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A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
+ A7FA10001302E096003860FE /* mantelcommand.h */,
+ A7FA10011302E096003860FE /* mantelcommand.cpp */,
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A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
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A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */,
A75790591301749D00A30DAB /* homovacommand.cpp in Sources */,
+ A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */,
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1DEB928A08733DD80010E9CD /* Debug */,
void AmovaCommand::help(){
try {
+ m->mothurOut("Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n");
m->mothurOut("The amova command can only be executed after a successful read.otu command of a list and group or shared file, or by providing a phylip formatted distance matrix.\n");
m->mothurOut("The amova command outputs a .amova file. \n");
m->mothurOut("The amova command parameters are phylip, iters, groups, label, design, sets and processors. The design parameter is required.\n");
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
trim = m->isTrue(temp);
+ //temp = validParameter.validFile(parameters, "trimera", false); if (temp == "not found") { temp = "f"; }
+ //trimera = m->isTrue(temp);
+
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
#endif
m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n");
+ //m->mothurOut("The trimera parameter allows you to check both peices of a chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n");
m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
Sequence* trimmed = chimera->print(out, out2);
if (trim) { trimmed->printSequence(out3); delete trimmed; }
+
+ //do you want to check both pieces for chimeras
+ //if (trimera) {}
}
count++;
}
MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
delete buf2;
}
+
+ //do you want to check both pieces for chimeras
+ //if (trimera) {}
}
}
int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
- bool abort, realign, trim;
+ bool abort, realign, trim, trimera;
string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;
#include "mergegroupscommand.h"
#include "amovacommand.h"
#include "homovacommand.h"
+#include "mantelcommand.h"
/*******************************************************/
commands["remove.rare"] = "remove.rare";
commands["amova"] = "amova";
commands["homova"] = "homova";
+ commands["mantel"] = "mantel";
commands["merge.groups"] = "merge.groups";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
else if(commandName == "merge.groups") { command = new MergeGroupsCommand(optionString); }
else if(commandName == "amova") { command = new AmovaCommand(optionString); }
else if(commandName == "homova") { command = new HomovaCommand(optionString); }
+ else if(commandName == "mantel") { command = new MantelCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
else if(commandName == "merge.groups") { pipecommand = new MergeGroupsCommand(optionString); }
else if(commandName == "amova") { pipecommand = new AmovaCommand(optionString); }
else if(commandName == "homova") { pipecommand = new HomovaCommand(optionString); }
+ else if(commandName == "mantel") { pipecommand = new MantelCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
return pipecommand;
else if(commandName == "merge.groups") { shellcommand = new MergeGroupsCommand(); }
else if(commandName == "amova") { shellcommand = new AmovaCommand(); }
else if(commandName == "homova") { shellcommand = new HomovaCommand(); }
+ else if(commandName == "mantel") { shellcommand = new MantelCommand(); }
else { shellcommand = new NoCommand(); }
return shellcommand;
#include "corraxescommand.h"
#include "sharedutilities.h"
-//********************************************************************************************************************
-//sorts highest to lowest
-inline bool compareSpearman(spearmanRank left, spearmanRank right){
- return (left.score > right.score);
-}
-//********************************************************************************************************************
-//sorts lowest to highest
-inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
- return (left.score < right.score);
-}
//**********************************************************************************************************************
vector<string> CorrAxesCommand::getValidParameters(){
try {
#include "sharedrabundfloatvector.h"
#include "inputdata.h"
-/***************************************************************/
-struct spearmanRank {
- string name;
- float score;
-
- spearmanRank(string n, float s) : name(n), score(s) {}
-};
-/***************************************************************/
class CorrAxesCommand : public Command {
public:
void HomovaCommand::help(){
try {
+ m->mothurOut("Referenced: Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71.\n");
m->mothurOut("The homova command can only be executed after a successful read.otu command of a list and group or shared file, or by providing a phylip formatted distance matrix.\n");
m->mothurOut("The homova command outputs a .homova file. \n");
m->mothurOut("The homova command parameters are phylip, iters, groups, label, design, sets and processors. The design parameter is required.\n");
}
catch(exception& e) {
- m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");
+ m->errorOut(e, "LinearAlgebra", "calcPearson");
exit(1);
}
}
/*********************************************************************************************************************************/
+//assumes both matrices are square and the same size
+double LinearAlgebra::calcSpearman(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
+ try {
+ double r;
+
+ //format data
+ map<float, int> tableX;
+ map<float, int>::iterator itTable;
+ vector<spearmanRank> scores;
+
+ for (int i = 0; i < euclidDists.size(); i++) {
+ for (int j = 0; j < i; j++) {
+ spearmanRank member(toString(scores.size()), euclidDists[i][j]);
+ scores.push_back(member);
+
+ //count number of repeats
+ itTable = tableX.find(euclidDists[i][j]);
+ if (itTable == tableX.end()) {
+ tableX[euclidDists[i][j]] = 1;
+ }else {
+ tableX[euclidDists[i][j]]++;
+ }
+ }
+ }
+
+ //sort scores
+ sort(scores.begin(), scores.end(), compareSpearman);
+
+ //calc LX
+ double Lx = 0.0;
+ for (itTable = tableX.begin(); itTable != tableX.end(); itTable++) {
+ double tx = (double) itTable->second;
+ Lx += ((pow(tx, 3.0) - tx) / 12.0);
+ }
+
+ //find ranks of xi
+ map<string, float> rankEuclid;
+ vector<spearmanRank> ties;
+ int rankTotal = 0;
+ for (int j = 0; j < scores.size(); j++) {
+ rankTotal += (j+1);
+ ties.push_back(scores[j]);
+
+ if (j != (scores.size()-1)) { // you are not the last so you can look ahead
+ if (scores[j].score != scores[j+1].score) { // you are done with ties, rank them and continue
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankEuclid[ties[k].name] = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankEuclid[ties[k].name] = thisrank;
+ }
+ }
+ }
+
+
+ //format data
+ map<float, int> tableY;
+ scores.clear();
+
+ for (int i = 0; i < userDists.size(); i++) {
+ for (int j = 0; j < i; j++) {
+ spearmanRank member(toString(scores.size()), userDists[i][j]);
+ scores.push_back(member);
+
+ //count number of repeats
+ itTable = tableY.find(userDists[i][j]);
+ if (itTable == tableY.end()) {
+ tableY[userDists[i][j]] = 1;
+ }else {
+ tableY[userDists[i][j]]++;
+ }
+ }
+ }
+
+ //sort scores
+ sort(scores.begin(), scores.end(), compareSpearman);
+
+ //calc LX
+ double Ly = 0.0;
+ for (itTable = tableY.begin(); itTable != tableY.end(); itTable++) {
+ double ty = (double) itTable->second;
+ Ly += ((pow(ty, 3.0) - ty) / 12.0);
+ }
+
+ //find ranks of yi
+ map<string, float> rankUser;
+ ties.clear();
+ rankTotal = 0;
+ for (int j = 0; j < scores.size(); j++) {
+ rankTotal += (j+1);
+ ties.push_back(scores[j]);
+
+ if (j != (scores.size()-1)) { // you are not the last so you can look ahead
+ if (scores[j].score != scores[j+1].score) { // you are done with ties, rank them and continue
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankUser[ties[k].name] = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankUser[ties[k].name] = thisrank;
+ }
+ }
+ }
+
+
+ double di = 0.0;
+ int count = 0;
+ for (int i = 0; i < userDists.size(); i++) {
+ for (int j = 0; j < i; j++) {
+
+ float xi = rankEuclid[toString(count)];
+ float yi = rankUser[toString(count)];
+
+ di += ((xi - yi) * (xi - yi));
+
+ count++;
+ }
+ }
+
+ double n = (double) count;
+
+ double SX2 = ((pow(n, 3.0) - n) / 12.0) - Lx;
+ double SY2 = ((pow(n, 3.0) - n) / 12.0) - Ly;
+
+ r = (SX2 + SY2 - di) / (2.0 * sqrt((SX2*SY2)));
+
+ //divide by zero error
+ if (isnan(r) || isinf(r)) { r = 0.0; }
+
+ return r;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcSpearman");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+//assumes both matrices are square and the same size
+double LinearAlgebra::calcKendall(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
+ try {
+ double r;
+
+ //format data
+ vector<spearmanRank> scores;
+ for (int i = 0; i < euclidDists.size(); i++) {
+ for (int j = 0; j < i; j++) {
+ spearmanRank member(toString(scores.size()), euclidDists[i][j]);
+ scores.push_back(member);
+ }
+ }
+
+ //sort scores
+ sort(scores.begin(), scores.end(), compareSpearman);
+
+ //find ranks of xi
+ map<string, float> rankEuclid;
+ vector<spearmanRank> ties;
+ int rankTotal = 0;
+ for (int j = 0; j < scores.size(); j++) {
+ rankTotal += (j+1);
+ ties.push_back(scores[j]);
+
+ if (j != (scores.size()-1)) { // you are not the last so you can look ahead
+ if (scores[j].score != scores[j+1].score) { // you are done with ties, rank them and continue
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankEuclid[ties[k].name] = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankEuclid[ties[k].name] = thisrank;
+ }
+ }
+ }
+
+ vector<spearmanRank> scoresUser;
+ for (int i = 0; i < userDists.size(); i++) {
+ for (int j = 0; j < i; j++) {
+ spearmanRank member(toString(scoresUser.size()), userDists[i][j]);
+ scoresUser.push_back(member);
+ }
+ }
+
+ //sort scores
+ sort(scoresUser.begin(), scoresUser.end(), compareSpearman);
+
+ //find ranks of yi
+ map<string, float> rankUser;
+ ties.clear();
+ rankTotal = 0;
+ for (int j = 0; j < scoresUser.size(); j++) {
+ rankTotal += (j+1);
+ ties.push_back(scoresUser[j]);
+
+ if (j != (scoresUser.size()-1)) { // you are not the last so you can look ahead
+ if (scoresUser[j].score != scoresUser[j+1].score) { // you are done with ties, rank them and continue
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankUser[ties[k].name] = thisrank;
+ }
+ ties.clear();
+ rankTotal = 0;
+ }
+ }else { // you are the last one
+
+ for (int k = 0; k < ties.size(); k++) {
+ float thisrank = rankTotal / (float) ties.size();
+ rankUser[ties[k].name] = thisrank;
+ }
+ }
+ }
+
+ int numCoor = 0;
+ int numDisCoor = 0;
+
+ //order user ranks
+ vector<spearmanRank> user;
+ for (int l = 0; l < scores.size(); l++) {
+ spearmanRank member(scores[l].name, rankUser[scores[l].name]);
+ user.push_back(member);
+ }
+
+ int count = 0;
+ for (int l = 0; l < scores.size(); l++) {
+
+ int numWithHigherRank = 0;
+ int numWithLowerRank = 0;
+ float thisrank = user[l].score;
+
+ for (int u = l; u < scores.size(); u++) {
+ if (user[u].score > thisrank) { numWithHigherRank++; }
+ else if (user[u].score < thisrank) { numWithLowerRank++; }
+ count++;
+ }
+
+ numCoor += numWithHigherRank;
+ numDisCoor += numWithLowerRank;
+ }
+
+ //comparing to yourself
+ count -= userDists.size();
+
+ r = (numCoor - numDisCoor) / (float) count;
+
+ //divide by zero error
+ if (isnan(r) || isinf(r)) { r = 0.0; }
+
+ return r;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calcKendall");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
#include "mothurout.h"
+
class LinearAlgebra {
public:
vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int); //pass in axes and number of dimensions
vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&); //pass in axes
double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
+ double calcSpearman(vector<vector<double> >&, vector<vector<double> >&);
+ double calcKendall(vector<vector<double> >&, vector<vector<double> >&);
private:
MothurOut* m;
--- /dev/null
+/*
+ * mantelcommand.cpp
+ * mothur
+ *
+ * Created by westcott on 2/9/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mantelcommand.h"
+#include "readphylipvector.h"
+
+//**********************************************************************************************************************
+vector<string> MantelCommand::getValidParameters(){
+ try {
+ string Array[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MantelCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"phylip1", "phylip2"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MantelCommand::MantelCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["mantel"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "MantelCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+vector<string> MantelCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MantelCommand::MantelCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"phylip1","phylip2","method","iters","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["mantel"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip1");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip1"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("phylip2");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip2"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ phylipfile1 = validParameter.validFile(parameters, "phylip1", true);
+ if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; }
+ else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; }
+
+ phylipfile2 = validParameter.validFile(parameters, "phylip2", true);
+ if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; }
+ else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true; }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(phylipfile1); }
+
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
+
+ string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, iters);
+
+ if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "MantelCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void MantelCommand::help(){
+ try {
+ m->mothurOut("The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n");
+ m->mothurOut("The mantel command parameters are phylip1, phylip2 and method. The phylip1 and phylip2 parameters are required. Matrices must be the same size and contain the same names.\n");
+ m->mothurOut("The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n");
+ m->mothurOut("The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n");
+ m->mothurOut("The mantel command outputs a .mantel file.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+MantelCommand::~MantelCommand(){}
+
+//**********************************************************************************************************************
+
+int MantelCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ /***************************************************/
+ // reading distance files //
+ /***************************************************/
+
+ //read phylip1
+ ReadPhylipVector readMatrix(phylipfile1);
+ vector< vector<double> > matrix1;
+ vector<string> names1 = readMatrix.read(matrix1);
+
+ if (m->control_pressed) { return 0; }
+
+ //read phylip2
+ ReadPhylipVector readMatrix2(phylipfile2);
+ vector<seqDist> temp; //seqDist - int, int, float
+ vector<string> names2 = readMatrix2.read(temp);
+
+ if (m->control_pressed) { return 0; }
+
+ //fill matrix2 making sure to make sure the distances are in the same order as matrix1
+ vector< vector<double> > matrix2;
+ if (names1 == names2) { //then everything is in same order and same size
+
+ //initialize space
+ matrix2.resize(names2.size());
+ for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
+
+ //fill matrix2
+ for (int i = 0; i < temp.size(); i++) {
+ matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
+ matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
+ }
+
+ }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
+ m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
+ m->control_pressed = true;
+ }else { //sizes are the same, but either the names are different or they are in different order
+
+ //map location of name in names1 to location of name in names2
+ map<string, int> names1Map;
+ map<string, int>::iterator it;
+ for (int i = 0; i < names1.size(); i++) { names1Map[names1[i]] = i; }
+
+ map<string, int> names2Map;
+ bool nameError = false;
+ for (int i = 0; i < names2.size(); i++) {
+
+ //if you find one name error stop looking
+ if (!nameError) {
+ it = names1Map.find(names2[i]);
+ if (it == names1Map.end()) { nameError = true; }
+ }
+
+ //are names different
+ names2Map[names2[i]] = i;
+ }
+
+ //initialize space
+ matrix2.resize(names2.size());
+ for (int i = 0; i < matrix2.size(); i++) { matrix2[i].resize(names2.size(), 0.0); }
+
+ //fill matrix2
+ //are we comparing apples to apples?
+ if (nameError) {
+ m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
+
+ for (int i = 0; i < temp.size(); i++) {
+ matrix2[temp[i].seq1][temp[i].seq2] = temp[i].dist;
+ matrix2[temp[i].seq2][temp[i].seq1] = temp[i].dist;
+ }
+
+ }else { //no name error just different orders, so reorder
+
+ for (int i = 0; i < temp.size(); i++) {
+
+ //what's the location of this distance comparison in matrix1
+ string matrix2NameI = names2[temp[i].seq1];
+ string matrix2NameJ = names2[temp[i].seq2];
+ int locationI = names1Map[matrix2NameI];
+ int locationJ = names1Map[matrix2NameJ];
+
+ matrix2[locationI][locationJ] = temp[i].dist;
+ matrix2[locationJ][locationI] = temp[i].dist;
+ }
+ }
+
+ }
+
+ //frees up space
+ temp.clear();
+
+ if (m->control_pressed) { return 0; }
+
+ /***************************************************/
+ // calculating mantel and signifigance //
+ /***************************************************/
+
+ //calc mantel coefficient
+ LinearAlgebra linear;
+ double mantel = 0.0;
+ if (method == "pearson") { mantel = linear.calcPearson(matrix1, matrix2); }
+ else if (method == "spearman") { mantel = linear.calcSpearman(matrix1, matrix2); }
+ else if (method == "kendall") { mantel = linear.calcKendall(matrix1, matrix2); }
+
+
+ //calc signifigance
+ int count = 0;
+ for (int i = 0; i < iters; i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ //randomize matrix2
+ vector< vector<double> > matrix2Copy = matrix2;
+ random_shuffle(matrix2Copy.begin(), matrix2Copy.end());
+
+ //calc random mantel
+ double randomMantel = 0.0;
+ if (method == "pearson") { randomMantel = linear.calcPearson(matrix1, matrix2Copy); }
+ else if (method == "spearman") { randomMantel = linear.calcSpearman(matrix1, matrix2Copy); }
+ else if (method == "kendall") { randomMantel = linear.calcKendall(matrix1, matrix2Copy); }
+
+ if (randomMantel >= mantel) { count++; }
+ }
+
+ double pValue = count / (float) iters;
+
+ if (m->control_pressed) { return 0; }
+
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel";
+ outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
+ ofstream out;
+
+ m->openOutputFile(outputFile, out);
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+
+ out << "Mantel\tpValue" << endl;
+ out << mantel << '\t' << pValue << endl;
+
+ out.close();
+
+ cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl;
+ m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n");
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
--- /dev/null
+#ifndef MANTELCOMMAND_H
+#define MANTELCOMMAND_H
+
+/*
+ * mantelcommand.h
+ * mothur
+ *
+ * Created by westcott on 2/9/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "linearalgebra.h"
+
+class MantelCommand : public Command {
+public:
+ MantelCommand(string);
+ MantelCommand();
+ ~MantelCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+
+ string phylipfile1, phylipfile2, outputDir, method;
+ bool abort;
+ int iters;
+
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+};
+
+
+#endif
+
+
+
int end;
};
+/***************************************************************/
+struct spearmanRank {
+ string name;
+ float score;
+
+ spearmanRank(string n, float s) : name(n), score(s) {}
+};
+//********************************************************************************************************************
+//sorts highest to lowest
+inline bool compareSpearman(spearmanRank left, spearmanRank right){
+ return (left.score > right.score);
+}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
+ return (left.score < right.score);
+}
/************************************************************/
//sorts lowest to highest
inline bool compareDistLinePairs(distlinePair left, distlinePair right){
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