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A7DA2006113FECD400BF472F /* bootstrap.h */,
A7DA2009113FECD400BF472F /* bstick.cpp */,
A7DA200A113FECD400BF472F /* bstick.h */,
+ A7F0C08A12B7EAE80048BC64 /* canberra.h */,
+ A7F0C08B12B7EAE80048BC64 /* canberra.cpp */,
A7DA200F113FECD400BF472F /* chao1.cpp */,
A7DA2010113FECD400BF472F /* chao1.h */,
A7DA2033113FECD400BF472F /* coverage.cpp */,
A7DA2059113FECD400BF472F /* geom.h */,
A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
A7DA206D113FECD400BF472F /* goodscoverage.h */,
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+ A7460B7912B9444800866BB6 /* hamming.cpp */,
7E5B2917121FF53C0005339C /* heip.h */,
7E5B2918121FF53C0005339C /* heip.cpp */,
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+ A7460A7412B8FCDC00866BB6 /* hellinger.cpp */,
A7DA2080113FECD400BF472F /* ignoregaps.h */,
7E962A40121F76B1007464B5 /* invsimpson.h */,
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A7DA2084113FECD400BF472F /* jackknife.h */,
A7DA2093113FECD400BF472F /* logsd.cpp */,
A7DA2094113FECD400BF472F /* logsd.h */,
+ A7460A9812B9061B00866BB6 /* manhattan.h */,
+ A7460A9912B9061B00866BB6 /* manhattan.cpp */,
A7DA20AE113FECD400BF472F /* npshannon.cpp */,
A7DA20AF113FECD400BF472F /* npshannon.h */,
A7DA20B0113FECD400BF472F /* nseqs.h */,
+ A7F0C06412B7D64F0048BC64 /* odum.h */,
+ A7F0C06512B7D64F0048BC64 /* odum.cpp */,
A7DA20B2113FECD400BF472F /* onegapdist.h */,
A7DA20B3113FECD400BF472F /* onegapignore.h */,
A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */,
7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */,
7E5B294A121FFADC0005339C /* smithwilson.h */,
7E5B294B121FFADC0005339C /* smithwilson.cpp */,
- A7DA2142113FECD400BF472F /* simpson.cpp */,
A7DA2143113FECD400BF472F /* simpson.h */,
+ A7DA2142113FECD400BF472F /* simpson.cpp */,
A7DA2149113FECD400BF472F /* sobs.h */,
+ A7460ADB12B914B700866BB6 /* soergel.h */,
+ A7460ADC12B914B700866BB6 /* soergel.cpp */,
A7DA214A113FECD400BF472F /* solow.cpp */,
A7DA214B113FECD400BF472F /* solow.h */,
+ A7460B5912B93F1F00866BB6 /* speciesprofile.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 */,
A7DA2160113FECD400BF472F /* treecalculator.h */,
A7DA216D113FECD400BF472F /* unweighted.cpp */,
A7DA216E113FECD400BF472F /* unweighted.h */,
class Calculator {
public:
- Calculator(){ m = MothurOut::getInstance(); }
+ Calculator(){ m = MothurOut::getInstance(); needsAll = false; }
virtual ~Calculator(){};
- Calculator(string n, int c, bool f) : name(n), cols(c), multiple(f) {};
+ Calculator(string n, int c, bool f) : name(n), cols(c), multiple(f) { m = MothurOut::getInstance(); needsAll = false; };
+ Calculator(string n, int c, bool f, bool a) : name(n), cols(c), multiple(f), needsAll(a) { m = MothurOut::getInstance(); };
virtual EstOutput getValues(SAbundVector*) = 0;
virtual EstOutput getValues(vector<SharedRAbundVector*>) = 0;
virtual void print(ostream& f) { f.setf(ios::fixed, ios::floatfield); f.setf(ios::showpoint);
virtual string getName() { return name; }
virtual int getCols() { return cols; }
virtual bool getMultiple() { return multiple; }
+ virtual bool getNeedsAll() { return needsAll; }
protected:
MothurOut* m;
EstOutput data;
string name;
int cols;
bool multiple;
+ bool needsAll;
};
--- /dev/null
+/*
+ * canberra.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/14/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "canberra.h"
+
+/***********************************************************************/
+
+EstOutput Canberra::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ int numSharedOTUS = 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);
+
+ //is this otu shared
+ if ((Aij != 0) && (Bij != 0)) { numSharedOTUS++; }
+
+ if ((Aij + Bij) != 0) {
+ sum += ((abs(Aij - Bij)) / (float) (Aij + Bij));
+ }
+ }
+
+ data[0] = (1 / (float) numSharedOTUS) * sum;
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Canberra", "getValues");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef CANBERRA_H
+#define CANBERRA_H
+
+/*
+ * canberra.h
+ * Mothur
+ *
+ * Created by westcott on 12/14/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Canberra : public Calculator {
+
+public:
+ Canberra() : Calculator("canberra", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
//how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
int n = 1;
+ bool pair = true;
for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
for (int l = n; l < lookup.size(); l++) {
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabund vectors
subset.push_back(lookup[k]); subset.push_back(lookup[l]);
- ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
+
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < lookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
+ }
+
+ ccd->updateSharedData(subset, i+1, globaldata->Groups.size(), pair);
}
n++;
}
//if this is a calculator that can do multiples then do them
- ccd->updateSharedData(lookup, i+1, globaldata->Groups.size());
+ pair = false;
+ ccd->updateSharedData(lookup, i+1, globaldata->Groups.size(), pair);
}
totalNumSeq = i+1;
}
if(numSeqs % increment != 0){
//how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
int n = 1;
+ bool pair = true;
for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
for (int l = n; l < lookup.size(); l++) {
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabund vectors
subset.push_back(lookup[k]); subset.push_back(lookup[l]);
- ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
+
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < lookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
+ }
+
+ ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size(), pair);
}
n++;
}
//if this is a calculator that can do multiples then do them
- ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size());
+ pair = false;
+ ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size(), pair);
}
//resets output files
bool isCalcMultiple() { return estimate->getMultiple(); }
+ bool calcNeedsAll() { return estimate->getNeedsAll(); }
bool hasLciHci() {
if (estimate->getCols() == 3) { return true; }
else{ return false; }
void registerDisplay(Display* o) { displays.insert(o); };
void removeDisplay(Display* o) { displays.erase(o); delete o; };
void SharedDataChanged() { notifyDisplays(); };
- void updateSharedData(vector<SharedRAbundVector*> s, int numSeqs, int numGroupComb) { shared = s; NumSeqs = numSeqs; NumGroupComb = numGroupComb; SharedDataChanged(); };
+ void updateSharedData(vector<SharedRAbundVector*> s, int numSeqs, int numGroupComb, bool p) { pairs = p; shared = s; NumSeqs = numSeqs; NumGroupComb = numGroupComb; SharedDataChanged(); };
void notifyDisplays(){
for(set<Display*>::iterator pos=displays.begin();pos!=displays.end();pos++){
-//cout << (*pos)->getName() << endl;
- if ( ( ((*pos)->isCalcMultiple() == true) && ((*pos)->getAll() == true) ) || (shared.size() == 2) ) {
+
+ if ((*pos)->calcNeedsAll() == true) {
(*pos)->update(shared, NumSeqs, NumGroupComb);
+ }else{
+
+ if ( ((*pos)->isCalcMultiple() == true) && ((*pos)->getAll() == true) && (!pairs) ) {
+ (*pos)->update(shared, NumSeqs, NumGroupComb);
+ }else {
+ vector<SharedRAbundVector*> temp; temp.push_back(shared[0]); temp.push_back(shared[1]);
+ shared = temp;
+
+ (*pos)->update(shared, NumSeqs, NumGroupComb);
+ }
}
}
};
vector<Display*> multiDisplays;
vector<SharedRAbundVector*> shared;
int NumSeqs, NumGroupComb;
+ bool pairs;
};
/***********************************************************************/
#include "sharedbraycurtis.h"
#include "sharedjackknife.h"
#include "whittaker.h"
-
+#include "odum.h"
+#include "canberra.h"
+#include "stricteuclidean.h"
+#include "strictchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "strictpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "strictkulczynski.h"
+#include "speciesprofile.h"
+#include "hamming.h"
//**********************************************************************************************************************
vector<string> CollectSharedCommand::getValidParameters(){
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
outputTypes["braycurtis"] = tempOutNames;
+ outputTypes["odum"] = tempOutNames;
+ outputTypes["canberra"] = tempOutNames;
+ outputTypes["stricteuclidean"] = tempOutNames;
+ outputTypes["strictchord"] = tempOutNames;
+ outputTypes["hellinger"] = tempOutNames;
+ outputTypes["manhattan"] = tempOutNames;
+ outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["soergel"] = tempOutNames;
+ outputTypes["spearman"] = tempOutNames;
+ outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["speciesprofile"] = tempOutNames;
+ outputTypes["hamming"] = tempOutNames;
}
catch(exception& e) {
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
outputTypes["braycurtis"] = tempOutNames;
+ outputTypes["odum"] = tempOutNames;
+ outputTypes["canberra"] = tempOutNames;
+ outputTypes["stricteuclidean"] = tempOutNames;
+ outputTypes["strictchord"] = tempOutNames;
+ outputTypes["hellinger"] = tempOutNames;
+ outputTypes["manhattan"] = tempOutNames;
+ outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["soergel"] = tempOutNames;
+ outputTypes["spearman"] = tempOutNames;
+ outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["speciesprofile"] = tempOutNames;
+ outputTypes["hamming"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
}else if (Estimators[i] == "braycurtis") {
cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
+ }else if (Estimators[i] == "odum") {
+ cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+"odum")));
+ outputNames.push_back(fileNameRoot+"odum"); outputTypes["odum"].push_back(fileNameRoot+"odum");
+ }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] == "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] == "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] == "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");
}
+
}
}
}
virtual void setAll(bool){}
virtual bool hasLciHci(){ return false; }
virtual bool getAll() { bool a; return a; }
+ virtual bool calcNeedsAll() { bool a; return a; }
virtual string getName() { return ""; };
virtual ~Display() {}
Display() { m = MothurOut::getInstance(); }
--- /dev/null
+/*
+ * hamming.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "hamming.h"
+
+/***********************************************************************/
+EstOutput Hamming::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ int numA = 0;
+ int numB = 0;
+ int numShared = 0;
+
+ //calc the 2 denominators
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ int A = shared[0]->getAbundance(i);
+ int B = shared[1]->getAbundance(i);
+
+ if (A != 0) { numA++; }
+ if (B != 0) { numB++; }
+ if ((A != 0) && (B != 0)) { numShared++; }
+ }
+
+ data[0] = numA + numB - (2 * numShared);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Hamming", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef HAMMING_H
+#define HAMMING_H
+
+/*
+ * hamming.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Hamming : public Calculator {
+
+public:
+ Hamming() : Calculator("hamming", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
--- /dev/null
+/*
+ * hellinger.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "hellinger.h"
+
+/***********************************************************************/
+EstOutput Hellinger::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumA = 0.0;
+ double sumB = 0.0;
+
+ //calc the 2 denominators
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ sumA += shared[0]->getAbundance(i);
+ sumB += shared[1]->getAbundance(i);
+ }
+
+
+ //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);
+
+ double term1 = sqrt((Aij / sumA));
+ double term2 = sqrt((Bij / sumB));
+
+ sum += ((term1 - term2) * (term1 - term2));
+ }
+
+ data[0] = sqrt(sum);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Hellinger", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+
--- /dev/null
+#ifndef HELLINGER_H
+#define HELLINGER_H
+
+/*
+ * hellinger.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Hellinger : public Calculator {
+
+public:
+ Hellinger() : Calculator("hellinger", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
+
--- /dev/null
+/*
+ * manhattan.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "manhattan.h"
+
+/***********************************************************************/
+EstOutput Manhattan::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);
+
+ sum += abs((Aij - Bij));
+ }
+
+ data[0] = sum;
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Manhattan", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
--- /dev/null
+#ifndef MANHATTAN_H
+#define MANHATTAN_H
+
+/*
+ * manhattan.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Manhattan : public Calculator {
+
+public:
+ Manhattan() : Calculator("manhattan", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
//check for blank file
gobble(fileHandle);
if (fileHandle.eof()) { fileHandle.close(); return true; }
+ fileHandle.close();
}
return false;
}
--- /dev/null
+/*
+ * odum.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/14/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "odum.h"
+
+/***********************************************************************/
+
+EstOutput Odum::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumNum = 0.0;
+ double sumDenom = 0.0;
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+
+ int Aij = shared[0]->getAbundance(i);
+ int Bij = shared[1]->getAbundance(i);
+
+ sumNum += abs(Aij - Bij);
+ sumDenom += Aij + Bij;
+ }
+
+ data[0] = sumNum / sumDenom;
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Odum", "getValues");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef ODUM_H
+#define ODUM_H
+
+/*
+ * odum.h
+ * Mothur
+ *
+ * Created by westcott on 12/14/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Odum : public Calculator {
+
+public:
+ Odum() : Calculator("odum", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
+
--- /dev/null
+/*
+ * soergel.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "soergel.h"
+
+/***********************************************************************/
+EstOutput Soergel::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumNum = 0.0;
+ double sumMax = 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);
+
+ sumNum += abs((Aij - Bij));
+ sumMax += max(Aij, Bij);
+ }
+
+ data[0] = sumNum / sumMax;
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Soergel", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef SOERGEL_H
+#define SOERGEL_H
+
+/*
+ * soergel.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Soergel : public Calculator {
+
+public:
+ Soergel() : Calculator("soergel", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * spearman.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "spearman.h"
+
+/***********************************************************************/
+EstOutput Spearman::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ SAbundVector savA = shared[0]->getSAbundVector();
+ SAbundVector savB = shared[1]->getSAbundVector();
+
+ double sumRanks = 0.0;
+ int numOTUS = shared[0]->getNumBins();
+
+ //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);
+
+ int rankA = savA.get(Aij);
+ int rankB = savB.get(Bij);
+
+ sumRanks += ((rankA - rankB) * (rankA - rankB));
+ }
+
+ data[0] = 1.0 - ((6 * sumRanks) / (float) (numOTUS * (numOTUS-1)));
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Soergel", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef SPEARMAN_H
+#define SPEARMAN_H
+
+/*
+ * spearman.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class Spearman : public Calculator {
+
+public:
+ Spearman() : Calculator("spearman", 1, false) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(vector<SharedRAbundVector*>);
+private:
+
+};
+
+/***********************************************************************/
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * speciesprofile.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "speciesprofile.h"
+
+/***********************************************************************/
+EstOutput SpeciesProfile::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ data.resize(1,0);
+
+ double sumA = 0.0;
+ double sumB = 0.0;
+
+ for (int i = 0; i < shared[0]->getNumBins(); i++) {
+ sumA += shared[0]->getAbundance(i);
+ sumB += shared[1]->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);
+
+ sum += (((A / sumA) - (B / sumB)) * ((A / sumA) - (B / sumB)));
+ }
+
+ data[0] = sqrt(sum);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SpeciesProfile", "getValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
--- /dev/null
+#ifndef SPECIESPROFILE_H
+#define SPECIESPROFILE_H
+
+/*
+ * speciesprofile.h
+ * Mothur
+ *
+ * Created by westcott on 12/15/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "calculator.h"
+
+/***********************************************************************/
+
+class SpeciesProfile : public Calculator {
+
+public:
+ SpeciesProfile() : Calculator("speciesprofile", 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
+
+
#include "sharedbraycurtis.h"
#include "sharedjackknife.h"
#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "stricteuclidean.h"
+#include "strictchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "strictpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "strictkulczynski.h"
+#include "speciesprofile.h"
+#include "hamming.h"
//**********************************************************************************************************************
vector<string> SummarySharedCommand::getValidParameters(){
sumCalculators.push_back(new BrayCurtis());
}else if (Estimators[i] == "whittaker") {
sumCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ 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] == "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] == "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] == "speciesprofile") {
+ sumCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ sumCalculators.push_back(new Hamming());
}
}
}
#endif
if (m->control_pressed) { return 0; }
-
- for(int i=0;i<fastaFileNames.size();i++){
- if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+ set<string> blanks;
+ for(int i=0;i<fastaFileNames.size();i++){
+ if (m->isBlank(fastaFileNames[i])) { blanks.insert(fastaFileNames[i]); }
else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
else {
ifstream inFASTA;
m->openInputFile(fastaFileNames[i], inFASTA);
ofstream outGroups;
string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
+
+ //if the fastafile is on the blanks list then the groups file should be as well
+ if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
+
m->openOutputFile(outGroupFilename, outGroups);
outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
}
}
+ for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
+
+ blanks.clear();
if(qFileName != ""){
for(int i=0;i<qualFileNames.size();i++){
- if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
+ if (m->isBlank(qualFileNames[i])) { blanks.insert(qualFileNames[i]); }
else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
- else {
- ifstream inQual;
- string seqName;
- m->openInputFile(qualFileNames[i], inQual);
-// ofstream outGroups;
-//
-// string thisGroup = "";
-// if (i > comboStarts) {
-// map<string, int>::iterator itCombo;
-// for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
-// if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
-// }
-// }
-// else{ thisGroup = groupVector[i]; }
-
- inQual.close();
- }
}
}
+ for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
shared["lennon"] = "lennon";
shared["morisitahorn"] = "morisitahorn";
shared["braycurtis"] = "braycurtis";
+ shared["odum"] = "odum";
+ shared["canberra"] = "canberra";
+ shared["stricteuclidean"] = "stricteuclidean";
+ shared["strictchord"] = "strictchord";
+ shared["hellinger"] = "hellinger";
+ shared["manhattan"] = "manhattan";
+ shared["strictpearson"] = "strictpearson";
+ shared["soergel"] = "soergel";
+ shared["spearman"] = "spearman";
+ shared["strictkulczynski"] = "strictkulczynski";
+ shared["speciesprofile"] = "speciesprofile";
+ shared["hamming"] = "hamming";
shared["default"] = "default";
}
catch(exception& e) {
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["stricteuclidean"] = "stricteuclidean";
+ sharedsummary["strictchord"] = "strictchord";
+ sharedsummary["hellinger"] = "hellinger";
+ sharedsummary["manhattan"] = "manhattan";
+ sharedsummary["strictpearson"] = "strictpearson";
+ sharedsummary["strictkulczynski"] = "strictkulczynski";
+ sharedsummary["soergel"] = "soergel";
+ sharedsummary["spearman"] = "spearman";
+ sharedsummary["speciesprofile"] = "speciesprofile";
+ sharedsummary["hamming"] = "hamming";
sharedsummary["default"] = "default";
}
catch(exception& e) {
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