1 #ifndef SUMMARYSHAREDCOMMAND_H
2 #define SUMMARYSHAREDCOMMAND_H
4 * summarysharedcommand.h
7 * Created by Sarah Westcott on 1/2/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundvector.h"
15 #include "inputdata.h"
16 #include "calculator.h"
17 #include "validcalculator.h"
18 #include "sharedsobscollectsummary.h"
19 #include "sharedchao1.h"
20 #include "sharedace.h"
21 #include "sharednseqs.h"
22 #include "sharedjabund.h"
23 #include "sharedsorabund.h"
24 #include "sharedjclass.h"
25 #include "sharedsorclass.h"
26 #include "sharedjest.h"
27 #include "sharedsorest.h"
28 #include "sharedthetayc.h"
29 #include "sharedthetan.h"
30 #include "sharedkstest.h"
31 #include "whittaker.h"
32 #include "sharedochiai.h"
33 #include "sharedanderbergs.h"
34 #include "sharedkulczynski.h"
35 #include "sharedkulczynskicody.h"
36 #include "sharedlennon.h"
37 #include "sharedmorisitahorn.h"
38 #include "sharedbraycurtis.h"
39 #include "sharedjackknife.h"
40 #include "whittaker.h"
43 #include "structeuclidean.h"
44 #include "structchord.h"
45 #include "hellinger.h"
46 #include "manhattan.h"
47 #include "structpearson.h"
50 #include "structkulczynski.h"
51 #include "structchi2.h"
52 #include "speciesprofile.h"
57 #include "memeuclidean.h"
58 #include "mempearson.h"
60 class SummarySharedCommand : public Command {
63 SummarySharedCommand(string);
64 SummarySharedCommand();
65 ~SummarySharedCommand() {}
67 vector<string> setParameters();
68 string getCommandName() { return "summary.shared"; }
69 string getCommandCategory() { return "OTU-Based Approaches"; }
71 string getHelpString();
72 string getOutputPattern(string);
73 string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
74 string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
77 void help() { m->mothurOut(getHelpString()); }
85 vector<linePair> lines;
86 vector<Calculator*> sumCalculators;
89 bool abort, allLines, mult, all, createPhylip, subsample;
90 set<string> labels; //holds labels to be used
91 string label, calc, groups, sharedfile, output;
92 vector<string> Estimators, Groups, outputNames;
93 vector<SharedRAbundVector*> lookup;
94 string format, outputDir;
95 int numGroups, processors, subsampleSize, iters;
96 int process(vector<SharedRAbundVector*>, string, string);
97 int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
98 int printSims(ostream&, vector< vector<double> >&);
102 /**************************************************************************************************/
103 //custom data structure for threads to use.
104 //main process handling the calcs that can do more than 2 groups
105 // This is passed by void pointer so it can be any data type
106 // that can be passed using a single void pointer (LPVOID).
107 struct summarySharedData {
108 vector<SharedRAbundVector*> thisLookup;
109 vector< vector<seqDist> > calcDists;
110 vector<string> Estimators;
111 unsigned long long start;
112 unsigned long long end;
117 summarySharedData(){}
118 summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
128 /**************************************************************************************************/
129 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
131 static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
132 summarySharedData* pDataArray;
133 pDataArray = (summarySharedData*)lpParam;
137 vector<Calculator*> sumCalculators;
138 ValidCalculators validCalculator;
139 for (int i=0; i<pDataArray->Estimators.size(); i++) {
140 if (validCalculator.isValidCalculator("sharedsummary", pDataArray->Estimators[i]) == true) {
141 if (pDataArray->Estimators[i] == "sharedsobs") {
142 sumCalculators.push_back(new SharedSobsCS());
143 }else if (pDataArray->Estimators[i] == "sharedchao") {
144 sumCalculators.push_back(new SharedChao1());
145 }else if (pDataArray->Estimators[i] == "sharedace") {
146 sumCalculators.push_back(new SharedAce());
147 }else if (pDataArray->Estimators[i] == "jabund") {
148 sumCalculators.push_back(new JAbund());
149 }else if (pDataArray->Estimators[i] == "sorabund") {
150 sumCalculators.push_back(new SorAbund());
151 }else if (pDataArray->Estimators[i] == "jclass") {
152 sumCalculators.push_back(new Jclass());
153 }else if (pDataArray->Estimators[i] == "sorclass") {
154 sumCalculators.push_back(new SorClass());
155 }else if (pDataArray->Estimators[i] == "jest") {
156 sumCalculators.push_back(new Jest());
157 }else if (pDataArray->Estimators[i] == "sorest") {
158 sumCalculators.push_back(new SorEst());
159 }else if (pDataArray->Estimators[i] == "thetayc") {
160 sumCalculators.push_back(new ThetaYC());
161 }else if (pDataArray->Estimators[i] == "thetan") {
162 sumCalculators.push_back(new ThetaN());
163 }else if (pDataArray->Estimators[i] == "kstest") {
164 sumCalculators.push_back(new KSTest());
165 }else if (pDataArray->Estimators[i] == "sharednseqs") {
166 sumCalculators.push_back(new SharedNSeqs());
167 }else if (pDataArray->Estimators[i] == "ochiai") {
168 sumCalculators.push_back(new Ochiai());
169 }else if (pDataArray->Estimators[i] == "anderberg") {
170 sumCalculators.push_back(new Anderberg());
171 }else if (pDataArray->Estimators[i] == "kulczynski") {
172 sumCalculators.push_back(new Kulczynski());
173 }else if (pDataArray->Estimators[i] == "kulczynskicody") {
174 sumCalculators.push_back(new KulczynskiCody());
175 }else if (pDataArray->Estimators[i] == "lennon") {
176 sumCalculators.push_back(new Lennon());
177 }else if (pDataArray->Estimators[i] == "morisitahorn") {
178 sumCalculators.push_back(new MorHorn());
179 }else if (pDataArray->Estimators[i] == "braycurtis") {
180 sumCalculators.push_back(new BrayCurtis());
181 }else if (pDataArray->Estimators[i] == "whittaker") {
182 sumCalculators.push_back(new Whittaker());
183 }else if (pDataArray->Estimators[i] == "odum") {
184 sumCalculators.push_back(new Odum());
185 }else if (pDataArray->Estimators[i] == "canberra") {
186 sumCalculators.push_back(new Canberra());
187 }else if (pDataArray->Estimators[i] == "structeuclidean") {
188 sumCalculators.push_back(new StructEuclidean());
189 }else if (pDataArray->Estimators[i] == "structchord") {
190 sumCalculators.push_back(new StructChord());
191 }else if (pDataArray->Estimators[i] == "hellinger") {
192 sumCalculators.push_back(new Hellinger());
193 }else if (pDataArray->Estimators[i] == "manhattan") {
194 sumCalculators.push_back(new Manhattan());
195 }else if (pDataArray->Estimators[i] == "structpearson") {
196 sumCalculators.push_back(new StructPearson());
197 }else if (pDataArray->Estimators[i] == "soergel") {
198 sumCalculators.push_back(new Soergel());
199 }else if (pDataArray->Estimators[i] == "spearman") {
200 sumCalculators.push_back(new Spearman());
201 }else if (pDataArray->Estimators[i] == "structkulczynski") {
202 sumCalculators.push_back(new StructKulczynski());
203 }else if (pDataArray->Estimators[i] == "speciesprofile") {
204 sumCalculators.push_back(new SpeciesProfile());
205 }else if (pDataArray->Estimators[i] == "hamming") {
206 sumCalculators.push_back(new Hamming());
207 }else if (pDataArray->Estimators[i] == "structchi2") {
208 sumCalculators.push_back(new StructChi2());
209 }else if (pDataArray->Estimators[i] == "gower") {
210 sumCalculators.push_back(new Gower());
211 }else if (pDataArray->Estimators[i] == "memchi2") {
212 sumCalculators.push_back(new MemChi2());
213 }else if (pDataArray->Estimators[i] == "memchord") {
214 sumCalculators.push_back(new MemChord());
215 }else if (pDataArray->Estimators[i] == "memeuclidean") {
216 sumCalculators.push_back(new MemEuclidean());
217 }else if (pDataArray->Estimators[i] == "mempearson") {
218 sumCalculators.push_back(new MemPearson());
223 pDataArray->calcDists.resize(sumCalculators.size());
225 ofstream outputFileHandle;
226 pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle);
228 vector<SharedRAbundVector*> subset;
229 for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
231 for (int l = 0; l < k; l++) {
233 outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';
235 subset.clear(); //clear out old pair of sharedrabunds
236 //add new pair of sharedrabunds
237 subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
239 //sort groups to be alphanumeric
240 if (pDataArray->thisLookup[k]->getGroup() > pDataArray->thisLookup[l]->getGroup()) {
241 outputFileHandle << (pDataArray->thisLookup[l]->getGroup() +'\t' + pDataArray->thisLookup[k]->getGroup()) << '\t'; //print out groups
243 outputFileHandle << (pDataArray->thisLookup[k]->getGroup() +'\t' + pDataArray->thisLookup[l]->getGroup()) << '\t'; //print out groups
246 for(int i=0;i<sumCalculators.size();i++) {
248 //if this calc needs all groups to calculate the pair load all groups
249 if (sumCalculators[i]->getNeedsAll()) {
250 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
251 for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
252 if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
256 vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
258 if (pDataArray->m->control_pressed) { for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } outputFileHandle.close(); return 1; }
260 outputFileHandle << '\t';
261 sumCalculators[i]->print(outputFileHandle);
263 seqDist temp(l, k, tempdata[0]);
264 pDataArray->calcDists[i].push_back(temp);
266 outputFileHandle << endl;
270 outputFileHandle.close();
271 for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
276 catch(exception& e) {
277 pDataArray->m->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction");