+++ /dev/null
-#ifndef TREEGROUPCOMMAND_H
-#define TREEGROUPCOMMAND_H
-
-/*
- * treegroupscommand.h
- * Mothur
- *
- * Created by Sarah Westcott on 4/8/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "inputdata.h"
-#include "groupmap.h"
-#include "validcalculator.h"
-#include "tree.h"
-#include "treemap.h"
-#include "readmatrix.hpp"
-#include "readcolumn.h"
-#include "readphylip.h"
-#include "sparsematrix.hpp"
-#include "sharedsobscollectsummary.h"
-#include "sharedchao1.h"
-#include "sharedace.h"
-#include "sharednseqs.h"
-#include "sharedjabund.h"
-#include "sharedsorabund.h"
-#include "sharedjclass.h"
-#include "sharedsorclass.h"
-#include "sharedjest.h"
-#include "sharedsorest.h"
-#include "sharedthetayc.h"
-#include "sharedthetan.h"
-#include "sharedkstest.h"
-#include "whittaker.h"
-#include "sharedochiai.h"
-#include "sharedanderbergs.h"
-#include "sharedkulczynski.h"
-#include "sharedkulczynskicody.h"
-#include "sharedlennon.h"
-#include "sharedmorisitahorn.h"
-#include "sharedbraycurtis.h"
-#include "sharedjackknife.h"
-#include "whittaker.h"
-#include "odum.h"
-#include "canberra.h"
-#include "structeuclidean.h"
-#include "structchord.h"
-#include "hellinger.h"
-#include "manhattan.h"
-#include "structpearson.h"
-#include "soergel.h"
-#include "spearman.h"
-#include "structkulczynski.h"
-#include "structchi2.h"
-#include "speciesprofile.h"
-#include "hamming.h"
-#include "gower.h"
-#include "memchi2.h"
-#include "memchord.h"
-#include "memeuclidean.h"
-#include "mempearson.h"
-
-
-
-/* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups.
- The user can select the lines or labels they wish to use as well as the groups they would like included.
- They can also use as many or as few calculators as they wish. */
-
-
-typedef list<PCell>::iterator MatData;
-
-class TreeGroupCommand : public Command {
-
-public:
- TreeGroupCommand(string);
- TreeGroupCommand();
- ~TreeGroupCommand();
-
- vector<string> setParameters();
- string getCommandName() { return "tree.shared"; }
- string getCommandCategory() { return "OTU-Based Approaches"; }
- string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
- string getDescription() { return "generate a tree file that describes the dissimilarity among groups"; }
-
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-private:
-
- struct linePair {
- int start;
- int end;
- };
- vector<linePair> lines;
-
- Tree* createTree(vector< vector<double> >&);
- void printSims(ostream&, vector< vector<double> >&);
- int makeSimsShared();
- vector< vector<double> > makeSimsDist();
- int writeTree(string, Tree*);
- int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
-
- ReadMatrix* readMatrix;
- SparseMatrix* matrix;
- NameAssignment* nameMap;
- ListVector* list;
- TreeMap* tmap;
- Tree* t;
- InputData* input;
- vector<Calculator*> treeCalculators;
- vector<SharedRAbundVector*> lookup;
- string lastLabel;
- string format, groupNames, filename, sharedfile, inputfile;
- int numGroups, subsampleSize, iters, processors;
- ofstream out;
- float precision, cutoff;
-
- bool abort, allLines, subsample;
- set<string> labels; //holds labels to be used
- string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
- vector<string> Estimators, Groups, outputNames; //holds estimators to be used
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- int process(vector<SharedRAbundVector*>);
-
-
-
-};
-
-/**************************************************************************************************/
-//custom data structure for threads to use.
-// This is passed by void pointer so it can be any data type
-// that can be passed using a single void pointer (LPVOID).
-struct treeSharedData {
- vector<SharedRAbundVector*> thisLookup;
- vector< vector<seqDist> > calcDists;
- vector<string> Estimators;
- unsigned long long start;
- unsigned long long end;
- MothurOut* m;
-
- treeSharedData(){}
- treeSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
- m = mout;
- start = st;
- end = en;
- Estimators = est;
- thisLookup = lu;
- }
-};
-/**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
-static DWORD WINAPI MyTreeSharedThreadFunction(LPVOID lpParam){
- treeSharedData* pDataArray;
- pDataArray = (treeSharedData*)lpParam;
-
- try {
-
- vector<Calculator*> treeCalculators;
- ValidCalculators validCalculator;
- for (int i=0; i<pDataArray->Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("matrix", pDataArray->Estimators[i]) == true) {
- if (pDataArray->Estimators[i] == "sharedsobs") {
- treeCalculators.push_back(new SharedSobsCS());
- }else if (pDataArray->Estimators[i] == "sharedchao") {
- treeCalculators.push_back(new SharedChao1());
- }else if (pDataArray->Estimators[i] == "sharedace") {
- treeCalculators.push_back(new SharedAce());
- }else if (pDataArray->Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (pDataArray->Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (pDataArray->Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (pDataArray->Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (pDataArray->Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (pDataArray->Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (pDataArray->Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (pDataArray->Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (pDataArray->Estimators[i] == "kstest") {
- treeCalculators.push_back(new KSTest());
- }else if (pDataArray->Estimators[i] == "sharednseqs") {
- treeCalculators.push_back(new SharedNSeqs());
- }else if (pDataArray->Estimators[i] == "ochiai") {
- treeCalculators.push_back(new Ochiai());
- }else if (pDataArray->Estimators[i] == "anderberg") {
- treeCalculators.push_back(new Anderberg());
- }else if (pDataArray->Estimators[i] == "kulczynski") {
- treeCalculators.push_back(new Kulczynski());
- }else if (pDataArray->Estimators[i] == "kulczynskicody") {
- treeCalculators.push_back(new KulczynskiCody());
- }else if (pDataArray->Estimators[i] == "lennon") {
- treeCalculators.push_back(new Lennon());
- }else if (pDataArray->Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (pDataArray->Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
- }else if (pDataArray->Estimators[i] == "whittaker") {
- treeCalculators.push_back(new Whittaker());
- }else if (pDataArray->Estimators[i] == "odum") {
- treeCalculators.push_back(new Odum());
- }else if (pDataArray->Estimators[i] == "canberra") {
- treeCalculators.push_back(new Canberra());
- }else if (pDataArray->Estimators[i] == "structeuclidean") {
- treeCalculators.push_back(new StructEuclidean());
- }else if (pDataArray->Estimators[i] == "structchord") {
- treeCalculators.push_back(new StructChord());
- }else if (pDataArray->Estimators[i] == "hellinger") {
- treeCalculators.push_back(new Hellinger());
- }else if (pDataArray->Estimators[i] == "manhattan") {
- treeCalculators.push_back(new Manhattan());
- }else if (pDataArray->Estimators[i] == "structpearson") {
- treeCalculators.push_back(new StructPearson());
- }else if (pDataArray->Estimators[i] == "soergel") {
- treeCalculators.push_back(new Soergel());
- }else if (pDataArray->Estimators[i] == "spearman") {
- treeCalculators.push_back(new Spearman());
- }else if (pDataArray->Estimators[i] == "structkulczynski") {
- treeCalculators.push_back(new StructKulczynski());
- }else if (pDataArray->Estimators[i] == "speciesprofile") {
- treeCalculators.push_back(new SpeciesProfile());
- }else if (pDataArray->Estimators[i] == "hamming") {
- treeCalculators.push_back(new Hamming());
- }else if (pDataArray->Estimators[i] == "structchi2") {
- treeCalculators.push_back(new StructChi2());
- }else if (pDataArray->Estimators[i] == "gower") {
- treeCalculators.push_back(new Gower());
- }else if (pDataArray->Estimators[i] == "memchi2") {
- treeCalculators.push_back(new MemChi2());
- }else if (pDataArray->Estimators[i] == "memchord") {
- treeCalculators.push_back(new MemChord());
- }else if (pDataArray->Estimators[i] == "memeuclidean") {
- treeCalculators.push_back(new MemEuclidean());
- }else if (pDataArray->Estimators[i] == "mempearson") {
- treeCalculators.push_back(new MemPearson());
- }
- }
- }
-
- pDataArray->calcDists.resize(treeCalculators.size());
-
- vector<SharedRAbundVector*> subset;
- for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
-
- for (int l = 0; l < k; l++) {
-
- if (k != l) { //we dont need to similiarity of a groups to itself
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
-
- for(int i=0;i<treeCalculators.size();i++) {
-
- //if this calc needs all groups to calculate the pair load all groups
- if (treeCalculators[i]->getNeedsAll()) {
- //load subset with rest of lookup for those calcs that need everyone to calc for a pair
- for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
- if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
- }
- }
-
- vector<double> tempdata = treeCalculators[i]->getValues(subset); //saves the calculator outputs
-
- if (pDataArray->m->control_pressed) { return 1; }
-
- seqDist temp(l, k, -(tempdata[0]-1.0));
- pDataArray->calcDists[i].push_back(temp);
- }
- }
- }
- }
-
- for(int i=0;i<treeCalculators.size();i++){ delete treeCalculators[i]; }
-
- return 0;
-
- }
- catch(exception& e) {
- pDataArray->m->errorOut(e, "TreeGroupsCommand", "MyTreeSharedThreadFunction");
- exit(1);
- }
-}
-#endif
-
-
-
-#endif
-
-
projects / mothur.git / blobdiff