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- 3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */,
- 374CD63F0F65832000D90B4A /* libshuffcommand.cpp in Sources */,
- 374CD6F10F65A4C100D90B4A /* coverage.cpp in Sources */,
- 3765B47A0F77D15900C3EDC5 /* nocommands.cpp in Sources */,
- 3765B4E20F78055000C3EDC5 /* sharedochiai.cpp in Sources */,
- 3765B5160F780A7F00C3EDC5 /* sharedanderberg.cpp in Sources */,
- 217595330F791EEE001CC3C6 /* sharedkulczynski.cpp in Sources */,
- 2175953F0F792111001CC3C6 /* sharedkulczynskicody.cpp in Sources */,
- 217595590F792490001CC3C6 /* sharedlennon.cpp in Sources */,
- 217595640F7927BB001CC3C6 /* sharedmorisitahorn.cpp in Sources */,
- 217595710F792A33001CC3C6 /* sharedbraycurtis.cpp in Sources */,
- 3765B5380F7A5A9E00C3EDC5 /* heatmapcommand.cpp in Sources */,
- 3765B5460F7A62A000C3EDC5 /* heatmap.cpp in Sources */,
+ EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */,
+ EB9303F90F53517300E8EF26 /* geom.cpp in Sources */,
+ EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */,
+ EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
+ EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
+ EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
+ EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
+ EBE2A41E0F7D5C6100A54BF8 /* jackknife2.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
GCC_DYNAMIC_NO_PIC = NO;
GCC_ENABLE_FIX_AND_CONTINUE = YES;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"_GLIBCXX_DEBUG=1",
"_GLIBCXX_DEBUG_PEDANTIC=1",
buildSettings = {
DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 3;
INSTALL_PATH = /usr/local/bin;
PRODUCT_NAME = mothur;
};
GCC_OPTIMIZATION_LEVEL = 3;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
- INSTALL_MODE_FLAG = "a-w,a+rX";
PREBINDING = NO;
SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
};
GCC_OPTIMIZATION_LEVEL = 0;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
- INSTALL_MODE_FLAG = "a-w,a+rX";
PREBINDING = NO;
SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
};
--- /dev/null
+/*
+ * ssbp.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/6/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "bergerparker.h"
+#include "calculator.h"
+
+/***************************************************************/
+
+EstOutput BergerParker::getValues(SAbundVector* rank){
+ try {
+ data.resize(1,0);
+ //Berger-Parker index
+ double BP = (double)rank->getNumSeqs()/(double)rank->getMaxRank();
+ //cout << "BP index = " << 1/BP << "\n\n";
+
+ data[0] = BP;
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
--- /dev/null
+#ifndef BERGERPARKER_H
+#define BERGERPARKER_H
+/*
+ * bergerparker.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/6/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "calculator.h"
+
+/*This class implements the SSBP estimator on single group.
+It is a child of the calculator class.*/
+
+/***********************************************************************/
+
+class BergerParker : public Calculator {
+
+public:
+ BergerParker() : Calculator("bergerparker", 1) {};
+ EstOutput getValues(SAbundVector*);
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
+
+private:
+};
+
+/***********************************************************************/
+
+#endif
+
--- /dev/null
+/*
+ * bstick.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/6/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "bstick.h"
+#include "calculator.h"
+
+/***********************************************************************/
+double BStick::invSum(int index, double numSpec)
+{
+ double sum = 0;
+ for(int i = index; i <= numSpec; i++)
+ sum += 1/(double)i;
+ return sum;
+}
+
+RAbundVector BStick::getRAbundVector(SAbundVector* rank){
+ vector <int> rData;
+ int mr = 1;
+ int nb = 0;
+ int ns = 0;
+
+ for(int i = rank->size()-1; i > 0; i--)
+ {
+ int cur = rank->get(i);
+ if(mr == 1 && cur > 0)
+ mr = i;
+ nb += cur;
+ ns += i*cur;
+ for(int j = 0; j < cur; j++)
+ rData.push_back(i);
+ }
+
+ RAbundVector rav = RAbundVector(rData, mr, nb, ns);
+ rav.setLabel(rank->getLabel());
+ return rav;
+}
+
+/***************************************************************************/
+
+/***************************************************************************/
+EstOutput BStick::getValues(SAbundVector* rank){
+ try {
+ data.resize(2,0);
+ rdata = getRAbundVector(rank);
+ double numInd = (double)rdata.getNumSeqs();
+ double numSpec = (double)rdata.getNumBins();
+
+ double sumExp = 0;
+ double sumObs = 0;
+ double maxDiff = 0;
+
+ for(int i = 0; i < rdata.size(); i++)
+ {
+ sumObs += rdata.get(i);
+ sumExp += numInd/numSpec*invSum(i+1,numSpec);
+ double diff = fabs(sumObs-sumExp);
+ if(diff > maxDiff)
+ maxDiff = diff;
+ }
+
+ double DStatistic = maxDiff/numInd;
+ double critVal = 0;
+ /*cout << "BStick:\n";
+ cout << "D-Statistic = " << DStatistic << "\n";
+ cout << "Critical value for 95% confidence interval = ";*/
+ if(rdata.size() > 20)
+ {
+ critVal = .886/sqrt(rdata.size());
+ }
+ else
+ {
+ KOSTable table;
+ critVal = table.getConfLimit(numSpec);
+ }
+ /*cout << critVal << "\n";
+ cout << "If D-Statistic is less than the critical value then the data fits the Broken Stick model w/ 95% confidence.\n\n";*/
+
+ data[0] = DStatistic;
+ data[1] = critVal;
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+ if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+
--- /dev/null
+#ifndef BSTICK_H
+#define BSTICK_H
+/*
+ * bstick.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/6/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/*This class implements the BStick estimator on single group.
+It is a child of the calculator class.*/
+
+/***********************************************************************/
+
+class BStick : public Calculator {
+
+public:
+ BStick() : Calculator("bstick", 3) {};
+ EstOutput getValues(SAbundVector*);
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
+
+private:
+ double invSum(int, double);
+ RAbundVector getRAbundVector(SAbundVector*);
+ RAbundVector rdata;
+};
+
+/***********************************************************************/
+
+#endif
exit(1);
}
}
+/***********************************************************************/
+int VecCalc::sumElements(vector<int> vec){
+ try {
+ return sumElements(vec,0);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+int VecCalc::sumElements(vector<int> vec, int index){
+ try {
+ int sum = 0;
+ for(int i = index; i < vec.size(); i++)
+ sum += vec.at(i);
+ return sum;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function sumElements. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/***********************************************************************/
double VecCalc::sumElements(vector<double> vec){
try {
}
}
/***********************************************************************/
+int VecCalc::numNZ(vector<int> vec){
+ try {
+ int numNZ = 0;
+ for(int i = 0; i < vec.size(); i++)
+ if(vec.at(i) != 0)
+ numNZ++;
+ return numNZ;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the VecCalc class Function numNZ. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the VecCalc class function numNZ. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
double VecCalc::numNZ(vector<double> vec){
try {
double numNZ = 0;
}
}
/***********************************************************************/
-double BDiversity::getWhitt(vector<double> vec1, vector<double> vec2){
- try {
- VecCalc vecCalc;
- double numSpec = vecCalc.numNZ(vecCalc.addVecs(vec1,vec2));
- return 2*numSpec/(vecCalc.numNZ(vec1)+vecCalc.numNZ(vec2))-1;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getWhitt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BDiversity class function getWhitt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************************/
-double BDiversity::getMS(vector<double> vec1, vector<double> vec2){
- try {
- VecCalc vecCalc;
- double a = vecCalc.numNZ(vecCalc.multVecs(vec1, vec2));
- double b = vecCalc.numPos(vecCalc.addVecs(vecCalc.addVecs(vec1, vecCalc.multiply(vec2, -1)), vecCalc.multiply(vecCalc.multVecs(vec1, vec2), -1)));
- double c = vecCalc.numPos(vecCalc.addVecs(vecCalc.addVecs(vec2, vecCalc.multiply(vec1, -1)), vecCalc.multiply(vecCalc.multVecs(vec2, vec1), -1)));
- return a/(a+b+c);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getMS. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BDiversity class function getMS. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************************/
-double BDiversity::getSor(vector<double> vec1, vector<double> vec2){
- try {
- double sum = 0;
- double asum = 0;
- double bsum = 0;
- for(int i = 0; i < vec1.size(); i++)
- {
- asum += vec1.at(i);
- bsum += vec2.at(i);
- if(vec1.at(i) >= vec2.at(i))
- sum += vec2.at(i);
- else
- sum += vec1.at(i);
- }
- return 2*sum/(asum+bsum);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getSor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BDiversity class function getSor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************************/
-double BDiversity::getMor(vector<double> vec1, vector<double> vec2){
- try {
- double sum = 0;
- double asum = 0;
- double bsum = 0;
- double sum1 = 0;
- double sum2 = 0;
- for(int i = 0; i < vec1.size(); i++)
- {
- sum += vec1.at(i)*vec2.at(i);
- asum += pow(vec1.at(i),2);
- bsum += pow(vec2.at(i),2);
- sum1 += vec1.at(i);
- sum2 += vec2.at(i);
- }
- return 2*sum/((asum/pow(sum1,2)+bsum/pow(sum2,2))*(sum1*sum2));
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function getMor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BDiversity class function getMor. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************************/
-void BDiversity::printD(vector<vector<double> > columns, int type){
- try {
- cout << " ";
- for(int i = 0; i < columns.size(); i++)
- cout << "Column:" << i << " ";
- cout << "\n";
- for(int i = 0; i < columns.size(); i++)
- {
- cout << "Column " << i << ":";
- for(int j = 0; j < columns.size(); j++)
- {
- if(j > i)
- {
- double B;
- if(type == 1)
- B = getWhitt(columns.at(i), columns.at(j));
- else if(type == 2)
- B = 1-getMS(columns.at(i), columns.at(j));
- else if(type == 3)
- B = 1-getSor(columns.at(i), columns.at(j));
- else if(type == 4)
- B = 1-getMor(columns.at(i), columns.at(j));
-
- cout << B << " ";
- }
- else
- cout << " ";
- }
- cout << "\n";
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function printD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BDiversity class function printD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/***********************************************************************/
-void BDiversity::doBD(vector<double> vec, double cols)//vec = The data vector if the data table was read left-to-right, top-to-bottom. cols = the number of columns in the data table.
-{ try {
- VecCalc vecCalc;
- vector<vector<double> > columns = vecCalc.gen2DVec(vec,cols,1);
-
- cout.setf(ios_base::fixed, ios_base::floatfield);
- cout.precision(6);//This formats the data so the tables look pretty.
-
- //Whittaker's measure Bw (presence/absence data)
- cout << "Whittaker's measure Bw (presence/absence data):\n";
- printD(columns, 1);
- double sum = 0;
- for(int i = 0; i < cols; i++)
- sum += vecCalc.numNZ(columns.at(i));
- double meanRichness = sum/cols;
- vector<double> totVec = vecCalc.genTotVec(columns);
- double totRichness = vecCalc.numNZ(totVec);
- cout << "\nOverall B Diversity = " << totRichness/meanRichness << "\n\n\n";//The overall B Diversity
-
- //Marczewski-Steinhaus(MS) distance(Jaccard index) (presence/abscence data)
- cout << "Marczewski-Steinhaus(MS) distance(Jaccard index) (presence/abscence data):\n";
- printD(columns, 2);
- sum = 0;
- for(int i = 0; i < cols; i++)
- for(int j = 0; j < cols; j++)
- if(j > i)
- sum += vecCalc.numNZ(columns.at(i))+vecCalc.numNZ(columns.at(j)) - 2*vecCalc.numNZ(vecCalc.multVecs(columns.at(i), columns.at(j)));
- cout << "\nOverall B Diversity = " << sum/cols << "\n\n\n";//The overall B Diversity
-
- //Sorensen quantitative index (abundance data)
- cout << "Sorensen quantitative index (abundance data):\n";
- printD(columns, 3);
- cout << "\n\n";
-
- //Sorensen quantitative index (abundance data)
- cout << "Morisita-Horn index (abundance data):\n";
- printD(columns,4);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BDiversity class Function doBD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BDiversity class function doBD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
/***********************************************************************/
void BrokenStick::doBStick(vector<double> vec)//vec = The data vector.
return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
}
/***********************************************************************/
-void GeometricSeries::doGeomTest(vector<double> vec)//vec = the data vector
+/*void GeometricSeries::doGeomTest(vector<double> vec)//vec = the data vector
{ try {
VecCalc vecCalc;
vec = vecCalc.quicksort(vec);//Sorts vec
cout << "An unknown error has occurred in the GeometricSeries class function doGeomTest. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-}
+}*/
/***********************************************************************/
void Jackknifing::doJK(vector<double> vec, double cols)//vec = the data vector if the data table was read left-to-right, top-to-bottom. cols = The number of columns in the data table.
}
/***********************************************************************/
-void LogSD::doLogSD(vector<double> indVec, vector<double> specVec) //indVec = individuals vector, specVec = species vector
+/*void LogSD::doLogSD(vector<double> indVec, vector<double> specVec) //indVec = individuals vector, specVec = species vector
{ try {
VecCalc vecCalc;
double numSpec = vecCalc.sumElements(specVec);//numSpec = The total number of species
cout << "An unknown error has occurred in the LogSD class function doLogSD. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-}
+}*/
/***********************************************************************/
void QStatistic::doQStat(vector<double> vec)//vec = The data vector.
{ try {
/***********************************************************************/
double TDTable::getConfLimit(int row, int col) //Rows are the degrees of freedom
{ try {
- //Confidence Level .80 .90 .95 .98 .99 .998 .999
+ //Found on http://www.vgtu.lt/leidiniai/elektroniniai/Probability.pdf/Table%203.pdf
+
+ //Confidence Level .90 .95 .975 .99 .995 .999 .9995
double values[33][7] = {{3.078, 6.314, 12.706, 31.821, 63.656, 318.289, 636.578},
- {1.886, 2.920, 4.303, 6.965, 9.925, 22.328, 31.600},
- {1.638, 2.353, 3.182, 4.541, 5.841, 10.214, 12.924},
- {1.533, 2.132, 2.776, 3.747, 4.604, 7.173, 8.610},
- {1.476, 2.015, 2.571, 3.365, 4.032, 5.894, 6.869},
- {1.440, 1.943, 2.447, 3.143, 3.707, 5.208, 5.959},
- {1.415, 1.895, 2.365, 2.998, 3.499, 4.785, 5.408},
- {1.397, 1.860, 2.306, 2.896, 3.355, 4.501, 5.041},
- {1.383, 1.833, 2.262, 2.821, 3.250, 4.297, 4.781},
- {1.372, 1.812, 2.228, 2.764, 3.169, 4.144, 4.587},
- {1.363, 1.796, 2.201, 2.718, 3.106, 4.025, 4.437},
- {1.356, 1.782, 2.179, 2.681, 3.055, 3.930, 4.318},
- {1.350, 1.771, 2.160, 2.650, 3.012, 3.852, 4.221},
- {1.345, 1.761, 2.145, 2.624, 2.977, 3.787, 4.140},
- {1.341, 1.753, 2.131, 2.602, 2.947, 3.733, 4.073},
- {1.337, 1.746, 2.120, 2.583, 2.921, 3.686, 4.015},
- {1.333, 1.740, 2.110, 2.567, 2.898, 3.646, 3.965},
- {1.330, 1.734, 2.101, 2.552, 2.878, 3.610, 3.922},
- {1.328, 1.729, 2.093, 2.539, 2.861, 3.579, 3.883},
- {1.325, 1.725, 2.086, 2.528, 2.845, 3.552, 3.850},
- {1.323, 1.721, 2.080, 2.518, 2.831, 3.527, 3.819},
- {1.321, 1.717, 2.074, 2.508, 2.819, 3.505, 3.792},
- {1.319, 1.714, 2.069, 2.500, 2.807, 3.485, 3.768},
- {1.318, 1.711, 2.064, 2.492, 2.797, 3.467, 3.745},
- {1.316, 1.708, 2.060, 2.485, 2.787, 3.450, 3.725},
- {1.315, 1.706, 2.056, 2.479, 2.779, 3.435, 3.707},
- {1.314, 1.703, 2.052, 2.473, 2.771, 3.421, 3.689},
- {1.313, 1.701, 2.048, 2.467, 2.763, 3.408, 3.674},
- {1.311, 1.699, 2.045, 2.462, 2.756, 3.396, 3.660},
- {1.310, 1.697, 2.042, 2.457, 2.750, 3.385, 3.646},
- {1.296, 1.671, 2.000, 2.390, 2.660, 3.232, 3.460},
- {1.289, 1.658, 1.980, 2.358, 2.617, 3.160, 3.373},
- {1.282, 1.645, 1.960, 2.326, 2.576, 3.091, 3.291}};
+ {1.886, 2.920, 4.303, 6.965, 9.925, 22.328, 31.600},
+ {1.638, 2.353, 3.182, 4.541, 5.841, 10.214, 12.924},
+ {1.533, 2.132, 2.776, 3.747, 4.604, 7.173, 8.610},
+ {1.476, 2.015, 2.571, 3.365, 4.032, 5.894, 6.869},
+ {1.440, 1.943, 2.447, 3.143, 3.707, 5.208, 5.959},
+ {1.415, 1.895, 2.365, 2.998, 3.499, 4.785, 5.408},
+ {1.397, 1.860, 2.306, 2.896, 3.355, 4.501, 5.041},
+ {1.383, 1.833, 2.262, 2.821, 3.250, 4.297, 4.781},
+ {1.372, 1.812, 2.228, 2.764, 3.169, 4.144, 4.587},
+ {1.363, 1.796, 2.201, 2.718, 3.106, 4.025, 4.437},
+ {1.356, 1.782, 2.179, 2.681, 3.055, 3.930, 4.318},
+ {1.350, 1.771, 2.160, 2.650, 3.012, 3.852, 4.221},
+ {1.345, 1.761, 2.145, 2.624, 2.977, 3.787, 4.140},
+ {1.341, 1.753, 2.131, 2.602, 2.947, 3.733, 4.073},
+ {1.337, 1.746, 2.120, 2.583, 2.921, 3.686, 4.015},
+ {1.333, 1.740, 2.110, 2.567, 2.898, 3.646, 3.965},
+ {1.330, 1.734, 2.101, 2.552, 2.878, 3.610, 3.922},
+ {1.328, 1.729, 2.093, 2.539, 2.861, 3.579, 3.883},
+ {1.325, 1.725, 2.086, 2.528, 2.845, 3.552, 3.850},
+ {1.323, 1.721, 2.080, 2.518, 2.831, 3.527, 3.819},
+ {1.321, 1.717, 2.074, 2.508, 2.819, 3.505, 3.792},
+ {1.319, 1.714, 2.069, 2.500, 2.807, 3.485, 3.768},
+ {1.318, 1.711, 2.064, 2.492, 2.797, 3.467, 3.745},
+ {1.316, 1.708, 2.060, 2.485, 2.787, 3.450, 3.725},
+ {1.315, 1.706, 2.056, 2.479, 2.779, 3.435, 3.707},
+ {1.314, 1.703, 2.052, 2.473, 2.771, 3.421, 3.689},
+ {1.313, 1.701, 2.048, 2.467, 2.763, 3.408, 3.674},
+ {1.311, 1.699, 2.045, 2.462, 2.756, 3.396, 3.660},
+ {1.310, 1.697, 2.042, 2.457, 2.750, 3.385, 3.646},
+ {1.296, 1.671, 2.000, 2.390, 2.660, 3.232, 3.460},
+ {1.289, 1.658, 1.980, 2.358, 2.617, 3.160, 3.373},
+ {1.282, 1.645, 1.960, 2.326, 2.576, 3.091, 3.291}};
return values[row][col];
}
catch(exception& e) {
exit(1);
}
}
+
+/***********************************************************************/
+double KOSTable::getConfLimit(int index) //Table of Critical values for N = 4-20 for One-Sample Kolmogorov-Smirnov Test
+{ try {
+ //Confidence Level = .05
+ //Sample size = 4-20.
+ //Found on http://www.utdallas.edu/~herve/MolinAbdi1998-LillieforsTechReport.pdf
+
+ double values[21] = {.9011,
+ .6372,
+ .5203,
+ .4506,
+ 0.3754,
+ 0.3427,
+ 0.3245,
+ 0.3041,
+ 0.2875,
+ 0.2744,
+ 0.2616,
+ 0.2506,
+ 0.2426,
+ 0.2337,
+ 0.2257,
+ 0.2196,
+ 0.2128,
+ 0.2071,
+ 0.2018,
+ 0.1965,
+ 0.1920,
+ };
+ return values[index];
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TDTable class Function getConfLimit. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TDTable class function getConfLimit. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/***********************************************************************
void TrunLN::doTrunLN(vector<double> indVec, vector<double> specVec) //indVec = individuals vector, specVec = species vector
{
{
// The methods seen in the order here is how they are ordered throughout the class.
public:
+ VecCalc(){};
void printElements(vector<double>); //This prints the values of the vector on one line with a space between each value.
void printElements(vector<string>); //This prints the values of the vector on one line with a space between each value.
int findString(vector<string>, string);//This returns the index of the given string in the given <string> vector, if the string does not exist in the vector it returns -1.
double mean(vector<double>); //This returns the mean value of the vector.
double stError(vector<double>); //This returns the standard error of the vector.
+ int sumElements(vector<int>, int);
+ int sumElements(vector<int>);
double sumElements(vector<double>); //This returns the sum of all the values in the vector.
double sumElements(vector<double>, int); //This returns the sum of all the values in the vector excluding those whose index is before the given index.
double findMax(vector<double>); //This returns the maximum value in the vector.
+ int numNZ(vector<int>); //This returns the number of non-zero values in the vector.
double numNZ(vector<double>); //This returns the number of non-zero values in the vector.
double numPos(vector<double>); //This returns the number of positive values in the vector.
double findMaxDiff(vector<double>, vector<double>); //This returns the absolute value of the maximum difference between the two vectors.
the Marczewski-Steinhaus distance.*/
-class BDiversity
+/*class BDiversity
{
public:
void doBD(vector<double>, double);//Main method
double getSor(vector<double>, vector<double>);//Sorensen quantitative index
double getMor(vector<double>, vector<double>);//Morisita-Horn index
void printD(vector<vector<double> >, int);//This prints a table that represents the given 2D vector, the second paramter specifies which method is to be used (1 for Whitt, 2 for MS, 3 for Sor, and 4 for Mor)
-};
+};*/
/**************************************************************************************************/
It prints the D-Statistic and the critical values for the Kolmogorov-Smirnov
1-sample test at the 95% confidence interval.*/
-class GeometricSeries
+/*class GeometricSeries
{
public:
void doGeomTest(vector<double>);
-};
+};*/
/**************************************************************************************************/
//This Class calculates the jackknifed estimate of the data and
It then generates a D-Statistic and prints the D-Statistic and
the critical values for the Kolmogorov-Smirnov 1 sample test.*/
-class LogSD
+/*class LogSD
{
public:
void doLogSD(vector<double>, vector<double>);
-};
+};*/
/**************************************************************************************************/
//This Class calculates and prints the Q-Statistic for the data.
double getConfLimit(int,int);
};
+/**************************************************************************************************/
+//This Class stores the table of the confidence limits of the One-Sample Kolmogorov-Smirnov Test.
+class KOSTable
+{
+ public:
+ double getConfLimit(int);
+};
+
/**************************************************************************************************/
/*This Class calculates the truncated lognormal for the data.
It then prints the D-Statistic and the critical values for the
#include "npshannon.h"
#include "shannon.h"
#include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
//**********************************************************************************************************************
fileNameRoot = getRootName(globaldata->inputFileName);
int i;
validCalculator = new ValidCalculators();
-
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
if (globaldata->Estimators[i] == "sobs") {
cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
}else if (globaldata->Estimators[i] == "bootstrap") {
cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
+ }else if (globaldata->Estimators[i] == "geom") {
+ cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geom")));
+ }else if (globaldata->Estimators[i] == "qstat") {
+ cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
+ }else if (globaldata->Estimators[i] == "logsd") {
+ cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logsd")));
+ }else if (globaldata->Estimators[i] == "bergerparker") {
+ cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
+ }else if (globaldata->Estimators[i] == "bstick") {
+ cDisplays.push_back(new CollectDisplay(new BStick(), new OneColumnFile(fileNameRoot+"bstick")));
}
}
}
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+<<<<<<< collectsharedcommand.cpp
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
+=======
#include "sharednseqs.h"
#include "sharedochiai.h"
#include "sharedanderberg.h"
#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+>>>>>>> 1.13
//**********************************************************************************************************************
cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
}else if (globaldata->Estimators[i] == "sharedthetan") {
cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
+ }else if (globaldata->Estimators[i] == "sharedkstest") {
+ cDisplays.push_back(new CollectDisplay(new SharedKSTest(), new SharedOneColumnFile(fileNameRoot+"shared.kstest")));
+ }else if (globaldata->Estimators[i] == "sharedbdiversity") {
+ cDisplays.push_back(new CollectDisplay(new SharedBDiversity(), new SharedOneColumnFile(fileNameRoot+"shared.bdiversity")));
}else if (globaldata->Estimators[i] == "sharednseqs") {
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
}else if (globaldata->Estimators[i] == "sharedochiai") {
splitAtComma(value, optionText);
splitAtEquals(parameter, value);
- //is it a valid parameter for the command
- if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
+ //is it a valid parameter
+ if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (errorFree) { //gets the last parameter and value
value = optionText;
splitAtEquals(parameter, value);
-
- //is it a valid parameter for the command
- if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
+ //is it a valid parameter
+ if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
}else if (sabundfile != "") {
if ((listfile != "") || (rabundfile != "")) {
cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
- }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
}
--- /dev/null
+/*
+ * geom.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 2/23/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "geom.h"
+#include "calculator.h"
+
+/***********************************************************************/
+
+double Geom::kEq(double k, double spec){
+ return k/(1-k)*pow(1-k, spec)/(1-pow(1-k, spec));
+}
+
+RAbundVector Geom::getRAbundVector(SAbundVector* rank){
+ vector <int> rData;
+ int mr = 1;
+ int nb = 0;
+ int ns = 0;
+
+ for(int i = rank->size()-1; i > 0; i--)
+ {
+ int cur = rank->get(i);
+ if(mr == 1 && cur > 0)
+ mr = i;
+ nb += cur;
+ ns += i*cur;
+ for(int j = 0; j < cur; j++)
+ rData.push_back(i);
+ }
+
+ RAbundVector rav = RAbundVector(rData, mr, nb, ns);
+ rav.setLabel(rank->getLabel());
+ return rav;
+}
+
+/***********************************************************************************/
+
+/***********************************************************************************/
+EstOutput Geom::getValues(SAbundVector* rank){
+ try {
+ data.resize(2,0);
+
+ rdata = getRAbundVector(rank);
+ int numInd = rdata.getNumSeqs();
+ int numSpec = rdata.getNumBins();
+ int min = rdata.get(rdata.size()-1);
+ double k = .5;
+ double step = .49999;
+
+ while(fabs(min - numInd*kEq(k, (double)numSpec)) > .0001) //This uses a binary search to find the value of k.
+ {
+ if(numInd*kEq(k, numSpec) > min)
+ k += step;
+ else
+ k -= step;
+ step /= 2;
+ }
+
+ double cK = 1/(1-pow(1-k, numSpec));
+ double sumExp = 0;
+ double sumObs = 0;
+ double maxDiff = 0;
+
+ for(int i = 0; i < rdata.size(); i++)
+ {
+ sumObs += rdata.get(i);
+ sumExp += numInd*cK*k*pow(1-k, i);
+ double diff = fabs(sumObs-sumExp);
+ if(diff > maxDiff)
+ maxDiff = diff;
+ }
+
+ double DStatistic = maxDiff/numInd;
+ double critVal = 0;
+ /*cout << "Geom:\n";
+ cout << "D-Statistic = " << DStatistic << "\n";
+ cout << "Critical value for 95% confidence interval = ";*/
+ if(rdata.size() > 20)
+ {
+ critVal = .886/sqrt(rdata.size());
+ }
+ else
+ {
+ KOSTable table;
+ critVal = table.getConfLimit(numSpec);
+ }
+ /*cout << critVal << "\n";
+ cout << "If D-Statistic is less than the critical value then the data fits the Geometric Series model w/ 95% confidence.\n\n";*/
+
+ data[0] = DStatistic;
+ data[1] = critVal;
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+ if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+
+
+
+
+
+
--- /dev/null
+#ifndef GEOM_H
+#define GEOM_H
+
+/*
+ * geom.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 2/23/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/* This class implements the LogSD estimator on single group.
+It is a child of the calculator class. */
+
+/***********************************************************************/
+
+class Geom : public Calculator {
+
+public:
+ Geom() : Calculator("geom", 3) {};
+ EstOutput getValues(SAbundVector*);
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
+
+private:
+ double kEq(double, double);
+ RAbundVector getRAbundVector(SAbundVector*);
+ RAbundVector rdata;
+};
+
+/***********************************************************************/
+
+#endif
+
+
+
+
+
//input defaults for calculators
if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
splitAtDash(calc, Estimators);
}
if (commandName == "collect.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
--- /dev/null
+/*
+ * logsd.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 2/23/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "logsd.h"
+#include "calculator.h"
+
+/***********************************************************************/
+
+double LogSD::logS(double x){
+ return -(1-x)*log(1-x)/x;
+}
+EstOutput LogSD::getValues(SAbundVector* rank){
+ try {
+
+ /*test data VVV
+ int dstring[] = {0,37,22,12,12,11,11,6,4,3,5,2,4,2,3,2,2,4,2,0,4,4,1,1,0,1,0,0,2,2,0,0,0,2,2,0,0,0,1,1,3,0,2,0,0,0,0,0,2,0,0,1,1,1,0,0,0,0,1,0,0,1,0,0,2,0,0,0,0,1,0,0,0,1,0,1,0,0,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1};
+ vector<int> dvec;
+ for(int i = 0; i < 1800; i++)
+ dvec.push_back(dstring[i]);
+ int mr = 1799;
+ int nb = 197;
+ int ns = 6815;
+ SAbundVector rankw = SAbundVector(dvec, mr,nb,ns);
+ SAbundVector *rank = &rankw;*/
+
+ data.resize(2,0);
+ int numInd = rank->getNumSeqs();
+ int numSpec = rank->getNumBins();
+ double snRatio = (double)numSpec/numInd;
+ double x = .5;
+ double step = .4999999999;
+
+ while(fabs(snRatio - logS(x)) > .00001) //This uses a binary search to find the value of x.
+ {
+ if(logS(x) > snRatio)
+ x += step;
+ else
+ x -= step;
+ step /= 2;
+ }
+ double alpha = numInd*(1-x)/x;
+
+ int oct = 1;
+ double octSumObs = 0;
+ double sumObs = 0;
+ double octSumExp = 0;
+ double sumExp = 0;
+ double maxDiff = 0;
+ for(int y = 1; y < rank->size(); y++)
+ {
+ if(y - .5 < pow(2.0, oct))
+ {
+ octSumObs += rank->get(y);
+ octSumExp += alpha*pow(x,y)/(y);
+ }
+ else
+ {
+ sumObs += octSumObs;
+ octSumObs = rank->get(y);
+
+ sumExp += octSumExp;
+ octSumExp = alpha*pow(x,y)/(y);
+ oct++;
+ }
+
+ if(y == rank->size()-1)
+ {
+ sumObs += octSumObs;
+ sumExp += octSumExp;
+ }
+
+ double diff = fabs(sumObs - .5 - sumExp);
+ if(diff > maxDiff)
+ maxDiff = diff;
+ }
+
+ double DStatistic = (maxDiff + .5)/numSpec;
+ /*cout << "LogSD:\n";
+ cout << "D Test Statistic = " << DStatistic << "\n";
+ cout << ".05 confidence value = " << .89196/sqrt(numSpec) << "\n";
+ cout << "If D Test Statistic is greater than the critical value then the data fits the Log Series Distribution model w/ 95% confidence.\n\n";*/
+
+ data[0] = DStatistic;
+ data[1] = .89196/sqrt(numSpec);
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+ if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
--- /dev/null
+#ifndef LOGSD_H
+#define LOGSD_H
+
+/*
+ * logsd.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 2/23/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/*This class implements the LogSD estimator on single group.
+It is a child of the calculator class.*/
+
+/***********************************************************************/
+
+class LogSD : public Calculator {
+
+public:
+ LogSD() : Calculator("logsd", 3) {};
+ EstOutput getValues(SAbundVector*);
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
+
+private:
+ double logS(double);
+ RAbundVector rdata;
+};
+
+/***********************************************************************/
+
+#endif
+
+
+
+
+
--- /dev/null
+/*
+ * qstat.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/4/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "qstat.h"
+#include "calculator.h"
+
+/***********************************************************************/
+
+EstOutput QStat::getValues(SAbundVector* rank){
+ try {
+
+ /*test data VVV
+ int dstring[] = {0,0,1,4,2,0,2,1,1,1,1,1,0,1,1,2,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,2,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1};
+ vector<int> dvec;
+ for(int i = 0; i < 171; i++)
+ dvec.push_back(dstring[i]);
+ int mr = 170;
+ int nb = 29;
+ int ns = 884;
+ SAbundVector rankw = SAbundVector(dvec, mr,nb,ns);
+ SAbundVector *rank = &rankw;*/
+ data.resize(1,0);
+ int numSpec = rank->getNumBins();
+ int r1 = -1;
+ int r3 = -1;
+ int r1Ind = 0;
+ int r3Ind = 0;
+ int sumSpec = 0;
+ int iqSum = 0;
+ for(int i = 1; i < rank->size(); i++)
+ {
+ if(r1 != -1 && r3 != -1)
+ i = rank->size();
+
+ sumSpec += rank->get(i);
+
+ if(r1 == -1 && sumSpec >= numSpec*.25)
+ {
+ r1 = rank->get(i);
+ r1Ind = i;
+ }
+ else if(r3 == -1 && sumSpec >= numSpec*.75)
+ {
+ r3 = rank->get(i);
+ r3Ind = i;
+ }
+ else if(sumSpec >= numSpec*.25 && sumSpec < numSpec*.75)
+ iqSum += rank->get(i);
+ }
+
+ double qstat = (.5*r1 + iqSum + .5*r3)/log((double)r3Ind/r1Ind);
+ //cout << "QStat:\nQStatistic = " << qstat << "\n\n";
+
+ data[0] = qstat;
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
--- /dev/null
+#ifndef QSTAT_H
+#define QSTAT_H
+/*
+ * qstat.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/4/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/*This class implements the LogSD estimator on single group.
+It is a child of the calculator class.*/
+
+/***********************************************************************/
+
+class QStat : public Calculator {
+
+public:
+ QStat() : Calculator("qstat", 3) {};
+ EstOutput getValues(SAbundVector*);
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*) {return data;};
+
+private:
+ RAbundVector rdata;
+};
+
+/***********************************************************************/
+
+#endif
+
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "ordervector.hpp"
+#include "calculator.h"
/***********************************************************************/
}
}
+/***********************************************************************/
+
+RAbundVector::RAbundVector(vector<int> rav, int mr, int nb, int ns) {
+ try {
+ numBins = nb;
+ maxRank = mr;
+ numSeqs = ns;
+ data = rav;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the RAbundVector class Function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the RAbundVector class function RAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
/***********************************************************************/
/***********************************************************************/
+void RAbundVector::quicksort(){
+ sort(data.rbegin(), data.rend());
+}
+
+/***********************************************************************/
+
+int RAbundVector::sum(){
+ VecCalc vecCalc;
+ return vecCalc.sumElements(data);
+}
+
+/***********************************************************************/
+
+int RAbundVector::sum(int index){
+ VecCalc vecCalc;
+ return vecCalc.sumElements(data, index);
+}
+
+/***********************************************************************/
+
+int RAbundVector::numNZ(){
+ VecCalc vecCalc;
+ return vecCalc.numNZ(data);
+}
+
+/***********************************************************************/
+
vector<int>::reverse_iterator RAbundVector::rbegin(){
return data.rbegin();
}
public:
RAbundVector();
RAbundVector(int);
+ RAbundVector(vector<int>, int, int, int);
// RAbundVector(const RAbundVector&);
RAbundVector(string, vector<int>);
RAbundVector(const RAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs){};
void pop_back();
void resize(int);
int size();
+ void quicksort();
+ int sum();
+ int sum(int);
+ int numNZ();
vector<int>::reverse_iterator rbegin();
vector<int>::reverse_iterator rend();
#include "sabundvector.hpp"
#include "utilities.hpp"
+#include "calculator.h"
/***********************************************************************/
SAbundVector::SAbundVector(string id, vector<int> sav) : DataVector(id), data(sav) {
try {
-
for(int i=0;i<sav.size();i++){
if(data[i] != 0){ maxRank = i; }
numSeqs += i*data[i];
/***********************************************************************/
+SAbundVector::SAbundVector(vector <int> dataVec, int mr, int nb, int ns) {
+ try {
+ data = dataVec;
+ maxRank = mr;
+ numBins = nb;
+ numSeqs = ns;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SAbundVector class Function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SAbundVector class function SAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+
SAbundVector::SAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
int hold;
}
}
+
/***********************************************************************/
void SAbundVector::set(int sabund, int abundance){
}
}
+
/***********************************************************************/
int SAbundVector::get(int index){
exit(1);
}
}
+/***********************************************************************/
+
+void SAbundVector::quicksort(){
+ sort(data.rbegin(), data.rend());
+}
+
+/***********************************************************************/
+
+int SAbundVector::sum(){
+ VecCalc vecCalc;
+ return vecCalc.sumElements(data);
+}
/***********************************************************************/
#include "datavector.hpp"
#include "rabundvector.hpp"
#include "ordervector.hpp"
+#include "calculator.h"
/* This class is a child to datavector. It represents OTU information at a certain distance.
SAbundVector();
SAbundVector(int);
// SAbundVector(const SAbundVector&);
+ SAbundVector(vector<int>, int, int, int);
SAbundVector(string, vector<int>);
SAbundVector(const SAbundVector& rv) : DataVector(rv.label), data(rv.data), maxRank(rv.maxRank), numBins(rv.numBins), numSeqs(rv.numSeqs){};
SAbundVector(ifstream&);
void set(int, int);
int get(int);
void push_back(int);
+ void quicksort();
+ int sum();
void resize(int);
int size();
void print(ostream&);
void print(string, ostream&);
- RAbundVector getRAbundVector();
+ RAbundVector getRAbundVector();
SAbundVector getSAbundVector();
OrderVector getOrderVector(map<string,int>*);
vector<int> data;
// bool needToUpdate;
// void updateStats();
+
int maxRank;
int numBins;
int numSeqs;
--- /dev/null
+/*
+ * bdiversity.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/13/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "sharedbdiversity.h"
+#include "calculator.h"
+
+/***********************************************************************/
+
+double SharedBDiversity::whitt(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+ double nz1 = (double)shared1->numNZ();
+ double nz2 = (double)shared2->numNZ();
+ double sum = nz1;
+ for(int i = 1; i < shared1->size(); i++)
+ {
+ if(shared1->get(i).abundance == 0 && shared2->get(i).abundance != 0)
+ sum++;
+ }
+ return 2*sum/(nz1+nz2)-1;
+}
+
+/***********************************************************************/
+
+double SharedBDiversity::ms(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+ double a = 0;
+ double b = 0;
+ double c = 0;
+ for(int i = 1; i < shared1->size(); i++)
+ {
+ int abund1 = shared1->get(i).abundance;
+ int abund2 = shared2->get(i).abundance;
+
+ if(abund1 > 0 && abund2 > 0)
+ a++;
+ else if(abund1 > 0 && abund2 == 0)
+ b++;
+ else if(abund1 == 0 && abund2 > 0)
+ c++;
+ }
+ return (b+c)/(a+b+c);
+}
+
+/***********************************************************************/
+
+double SharedBDiversity::sor(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+ double sum = 0;
+ double asum = 0;
+ double bsum = 0;
+ for(int i = 1; i < shared1->size(); i++)
+ {
+ int abund1 = shared1->get(i).abundance;
+ int abund2 = shared2->get(i).abundance;
+
+ asum += abund1;
+ bsum += abund2;
+ if(abund1 >= abund2)
+ sum += abund2;
+ else
+ sum += abund1;
+ }
+ return 2*sum/(asum+bsum);
+}
+
+/***********************************************************************/
+
+double SharedBDiversity::mor(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+ double multSum = 0;
+ double powSum1 = 0;
+ double powSum2 = 0;
+ double ind1 = 0;
+ double ind2 = 0;
+ for(int i = 1; i < shared1->size(); i++)
+ {
+ double abund1 = (double)shared1->get(i).abundance;
+ double abund2 = (double)shared2->get(i).abundance;
+ multSum += abund1*abund2;
+ powSum1 += pow(abund1, 2);
+ powSum2 += pow(abund2, 2);
+ ind1 += abund1;
+ ind2 += abund2;
+ }
+ return 2*multSum / ((powSum1/pow(ind1, 2) + powSum2/pow(ind2, 2)) * (ind1*ind2));
+}
+/***********************************************************************/
+
+EstOutput SharedBDiversity::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+ try {
+ data.resize(4,0);
+
+ double whitt1 = whitt(shared1, shared2);
+ double jac1 = 1-ms(shared1, shared2);
+ double sor1 = sor(shared1, shared2);
+ double mor1 = mor(shared1, shared2);
+ /*cout << "Whittaker's Measure: " << whitt1 << "\n";
+ cout << "Marczewski-Steinhaus distance: " << jac1 << "\n";
+ cout << "Sorensen index: " << sor1 << "\n";
+ cout << "Morisita-Horn index: " << mor1 << "\n";*/
+
+ data[0] = whitt1;
+ data[1] = jac1;
+ data[2] = sor1;
+ data[3] = mor1;
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+ if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+ if (isnan(data[2]) || isinf(data[0])) { data[2] = 0; }
+ if (isnan(data[3]) || isinf(data[1])) { data[3] = 0; }
+
+ return data;
+ }
+
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
\ No newline at end of file
--- /dev/null
+#ifndef SHAREDBDIVERSITY_H
+#define SHAREDBDIVERSITY_H
+/*
+ * bdiversity.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/13/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/*This class implements the BDiversity estimator on 2 groups.
+It is a child of the calculator class.*/
+
+/***********************************************************************/
+
+class SharedBDiversity : public Calculator {
+
+public:
+ SharedBDiversity() : Calculator("sharedbdiversity", 3) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+ double whitt(SharedRAbundVector*, SharedRAbundVector*);
+ double ms(SharedRAbundVector*, SharedRAbundVector*);
+ double sor(SharedRAbundVector*, SharedRAbundVector*);
+ double mor(SharedRAbundVector*, SharedRAbundVector*);
+};
+
+/***********************************************************************/
+
+#endif
\ No newline at end of file
--- /dev/null
+/*
+ * kstest.cpp
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/6/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "sharedkstest.h"
+#include "calculator.h"
+#include <algorithm>
+
+/***********************************************************************/
+
+EstOutput SharedKSTest::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2){
+ try {
+ data.resize(2,0);
+
+ //Must return shared1 and shared2 to original order at conclusion of kstest
+ vector <individual> initData1 = shared1->getData();
+ vector <individual> initData2 = shared2->getData();
+ shared1->sortD();
+ shared2->sortD();
+
+ int numNZ1 = shared1->numNZ();
+ int numNZ2 = shared2->numNZ();
+ double numInd1 = (double)shared1->getNumSeqs();
+ double numInd2 = (double)shared2->getNumSeqs();
+
+ double maxDiff = -1;
+ double sum1 = 0;
+ double sum2 = 0;
+ for(int i = 1; i < shared1->getNumBins(); i++)
+ {
+ sum1 += shared1->get(i).abundance;
+ sum2 += shared2->get(i).abundance;
+ double diff = fabs((double)sum1/numInd1 - (double)sum2/numInd2);
+ if(diff > maxDiff)
+ maxDiff = diff;
+ }
+
+ double DStatistic = maxDiff*numNZ1*numNZ2;
+ double a = pow((double)(numNZ1 + numNZ2)/(numNZ1*numNZ2),.5);
+ double pVal = exp(-2*pow(maxDiff/a,2));
+ double critVal = 1.36*a*numNZ1*numNZ2;
+
+ /*cout << "Kolmogorov-Smirnov 2-sample test:\n";
+ if(numNZ1 > 25 && numNZ2 > 25) //If the sample sizes are both bigger than 25.
+ cout << "P-Value = " << pVal << "\nP-Value is the probability that the data sets are significantly different.\n";
+ else
+ {
+ //cout << "90% Confidence Critical Value = " << 1.22*a*numNZ1*numNZ2 << "\n";
+ cout << "D-Statistic = " << DStatistic << "\n";
+ cout << "95% Confidence Critical Value = " << critVal << "\n";
+ cout << "If D-Statistic is greater than the critical value then the data sets are significantly different at the 95% confidence level.\n\n";
+ }*/
+
+ shared1->setData(initData1);
+ shared2->setData(initData2);
+
+ data[0] = DStatistic;
+ data[1] = critVal;
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+ if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the NPShannon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the NPShannon class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
--- /dev/null
+#ifndef SHAREDKSTEST_H
+#define SHAREDKSTEST_H
+/*
+ * kstest.h
+ * Mothur
+ *
+ * Created by Thomas Ryabin on 3/6/09.
+ * Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+#include "calculator.h"
+
+/*This class implements the KSTest estimator on 2 groups.
+It is a child of the calculator class.*/
+
+/***********************************************************************/
+
+class SharedKSTest : public Calculator {
+
+public:
+ SharedKSTest() : Calculator("sharedkstest", 3) {};
+ EstOutput getValues(SAbundVector*) {return data;};
+ EstOutput getValues(SharedRAbundVector*, SharedRAbundVector*);
+private:
+};
+
+/***********************************************************************/
+
+#endif
string group;
int bin;
int abundance;
+ bool operator()(const individual& i1, const individual& i2) {
+ return (i1.abundance > i2.abundance);
+ }
};
#include "sabundvector.hpp"
#include "utilities.hpp"
#include "sabundvector.hpp"
#include "ordervector.hpp"
+#include <algorithm>
/***********************************************************************/
exit(1);
}
}
+/***********************************************************************/
+
+void SharedRAbundVector::setData(vector <individual> newData){
+ data = newData;
+}
/***********************************************************************/
return data[index].abundance;
}
+/***********************************************************************/
+
+int SharedRAbundVector::numNZ(){
+ int sum = 0;
+ for(int i = 1; i < numBins; i++)
+ if(data[i].abundance > 0)
+ sum++;
+ return sum;
+}
+/***********************************************************************/
+void SharedRAbundVector::sortD(){
+ struct individual indObj;
+ sort(data.begin()+1, data.end(), indObj);
+}
/***********************************************************************/
individual SharedRAbundVector::get(int index){
return data[index];
}
+/***********************************************************************/
+vector <individual> SharedRAbundVector::getData(){
+ return data;
+}
/***********************************************************************/
void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
int SharedRAbundVector::getMaxRank(){
return maxRank;
}
-
/***********************************************************************/
SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
exit(1);
}
}
+/***********************************************************************/
+RAbundVector SharedRAbundVector::getRAbundVector2() {
+ try {
+ RAbundVector rav;
+ for(int i = 0; i < numBins; i++)
+ if(data[i].abundance != 0)
+ rav.push_back(data[i].abundance-1);
+ return rav;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/***********************************************************************/
SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
SharedRAbundVector(int);
//SharedRAbundVector(string, vector<int>);
SharedRAbundVector(const SharedRAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs){};
-// SharedRAbundVector(ifstream&);
+ //SharedRAbundVector(ifstream&);
~SharedRAbundVector();
int getNumBins();
void setGroupIndex(int);
void set(int, int, string); //OTU, abundance, groupname
+ void setData(vector <individual>);
individual get(int);
+ vector <individual> getData();
int getAbundance(int);
+ int numNZ();
+ void sortD(); //Sorts the data in descending order.
void push_back(int, int, string); //abundance, OTU, groupname
void pop_back();
void resize(int);
void print(ostream&);
RAbundVector getRAbundVector();
+ RAbundVector getRAbundVector2();
SAbundVector getSAbundVector();
OrderVector getOrderVector(map<string,int>*);
SharedOrderVector getSharedOrderVector();
#include "npshannon.h"
#include "shannon.h"
#include "jackknife.h"
+#include "geom.h"
+#include "logsd.h"
+#include "qstat.h"
+#include "bergerparker.h"
+#include "bstick.h"
//**********************************************************************************************************************
for (i=0; i<globaldata->Estimators.size(); i++) {
if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
+
if(globaldata->Estimators[i] == "sobs"){
sumCalculators.push_back(new Sobs());
}else if(globaldata->Estimators[i] == "chao"){
sumCalculators.push_back(new Chao1());
+ }else if(globaldata->Estimators[i] == "geom"){
+ sumCalculators.push_back(new Geom());
+ }else if(globaldata->Estimators[i] == "logsd"){
+ sumCalculators.push_back(new LogSD());
+ }else if(globaldata->Estimators[i] == "qstat"){
+ sumCalculators.push_back(new QStat());
+ }else if(globaldata->Estimators[i] == "bergerparker"){
+ sumCalculators.push_back(new BergerParker());
+ }else if(globaldata->Estimators[i] == "bstick"){
+ sumCalculators.push_back(new BStick());
}else if(globaldata->Estimators[i] == "ace"){
convert(globaldata->getAbund(), abund);
if(abund < 5)
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
cout << sabund->getLabel() << '\t' << count << endl;
-
+
outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
vector<double> data = sumCalculators[i]->getValues(sabund);
outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
+ //sumCalculators[i]->print(outputFileHandle);
}
+
outputFileHandle << endl;
}
-
sabund = input->getSAbundVector();
count++;
}
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "sharedbdiversity.h"
#include "sharedochiai.h"
#include "sharedanderberg.h"
#include "sharedkulczynski.h"
sumCalculators.push_back(new SharedThetaYC());
}else if (globaldata->Estimators[i] == "sharedthetan") {
sumCalculators.push_back(new SharedThetaN());
+ }else if (globaldata->Estimators[i] == "sharedkstest") {
+ sumCalculators.push_back(new SharedKSTest());
}else if (globaldata->Estimators[i] == "sharednseqs") {
sumCalculators.push_back(new SharedNSeqs());
}else if (globaldata->Estimators[i] == "sharedochiai") {
}else if (globaldata->Estimators[i] == "sharedbraycurtis") {
sumCalculators.push_back(new SharedBrayCurtis());
}
+ else if (globaldata->Estimators[i] == "sharedbdiversity") {
+ sumCalculators.push_back(new SharedBDiversity());
+ }
+
}
}
-
//reset calc for next command
globaldata->setCalc("");
int n = 1;
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++) {
+ outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
outputFileHandle << order->getLabel() << '\t';
//sort groups to be alphanumeric
void ValidCalculators::initialSingle() {
try {
- single["sobs"] = "sobs";
- single["chao"] = "chao";
- single["ace"] = "ace";
- single["jack"] = "jack";
- single["shannon"] = "shannon";
- single["npshannon"] = "npshannon";
- single["simpson"] = "simpson";
- single["bootstrap"] = "bootstrap";
- single["default"] = "default";
+ single["sobs"] = "sobs";
+ single["chao"] = "chao";
+ single["ace"] = "ace";
+ single["jack"] = "jack";
+ single["shannon"] = "shannon";
+ single["npshannon"] = "npshannon";
+ single["simpson"] = "simpson";
+ single["bergerparker"] = "bergerparker";
+ single["bootstrap"] = "bootstrap";
+ single["geom"] = "geom";
+ single["logsd"] = "logsd";
+ single["qstat"] = "qstat";
+ single["bstick"] = "bstick";
single["nseqs"] = "nseqs";
+ single["default"] = "default";
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
shared["sharedsorest"] = "sharedsorest";
shared["sharedthetayc"] = "sharedthetayc";
shared["sharedthetan"] = "sharedthetan";
+ shared["sharedkstest"] = "sharedkstest";
+ shared["sharedbdiversity"] = "sharedbdiversity";
shared["sharednseqs"] = "sharednseqs";
shared["sharedochiai"] = "sharedochiai";
shared["sharedanderberg"] = "sharedanderberg";
summary["shannon"] = "shannon";
summary["npshannon"] = "npshannon";
summary["simpson"] = "simpson";
+ summary["bergerparker"] = "bergerparker";
+ summary["geom"] = "geom";
summary["bootstrap"] = "bootstrap";
+ summary["logsd"] = "logsd";
+ summary["qstat"] = "qstat";
+ summary["bstick"] = "bstick";
summary["nseqs"] = "nseqs";
summary["default"] = "default";
}
sharedsummary["sharedsorest"] = "sharedsorest";
sharedsummary["sharedthetayc"] = "sharedthetayc";
sharedsummary["sharedthetan"] = "sharedthetan";
+ sharedsummary["sharedkstest"] = "sharedkstest";
+ sharedsummary["sharedbdiversity"] = "sharedbdiversity";
sharedsummary["sharednseqs"] = "sharednseqs";
sharedsummary["sharedochiai"] = "sharedochiai";
sharedsummary["sharedanderberg"] = "sharedanderberg";
ValidParameters::ValidParameters() {
try {
- initialReaddist();
- initialReadotu();
- initialReadtree();
- initialCluster();
- initialDeconvolute();
- initialParsimony();
- initialCollectsingle();
- initialCollectshared();
- initialRarefactsingle();
- initialRarefactshared();
- initialSummarysingle();
- initialSummaryshared();
- initialUnifracweighted();
- initialUnifracunweighted();
- initialLibshuff();
+ parameters["phylip"] = "phylip";
+ parameters["column"] = "column";
+ parameters["list"] = "list";
+ parameters["rabund"] = "rabund";
+ parameters["sabund"] = "sabund";
+ parameters["name"] = "name";
+ parameters["group"] = "group";
+ parameters["order"] = "order";
+ parameters["fasta"] = "fasta";
+ parameters["tree"] = "tree";
+ parameters["fileroot"] = "fileroot";
+ parameters["cutoff"] = "cutoff";
+ parameters["method"] = "method";
+ parameters["format"] = "format";
+ parameters["precision"] = "precision";
+ parameters["label"] = "label";
+ parameters["line"] = "line";
+ parameters["iters"] = "iters";
+ parameters["jumble"] = "jumble";
+ parameters["freq"] = "freq";
+ parameters["abund"] = "abund";
+ parameters["random"] = "random";
+ parameters["groups"] = "groups";
+ parameters["calc"] = "calc";
+ parameters["sharedrarefaction"] = "sharedrarefaction";
+ parameters["sharedsummary"] = "sharedsummary";
+ parameters["shared"] = "shared";
+ parameters["single"] = "single";
+ parameters["rarefaction"] = "rarefaction";
+
+ initCommandParameters();
+ initParameterRanges();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
ValidParameters::~ValidParameters() {}
+
/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter, string command) {
+bool ValidParameters::isValidParameter(string parameter, string command, string value) {
try {
+ bool valid = false;
+ vector<string> cParams = commandParameters[command];
+ int numParams = cParams.size();
+ for(int i = 0; i < numParams; i++)
+ {
+ if(cParams.at(i).compare(parameter) == 0)
+ {
+ valid = true;
+ i = numParams;
+ }
+ }
+ if(!valid)
+ {
+ cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
+ return false;
+ }
+
+ if(parameterRanges.count(parameter) != 1)
+ return true;
- if (command == "read.dist") {
- //is it valid
- if ((readdist.find(parameter)) != (readdist.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = readdist.begin(); it != readdist.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "read.otu") {
- //is it valid
- if ((readotu.find(parameter)) != (readotu.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = readotu.begin(); it != readotu.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- //are you looking for a calculator for a rarefaction parameter
- }else if (command == "read.tree") {
- //is it valid
- if ((readtree.find(parameter)) != (readtree.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = readtree.begin(); it != readtree.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- //are you looking for a calculator for a summary parameter
- }else if (command == "cluster") {
- //is it valid
- if ((cluster.find(parameter)) != (cluster.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = cluster.begin(); it != cluster.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; } //are you looking for a calculator for a sharedsummary parameter
- }else if (command == "deconvolute") {
- //is it valid
- if ((deconvolute.find(parameter)) != (deconvolute.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = deconvolute.begin(); it != deconvolute.end(); it++) {
- cout << it->first;
- }
- cout << endl;
- return false; }
- }else if (command == "parsimony") {
- //is it valid
- if ((parsimony.find(parameter)) != (parsimony.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = parsimony.begin(); it != parsimony.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "collect.single") {
- //is it valid
- if ((collectsingle.find(parameter)) != (collectsingle.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = collectsingle.begin(); it != collectsingle.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "collect.shared") {
- //is it valid
- if ((collectshared.find(parameter)) != (collectshared.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = collectshared.begin(); it != collectshared.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "rarefaction.single") {
- //is it valid
- if ((rarefactsingle.find(parameter)) != (rarefactsingle.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = rarefactsingle.begin(); it != rarefactsingle.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "rarefaction.shared") {
- //is it valid
- if ((rarefactshared.find(parameter)) != (rarefactshared.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = rarefactshared.begin(); it != rarefactshared.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "summary.single") {
- //is it valid
- if ((summarysingle.find(parameter)) != (summarysingle.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = summarysingle.begin(); it != summarysingle.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "summary.shared") {
- //is it valid
- if ((summaryshared.find(parameter)) != (summaryshared.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = summaryshared.begin(); it != summaryshared.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "unifrac.weighted") {
- //is it valid
- if ((unifracweighted.find(parameter)) != (unifracweighted.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = unifracweighted.begin(); it != unifracweighted.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "unifrac.unweighted") {
- //is it valid
- if ((unifracunweighted.find(parameter)) != (unifracunweighted.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = unifracunweighted.begin(); it != unifracunweighted.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "libshuff") {
- //is it valid
- if ((libshuff.find(parameter)) != (libshuff.end())) {
+ int pVal;
+ double piSentinel = 3.14159;
+ vector<string> range = parameterRanges[parameter];
+
+ valid = convertTest(value, pVal);
+
+ if(!valid)
+ return false;
+
+
+
+ /********************************************************************************************************
+ Special Cases
+ *********************************************************************************************************/
+
+ if(parameter.compare("precision") == 0)
+ {
+ double logNum = log10((double)pVal);
+ double diff = (double)((int)logNum - logNum);
+ if(diff != 0)
+ {
+ cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+ return false;
+ }
+ }
+
+ /************************************************************************************************************/
+
+
+
+ double a,b,c,d,e;
+
+ if(range.at(1).compare("NA") == 0)
+ a = piSentinel;
+ else
+ a = atoi(range.at(1).c_str());
+
+ if(range.at(3).compare("NA") == 0)
+ b = piSentinel;
+ else
+ b = atoi(range.at(3).c_str());
+
+ if(range.at(4).compare("between") == 0)
+ c = 0;
+ else if(range.at(4).compare("only") == 0)
+ c = 1;
+ else
+ {
+ cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
+ return false;
+ }
+
+ if(range.at(0).compare(">") == 0)
+ d = 0;
+ else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
+ d = 1;
+ else
+ {
+ cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
+ return false;
+ }
+
+ if(range.at(2).compare("<") == 0)
+ e = 0;
+ else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
+ e = 1;
+ else
+ {
+ cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
+ return false;
+ }
+
+ bool a0 = pVal > a;
+ bool a1 = pVal >= a;
+ bool b0 = pVal < b;
+ bool b1 = pVal <= b;
+
+ if(c != 1)
+ {
+ if(a == piSentinel && b == piSentinel)
return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = libshuff.begin(); it != libshuff.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "heatmap") {
- //is it valid
- if ((heatmap.find(parameter)) != (heatmap.end())) {
+ if(a != piSentinel && b == piSentinel)
+ {
+ if(d == 0)
+ valid = a0;
+ else
+ valid = a1;
+ }
+ else if(a == piSentinel && b != piSentinel)
+ {
+ if(e == 0)
+ valid = b0;
+ else
+ valid = b1;
+ }
+ else
+ {
+ if(d == 0 && e == 0)
+ valid = (a0 && b0);
+ else if(d == 0 && e == 1)
+ valid = (a0 && b1);
+ else if(d == 1 && e == 0)
+ valid = (a1 && b0);
+ else
+ valid = (a1 && b1);
+ }
+ }
+ else
+ {
+ if(a == piSentinel && b == piSentinel)
return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = heatmap.begin(); it != heatmap.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
-
- //not a valid paramter
- }else if (command == "help") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "quit") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; }
+ if(a != piSentinel && b == piSentinel)
+ valid = (pVal == a);
+ else if(a == piSentinel && b != piSentinel)
+ valid = (pVal == b);
+ else
+ valid = (pVal == a || pVal == b);
+ }
- return false;
+ if(valid)
+ return true;
+ else
+ {
+ cout << "The '" << parameter << "' parameter needs to be ";
+ if(c == 1)
+ cout << "either '" << a << "' or '" << b << "'.\n";
+ else
+ {
+ if(a != piSentinel)
+ {
+ cout << ">";
+ if(d != 0)
+ cout << "=";
+ cout << " '" << a << "'";
+ }
+ if(b == piSentinel)
+ cout << ".\n";
+ else if(a != piSentinel)
+ cout << " and ";
+ if(b != piSentinel)
+ {
+ cout << "<";
+ if(e != 0)
+ cout << "=";
+ cout << " '" << b << ".\n";
+ }
+ }
+ return false;
+ }
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
/***********************************************************************/
-void ValidParameters::initialReaddist() {
- readdist["phylip"] = "phylip";
- readdist["column"] = "column";
- readdist["name"] = "name";
- readdist["group"] = "group";
- readdist["cutoff"] = "cutoff";
- readdist["precision"] = "precision";
-}
-/***********************************************************************/
-void ValidParameters::initialReadotu() {
- readotu["list"] = "list";
- readotu["rabund"] = "rabund";
- readotu["sabund"] = "sabund";
- readotu["shared"] = "shared";
- readotu["group"] = "group";
- readotu["order"] = "order";
- readotu["label"] = "label";
- readotu["line"] = "line";
-}
-/***********************************************************************/
-void ValidParameters::initialReadtree() {
- readtree["group"] = "group";
- readtree["tree"] = "tree";
-}
-/***********************************************************************/
-void ValidParameters::initialCluster() {
- cluster["cutoff"] = "cutoff";
- cluster["method"] = "method";
- cluster["precision"] = "precision";
-}
-/***********************************************************************/
-void ValidParameters::initialDeconvolute() {
- deconvolute["fasta"] = "fasta";
-}
-/***********************************************************************/
-void ValidParameters::initialParsimony() {
- parsimony["iters"] = "iters";
- parsimony["random"] = "random";
- parsimony["groups"] = "groups";
-}
-/***********************************************************************/
-void ValidParameters::initialCollectsingle() {
- collectsingle["label"] = "label";
- collectsingle["line"] = "line";
- collectsingle["freq"] = "freq";
- collectsingle["calc"] = "calc";
-}
-/***********************************************************************/
-void ValidParameters::initialCollectshared() {
- collectshared["label"] = "label";
- collectshared["line"] = "line";
- collectshared["freq"] = "freq";
- collectshared["calc"] = "calc";
- collectshared["jumble"] = "jumble";
-}
-/***********************************************************************/
-void ValidParameters::initialRarefactsingle() {
- rarefactsingle["label"] = "label";
- rarefactsingle["line"] = "line";
- rarefactsingle["freq"] = "freq";
- rarefactsingle["calc"] = "calc";
- rarefactsingle["iters"] = "iters";
-}
-/***********************************************************************/
-void ValidParameters::initialRarefactshared() {
- rarefactshared["label"] = "label";
- rarefactshared["line"] = "line";
- rarefactshared["jumble"] = "jumble";
- rarefactshared["calc"] = "calc";
- rarefactshared["iters"] = "iters";
-}
-/***********************************************************************/
-void ValidParameters::initialSummarysingle() {
- summarysingle["label"] = "label";
- summarysingle["line"] = "line";
- summarysingle["calc"] = "calc";
-}
+
/***********************************************************************/
-void ValidParameters::initialSummaryshared() {
- summaryshared["label"] = "label";
- summaryshared["line"] = "line";
- summaryshared["calc"] = "calc";
- summaryshared["jumble"] = "jumble";
+void ValidParameters::initCommandParameters() {
+ try {
+ //{"parameter1","parameter2",...,"last parameter"};
+
+ string readdistArray[] = {"phylip","name","cutoff","precision"};
+ commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
+
+ string readotuArray[] = {"list","order","group","shared", "sabund"};
+ commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
+
+ string clusterArray[] = {"cutoff","precision","method"};
+ commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
+
+ string deconvoluteArray[] = {"fasta"};
+ commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
+
+ string collectsingleArray[] = {"freq","line","label","single","precision","abund"};
+ commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
+
+ string collectsharedArray[] = {"jumble","freq","line","label","shared","groups"};
+ commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
+
+ string getgroupArray[] = {};
+ commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
+
+ string getlabelArray[] = {};
+ commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
+
+ string getlineArray[] = {};
+ commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
+ string rarefactionsingleArray[] = {"iters","freq","line","label","rarefaction","abund"};
+ commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
+
+ string rarefactionsharedArray[] = {"iters","jumble","line","label","sharedrarefaction"};
+ commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
+
+ string summarysingleArray[] = {"line","label","summary","abund"};
+ commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
+
+ string summarysharedArray[] = {"jumble","line","label","sharedsummary"};
+ commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
+
+ string quitArray[] = {};
+ commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
+
/***********************************************************************/
-void ValidParameters::initialUnifracweighted() {
- unifracweighted["iters"] = "iters";
- unifracweighted["groups"] = "groups";
-}
+
/***********************************************************************/
-void ValidParameters::initialUnifracunweighted() {
- unifracunweighted["iters"] = "iters";
- unifracunweighted["groups"] = "groups";
+void ValidParameters::initParameterRanges() {
+ try {
+ int rangeSize = 5;
+
+ /**************************************************************************************************************
+ {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
+ A number representing the lower bound ("NA" if there is no lower bound),
+ "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
+ A number representing the upper bound ("NA" if there is no lower bound),
+ "between" if between lower and upper bounds or "only" if exactly one of the bounds};
+
+ # = parameter
+ # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
+ ***********************************************************************************************************/
+
+ string precisionArray[] = {">=","10", "<","NA", "between"};
+ parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
+
+ string itersArray[] = {">=","10", "<","NA", "between"};
+ parameterRanges["iters"] = addParameters(itersArray, rangeSize);
+
+ string jumbleArray[] = {">","0", "<","1", "only"};
+ parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
+
+ string freqArray[] = {">","1", "<","NA", "between"};
+ parameterRanges["freq"] = addParameters(freqArray, rangeSize);
+
+ string lineArray[] = {">=","1", "<","NA", "between"};
+ parameterRanges["line"] = addParameters(lineArray, rangeSize);
+
+ string abundArray[] = {">=","5", "<","NA", "between"};
+ parameterRanges["abund"] = addParameters(abundArray, rangeSize);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
+
/***********************************************************************/
-void ValidParameters::initialLibshuff() {
- libshuff["cutoff"] = "cutoff";
- libshuff["iters"] = "iters";
- libshuff["groups"] = "groups";
- libshuff["step"] = "step";
- libshuff["form"] = "form";
-}
+
/***********************************************************************/
-void ValidParameters::initialHeatmap() {
- heatmap["label"] = "label";
- heatmap["line"] = "line";
+vector<string> ValidParameters::addParameters(string parameters[], int size) {
+ try {
+ vector<string> pVector (parameters, parameters+size);
+ return pVector;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
+
using namespace std;
#include "mothur.h"
+#include "utilities.hpp"
//This class contains a list of all valid parameters in Mothur.
//It has a function which will tell you if your parameter is valid.
public:
ValidParameters();
~ValidParameters();
- bool isValidParameter(string, string);
-
+ bool isValidParameter(string);
+ bool isValidParameter(string, string, string);
+ vector <string> addParameters(string[], int);
+ void initCommandParameters();
+ void initParameterRanges();
+
private:
map<string, string> readdist;
map<string, string> readotu;
map<string, string> heatmap;
map<string, string>::iterator it;
-
- void initialReaddist();
- void initialReadotu();
- void initialReadtree();
- void initialCluster();
- void initialDeconvolute();
- void initialParsimony();
- void initialCollectsingle();
- void initialCollectshared();
- void initialRarefactsingle();
- void initialRarefactshared();
- void initialSummarysingle();
- void initialSummaryshared();
- void initialUnifracweighted();
- void initialUnifracunweighted();
- void initialLibshuff();
- void initialHeatmap();
+ map<string, vector<string> > commandParameters;
+ map<string, vector<string> > parameterRanges;
};
projects / mothur.git / commitdiff