--- /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