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"
59 #include "sharedjsd.h"
60 #include "sharedrjsd.h"
62 class SummarySharedCommand : public Command {
65 SummarySharedCommand(string);
66 SummarySharedCommand();
67 ~SummarySharedCommand() {}
69 vector<string> setParameters();
70 string getCommandName() { return "summary.shared"; }
71 string getCommandCategory() { return "OTU-Based Approaches"; }
73 string getHelpString();
74 string getOutputPattern(string);
75 string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
76 string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
79 void help() { m->mothurOut(getHelpString()); }
87 vector<linePair> lines;
88 vector<Calculator*> sumCalculators;
91 bool abort, allLines, mult, all, createPhylip, subsample;
92 set<string> labels; //holds labels to be used
93 string label, calc, groups, sharedfile, output;
94 vector<string> Estimators, Groups, outputNames;
95 vector<SharedRAbundVector*> lookup;
96 string format, outputDir;
97 int numGroups, processors, subsampleSize, iters;
98 int process(vector<SharedRAbundVector*>, string, string);
99 int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
100 int printSims(ostream&, vector< vector<double> >&);
104 /**************************************************************************************************/
105 //custom data structure for threads to use.
106 //main process handling the calcs that can do more than 2 groups
107 // This is passed by void pointer so it can be any data type
108 // that can be passed using a single void pointer (LPVOID).
109 struct summarySharedData {
110 vector<SharedRAbundVector*> thisLookup;
111 vector< vector<seqDist> > calcDists;
112 vector<string> Estimators;
113 unsigned long long start;
114 unsigned long long end;
119 summarySharedData(){}
120 summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
130 /**************************************************************************************************/
131 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
133 static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
134 summarySharedData* pDataArray;
135 pDataArray = (summarySharedData*)lpParam;
139 vector<Calculator*> sumCalculators;
140 ValidCalculators validCalculator;
141 for (int i=0; i<pDataArray->Estimators.size(); i++) {
142 if (validCalculator.isValidCalculator("sharedsummary", pDataArray->Estimators[i]) == true) {
143 if (pDataArray->Estimators[i] == "sharedsobs") {
144 sumCalculators.push_back(new SharedSobsCS());
145 }else if (pDataArray->Estimators[i] == "sharedchao") {
146 sumCalculators.push_back(new SharedChao1());
147 }else if (pDataArray->Estimators[i] == "sharedace") {
148 sumCalculators.push_back(new SharedAce());
149 }else if (pDataArray->Estimators[i] == "jabund") {
150 sumCalculators.push_back(new JAbund());
151 }else if (pDataArray->Estimators[i] == "sorabund") {
152 sumCalculators.push_back(new SorAbund());
153 }else if (pDataArray->Estimators[i] == "jclass") {
154 sumCalculators.push_back(new Jclass());
155 }else if (pDataArray->Estimators[i] == "sorclass") {
156 sumCalculators.push_back(new SorClass());
157 }else if (pDataArray->Estimators[i] == "jest") {
158 sumCalculators.push_back(new Jest());
159 }else if (pDataArray->Estimators[i] == "sorest") {
160 sumCalculators.push_back(new SorEst());
161 }else if (pDataArray->Estimators[i] == "thetayc") {
162 sumCalculators.push_back(new ThetaYC());
163 }else if (pDataArray->Estimators[i] == "thetan") {
164 sumCalculators.push_back(new ThetaN());
165 }else if (pDataArray->Estimators[i] == "kstest") {
166 sumCalculators.push_back(new KSTest());
167 }else if (pDataArray->Estimators[i] == "sharednseqs") {
168 sumCalculators.push_back(new SharedNSeqs());
169 }else if (pDataArray->Estimators[i] == "ochiai") {
170 sumCalculators.push_back(new Ochiai());
171 }else if (pDataArray->Estimators[i] == "anderberg") {
172 sumCalculators.push_back(new Anderberg());
173 }else if (pDataArray->Estimators[i] == "kulczynski") {
174 sumCalculators.push_back(new Kulczynski());
175 }else if (pDataArray->Estimators[i] == "kulczynskicody") {
176 sumCalculators.push_back(new KulczynskiCody());
177 }else if (pDataArray->Estimators[i] == "lennon") {
178 sumCalculators.push_back(new Lennon());
179 }else if (pDataArray->Estimators[i] == "morisitahorn") {
180 sumCalculators.push_back(new MorHorn());
181 }else if (pDataArray->Estimators[i] == "braycurtis") {
182 sumCalculators.push_back(new BrayCurtis());
183 }else if (pDataArray->Estimators[i] == "whittaker") {
184 sumCalculators.push_back(new Whittaker());
185 }else if (pDataArray->Estimators[i] == "odum") {
186 sumCalculators.push_back(new Odum());
187 }else if (pDataArray->Estimators[i] == "canberra") {
188 sumCalculators.push_back(new Canberra());
189 }else if (pDataArray->Estimators[i] == "structeuclidean") {
190 sumCalculators.push_back(new StructEuclidean());
191 }else if (pDataArray->Estimators[i] == "structchord") {
192 sumCalculators.push_back(new StructChord());
193 }else if (pDataArray->Estimators[i] == "hellinger") {
194 sumCalculators.push_back(new Hellinger());
195 }else if (pDataArray->Estimators[i] == "manhattan") {
196 sumCalculators.push_back(new Manhattan());
197 }else if (pDataArray->Estimators[i] == "structpearson") {
198 sumCalculators.push_back(new StructPearson());
199 }else if (pDataArray->Estimators[i] == "soergel") {
200 sumCalculators.push_back(new Soergel());
201 }else if (pDataArray->Estimators[i] == "spearman") {
202 sumCalculators.push_back(new Spearman());
203 }else if (pDataArray->Estimators[i] == "structkulczynski") {
204 sumCalculators.push_back(new StructKulczynski());
205 }else if (pDataArray->Estimators[i] == "speciesprofile") {
206 sumCalculators.push_back(new SpeciesProfile());
207 }else if (pDataArray->Estimators[i] == "hamming") {
208 sumCalculators.push_back(new Hamming());
209 }else if (pDataArray->Estimators[i] == "structchi2") {
210 sumCalculators.push_back(new StructChi2());
211 }else if (pDataArray->Estimators[i] == "gower") {
212 sumCalculators.push_back(new Gower());
213 }else if (pDataArray->Estimators[i] == "memchi2") {
214 sumCalculators.push_back(new MemChi2());
215 }else if (pDataArray->Estimators[i] == "memchord") {
216 sumCalculators.push_back(new MemChord());
217 }else if (pDataArray->Estimators[i] == "memeuclidean") {
218 sumCalculators.push_back(new MemEuclidean());
219 }else if (pDataArray->Estimators[i] == "mempearson") {
220 sumCalculators.push_back(new MemPearson());
221 }else if (pDataArray->Estimators[i] == "jsd") {
222 sumCalculators.push_back(new JSD());
223 }else if (pDataArray->Estimators[i] == "rjsd") {
224 sumCalculators.push_back(new RJSD());
229 pDataArray->calcDists.resize(sumCalculators.size());
231 ofstream outputFileHandle;
232 pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle);
234 vector<SharedRAbundVector*> subset;
235 for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
237 for (int l = 0; l < k; l++) {
239 outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';
241 subset.clear(); //clear out old pair of sharedrabunds
242 //add new pair of sharedrabunds
243 subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
245 //sort groups to be alphanumeric
246 if (pDataArray->thisLookup[k]->getGroup() > pDataArray->thisLookup[l]->getGroup()) {
247 outputFileHandle << (pDataArray->thisLookup[l]->getGroup() +'\t' + pDataArray->thisLookup[k]->getGroup()) << '\t'; //print out groups
249 outputFileHandle << (pDataArray->thisLookup[k]->getGroup() +'\t' + pDataArray->thisLookup[l]->getGroup()) << '\t'; //print out groups
252 for(int i=0;i<sumCalculators.size();i++) {
254 //if this calc needs all groups to calculate the pair load all groups
255 if (sumCalculators[i]->getNeedsAll()) {
256 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
257 for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
258 if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
262 vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
264 if (pDataArray->m->control_pressed) { for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } outputFileHandle.close(); return 1; }
266 outputFileHandle << '\t';
267 sumCalculators[i]->print(outputFileHandle);
269 seqDist temp(l, k, tempdata[0]);
270 pDataArray->calcDists[i].push_back(temp);
272 outputFileHandle << endl;
276 outputFileHandle.close();
277 for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
282 catch(exception& e) {
283 pDataArray->m->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction");