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37D9282C0F21331F001D4494 /* sharedjest.cpp */,
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);
runOnlyForDeploymentPostprocessing = 0;
};
#include "sharednseqs.h"
#include "sharedochiai.h"
#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
//**********************************************************************************************************************
cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
}else if (globaldata->Estimators[i] == "sharedanderberg") {
cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
+ }else if (globaldata->Estimators[i] == "sharedkulczynski") {
+ cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
+ }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
+ cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
+ }else if (globaldata->Estimators[i] == "sharedlennon") {
+ cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
+ }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
+ cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
+ }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
+ cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
}
-
}
}
--- /dev/null
+/*
+ * sharedbraycurtis.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedbraycurtis.h"
+
+/***********************************************************************/
+//This is used by SharedJAbund and SharedSorAbund
+EstOutput SharedBrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+ try {
+ EstOutput data;
+ data.resize(1,0);
+
+ int sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
+ sumSharedA = 0; sumSharedB = 0; sumSharedAB = 0;
+
+ /*Xi, Yi = abundance of the ith shared OTU in A and B
+ sumSharedA = the sum of all shared otus in A
+ sumSharedB = the sum of all shared otus in B
+ sumSharedAB = the sum of the minimum otus int all shared otus in AB.
+ */
+
+ for (int i = 0; i < shared1->size(); i++) {
+ //store in temps to avoid multiple repetitive function calls
+ tempA = shared1->getAbundance(i);
+ tempB = shared2->getAbundance(i);
+
+
+ if ((tempA != 0) && (tempB != 0)) {//they are shared
+ sumSharedA += tempA;
+ sumSharedB += tempB;
+
+ //sum the min of tempA and tempB
+ if (tempA < tempB) { sumSharedAB += tempA; }
+ else { sumSharedAB += tempB; }
+ }
+ }
+
+ data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedBrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedBrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef SHAREDBRAYCURTIS_H
+#define SHAREDBRAYCURTIS_H
+/*
+ * sharedbraycurtis.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SharedBrayCurtis : public Calculator {
+
+public:
+ SharedBrayCurtis() : Calculator("SharedBrayCurtis", 1) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+
+};
+
+/***********************************************************************/
+
+
+
+#endif
--- /dev/null
+/*
+ * sharedkulczynski.cpp
+ * Mothur
+ *
+ * Created by John Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedkulczynski.h"
+
+/***********************************************************************/
+
+EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+ try {
+ int S1, S2, S12, tempA, tempB;
+ S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0;
+
+ /*S1, S2 = number of OTUs observed or estimated in A and B
+ S12=number of OTUs shared between A and B */
+
+ data.resize(1,0);
+
+ for (int i = 0; i < shared1->size(); i++) {
+ //store in temps to avoid multiple repetitive function calls
+ tempA = shared1->getAbundance(i);
+ tempB = shared2->getAbundance(i);
+
+ if (tempA != 0) { S1++; }
+ if (tempB != 0) { S2++; }
+
+ //they are shared
+ if ((tempA != 0) && (tempB != 0)) { S12++; }
+ }
+
+ data[0] = S12 / (float)(S1 + S2 - (2 * S12));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef SHAREDKULCZYNSKI_H
+#define SHAREDKULCZYNSKI_H
+/*
+ * sharedkulczynski.h
+ * Mothur
+ *
+ * Created by John Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SharedKulczynski : public Calculator {
+
+public:
+ SharedKulczynski() : Calculator("SharedKulczynski", 1) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+
+};
+
+/***********************************************************************/
+
+
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * sharedkulczynskicody.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedkulczynskicody.h"
+
+/***********************************************************************/
+
+EstOutput SharedKulczynskiCody::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+ try {
+ int S1, S2, S12, tempA, tempB;
+ S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0;
+
+ /*S1, S2 = number of OTUs observed or estimated in A and B
+ S12=number of OTUs shared between A and B */
+
+ data.resize(1,0);
+
+ for (int i = 0; i < shared1->size(); i++) {
+ //store in temps to avoid multiple repetitive function calls
+ tempA = shared1->getAbundance(i);
+ tempB = shared2->getAbundance(i);
+
+ if (tempA != 0) { S1++; }
+ if (tempB != 0) { S2++; }
+
+ //they are shared
+ if ((tempA != 0) && (tempB != 0)) { S12++; }
+ }
+
+ data[0] = 0.5 * ((S12 / (float)S1) + (S12 / (float)S2));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedKulczynskiCody class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedKulczynskiCody class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef SHAREDKULCZYNSKICODY_H
+#define SHAREDKULCZYNSKICODY_H
+
+/*
+ * sharedkulczynskicody.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SharedKulczynskiCody : public Calculator {
+
+public:
+ SharedKulczynskiCody() : Calculator("SharedKulczynskiCody", 1) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+
+};
+
+/***********************************************************************/
+
+
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * sharedlennon.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedlennon.h"
+
+/***********************************************************************/
+
+EstOutput SharedLennon::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+ try {
+ int S1, S2, S12, tempA, tempB, min;
+ S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; min = 0;
+
+ /*S1, S2 = number of OTUs observed or estimated in A and B
+ S12=number of OTUs shared between A and B */
+
+ data.resize(1,0);
+
+ for (int i = 0; i < shared1->size(); i++) {
+ //store in temps to avoid multiple repetitive function calls
+ tempA = shared1->getAbundance(i);
+ tempB = shared2->getAbundance(i);
+
+ if (tempA != 0) { S1++; }
+ if (tempB != 0) { S2++; }
+
+ //they are shared
+ if ((tempA != 0) && (tempB != 0)) { S12++; }
+ }
+
+
+ tempA = S1 - S12; tempB = S2 - S12;
+
+ if (tempA < tempB) { min = tempA; }
+ else { min = tempB; }
+
+ data[0] = S12 / (float)(S12 + min);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedLennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedLennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef SHAREDLENNON_H
+#define SHAREDLENNON_H
+
+/*
+ * sharedlennon.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SharedLennon : public Calculator {
+
+public:
+ SharedLennon() : Calculator("SharedLennon", 1) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+
+};
+
+/***********************************************************************/
+
+
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * sharedmorisitahorn.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedmorisitahorn.h"
+
+/***********************************************************************/
+EstOutput SharedMorHorn::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+ try {
+ data.resize(1,0);
+
+ int Atotal, Btotal, tempA, tempB;
+ Atotal = 0; Btotal = 0;
+ float morhorn, sumSharedA, sumSharedB, a, b, d;
+ morhorn = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+
+ //get the total values we need to calculate the theta denominator sums
+ for (int i = 0; i < shared1->size(); i++) {
+ //store in temps to avoid multiple repetitive function calls
+ Atotal += shared1->getAbundance(i);
+ Btotal += shared2->getAbundance(i);
+ }
+
+ //calculate the theta denominator sums
+ for (int j = 0; j < shared1->size(); j++) {
+ //store in temps to avoid multiple repetitive function calls
+ tempA = shared1->getAbundance(j);
+ tempB = shared2->getAbundance(j);
+
+ //they are shared
+ if ((tempA != 0) && (tempB != 0)) {
+ if (Atotal != 0) { sumSharedA = (tempA / (float)Atotal); }
+ if (Btotal != 0) { sumSharedB = (tempB / (float)Btotal); }
+
+ a += sumSharedA * sumSharedA;
+ b += sumSharedB * sumSharedB;
+ d += sumSharedA * sumSharedB;
+ }
+ }
+
+ morhorn = (2 * d) / (float) (a + b);
+
+ if (isnan(morhorn) || isinf(morhorn)) { morhorn = 0; }
+
+ data[0] = morhorn;
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedMorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedMorHorn class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
\ No newline at end of file
--- /dev/null
+#ifndef SHAREDMORHORN_H
+#define SHAREDMORHORN_H
+/*
+ * sharedmorisitahorn.h
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/24/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SharedMorHorn : public Calculator {
+
+public:
+ SharedMorHorn() : Calculator("SharedMorisitaHorn", 1) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
int Atotal, Btotal, tempA, tempB;
Atotal = 0; Btotal = 0;
- float numerator, denominator, thetaYC, sumSharedA, sumSharedB, a, b, d;
- numerator = 0.0; denominator = 0.0; thetaYC = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+ float thetaYC, sumSharedA, sumSharedB, a, b, d;
+ thetaYC = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
//get the total values we need to calculate the theta denominator sums
for (int i = 0; i < shared1->size(); i++) {
#include "sharedthetan.h"
#include "sharedochiai.h"
#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
//**********************************************************************************************************************
sumCalculators.push_back(new SharedOchiai());
}else if (globaldata->Estimators[i] == "sharedanderberg") {
sumCalculators.push_back(new SharedAnderberg());
+ }else if (globaldata->Estimators[i] == "sharedkulczynski") {
+ sumCalculators.push_back(new SharedKulczynski());
+ }else if (globaldata->Estimators[i] == "sharedkulczynskicody") {
+ sumCalculators.push_back(new SharedKulczynskiCody());
+ }else if (globaldata->Estimators[i] == "sharedlennon") {
+ sumCalculators.push_back(new SharedLennon());
+ }else if (globaldata->Estimators[i] == "sharedmorisitahorn") {
+ sumCalculators.push_back(new SharedMorHorn());
+ }else if (globaldata->Estimators[i] == "sharedbraycurtis") {
+ sumCalculators.push_back(new SharedBrayCurtis());
}
-
-
}
}
shared["sharednseqs"] = "sharednseqs";
shared["sharedochiai"] = "sharedochiai";
shared["sharedanderberg"] = "sharedanderberg";
+ shared["sharedkulczynski"] = "sharedkulczynski";
+ shared["sharedkulczynskicody"] = "sharedkulczynskicody";
+ shared["sharedlennon"] = "sharedlennon";
+ shared["sharedmorisitahorn"] = "sharedmorisitahorn";
+ shared["sharedbraycurtis"] = "sharedbraycurtis";
shared["default"] = "default";
}
catch(exception& e) {
sharedsummary["sharednseqs"] = "sharednseqs";
sharedsummary["sharedochiai"] = "sharedochiai";
sharedsummary["sharedanderberg"] = "sharedanderberg";
+ sharedsummary["sharedkulczynski"] = "sharedkulczynski";
+ sharedsummary["sharedkulczynskicody"] = "sharedkulczynskicody";
+ sharedsummary["sharedlennon"] = "sharedlennon";
+ sharedsummary["sharedmorisitahorn"] = "sharedmorisitahorn";
+ sharedsummary["sharedbraycurtis"] = "sharedbraycurtis";
sharedsummary["default"] = "default";
}
catch(exception& e) {
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