());
+ }else if (Estimators[i] == "structpearson") {
+ sumCalculators.push_back(new StructPearson());
}else if (Estimators[i] == "soergel") {
sumCalculators.push_back(new Soergel());
}else if (Estimators[i] == "spearman") {
sumCalculators.push_back(new Spearman());
- }else if (Estimators[i] == "strictkulczynski") {
- sumCalculators.push_back(new StrictKulczynski());
+ }else if (Estimators[i] == "structkulczynski") {
+ sumCalculators.push_back(new StructKulczynski());
}else if (Estimators[i] == "speciesprofile") {
sumCalculators.push_back(new SpeciesProfile());
}else if (Estimators[i] == "hamming") {
sumCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ sumCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ sumCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ sumCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ sumCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ sumCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ sumCalculators.push_back(new MemPearson());
}
}
}
}
for(int i=0;i<sumCalculators.size();i++) {
-
+
+ //if this calc needs all groups to calculate the pair load all groups
+ if (sumCalculators[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]); }
+ }
+ }
+
vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
if (m->control_pressed) { outputFileHandle.close(); return 1; }
shared["braycurtis"] = "braycurtis";
shared["odum"] = "odum";
shared["canberra"] = "canberra";
- shared["stricteuclidean"] = "stricteuclidean";
- shared["strictchord"] = "strictchord";
+ shared["structeuclidean"] = "structeuclidean";
+ shared["structchord"] = "structchord";
shared["hellinger"] = "hellinger";
shared["manhattan"] = "manhattan";
- shared["strictpearson"] = "strictpearson";
+ shared["structpearson"] = "structpearson";
shared["soergel"] = "soergel";
shared["spearman"] = "spearman";
- shared["strictkulczynski"] = "strictkulczynski";
+ 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) {
sharedsummary["braycurtis"] = "braycurtis";
sharedsummary["odum"] = "odum";
sharedsummary["canberra"] = "canberra";
- sharedsummary["stricteuclidean"] = "stricteuclidean";
- sharedsummary["strictchord"] = "strictchord";
+ sharedsummary["structeuclidean"] = "structeuclidean";
+ sharedsummary["structchord"] = "structchord";
sharedsummary["hellinger"] = "hellinger";
sharedsummary["manhattan"] = "manhattan";
- sharedsummary["strictpearson"] = "strictpearson";
- sharedsummary["strictkulczynski"] = "strictkulczynski";
+ 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) {
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