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"
61 class SummarySharedCommand : public Command {
64 SummarySharedCommand(string);
65 SummarySharedCommand();
66 ~SummarySharedCommand() {}
68 vector<string> setParameters();
69 string getCommandName() { return "summary.shared"; }
70 string getCommandCategory() { return "OTU-Based Approaches"; }
72 string getHelpString();
73 string getOutputPattern(string);
74 string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
75 string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
78 void help() { m->mothurOut(getHelpString()); }
86 vector<linePair> lines;
87 vector<Calculator*> sumCalculators;
90 bool abort, allLines, mult, all, createPhylip, subsample;
91 set<string> labels; //holds labels to be used
92 string label, calc, groups, sharedfile, output;
93 vector<string> Estimators, Groups, outputNames;
94 vector<SharedRAbundVector*> lookup;
95 string format, outputDir;
96 int numGroups, processors, subsampleSize, iters;
97 int process(vector<SharedRAbundVector*>, string, string);
98 int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
99 int printSims(ostream&, vector< vector<double> >&);
103 /**************************************************************************************************/
104 //custom data structure for threads to use.
105 //main process handling the calcs that can do more than 2 groups
106 // This is passed by void pointer so it can be any data type
107 // that can be passed using a single void pointer (LPVOID).
108 struct summarySharedData {
109 vector<SharedRAbundVector*> thisLookup;
110 vector< vector<seqDist> > calcDists;
111 vector<string> Estimators;
112 unsigned long long start;
113 unsigned long long end;
118 summarySharedData(){}
119 summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
129 /**************************************************************************************************/
130 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
132 static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
133 summarySharedData* pDataArray;
134 pDataArray = (summarySharedData*)lpParam;
138 vector<Calculator*> sumCalculators;
139 ValidCalculators validCalculator;
140 for (int i=0; i<pDataArray->Estimators.size(); i++) {
141 if (validCalculator.isValidCalculator("sharedsummary", pDataArray->Estimators[i]) == true) {
142 if (pDataArray->Estimators[i] == "sharedsobs") {
143 sumCalculators.push_back(new SharedSobsCS());
144 }else if (pDataArray->Estimators[i] == "sharedchao") {
145 sumCalculators.push_back(new SharedChao1());
146 }else if (pDataArray->Estimators[i] == "sharedace") {
147 sumCalculators.push_back(new SharedAce());
148 }else if (pDataArray->Estimators[i] == "jabund") {
149 sumCalculators.push_back(new JAbund());
150 }else if (pDataArray->Estimators[i] == "sorabund") {
151 sumCalculators.push_back(new SorAbund());
152 }else if (pDataArray->Estimators[i] == "jclass") {
153 sumCalculators.push_back(new Jclass());
154 }else if (pDataArray->Estimators[i] == "sorclass") {
155 sumCalculators.push_back(new SorClass());
156 }else if (pDataArray->Estimators[i] == "jest") {
157 sumCalculators.push_back(new Jest());
158 }else if (pDataArray->Estimators[i] == "sorest") {
159 sumCalculators.push_back(new SorEst());
160 }else if (pDataArray->Estimators[i] == "thetayc") {
161 sumCalculators.push_back(new ThetaYC());
162 }else if (pDataArray->Estimators[i] == "thetan") {
163 sumCalculators.push_back(new ThetaN());
164 }else if (pDataArray->Estimators[i] == "kstest") {
165 sumCalculators.push_back(new KSTest());
166 }else if (pDataArray->Estimators[i] == "sharednseqs") {
167 sumCalculators.push_back(new SharedNSeqs());
168 }else if (pDataArray->Estimators[i] == "ochiai") {
169 sumCalculators.push_back(new Ochiai());
170 }else if (pDataArray->Estimators[i] == "anderberg") {
171 sumCalculators.push_back(new Anderberg());
172 }else if (pDataArray->Estimators[i] == "kulczynski") {
173 sumCalculators.push_back(new Kulczynski());
174 }else if (pDataArray->Estimators[i] == "kulczynskicody") {
175 sumCalculators.push_back(new KulczynskiCody());
176 }else if (pDataArray->Estimators[i] == "lennon") {
177 sumCalculators.push_back(new Lennon());
178 }else if (pDataArray->Estimators[i] == "morisitahorn") {
179 sumCalculators.push_back(new MorHorn());
180 }else if (pDataArray->Estimators[i] == "braycurtis") {
181 sumCalculators.push_back(new BrayCurtis());
182 }else if (pDataArray->Estimators[i] == "whittaker") {
183 sumCalculators.push_back(new Whittaker());
184 }else if (pDataArray->Estimators[i] == "odum") {
185 sumCalculators.push_back(new Odum());
186 }else if (pDataArray->Estimators[i] == "canberra") {
187 sumCalculators.push_back(new Canberra());
188 }else if (pDataArray->Estimators[i] == "structeuclidean") {
189 sumCalculators.push_back(new StructEuclidean());
190 }else if (pDataArray->Estimators[i] == "structchord") {
191 sumCalculators.push_back(new StructChord());
192 }else if (pDataArray->Estimators[i] == "hellinger") {
193 sumCalculators.push_back(new Hellinger());
194 }else if (pDataArray->Estimators[i] == "manhattan") {
195 sumCalculators.push_back(new Manhattan());
196 }else if (pDataArray->Estimators[i] == "structpearson") {
197 sumCalculators.push_back(new StructPearson());
198 }else if (pDataArray->Estimators[i] == "soergel") {
199 sumCalculators.push_back(new Soergel());
200 }else if (pDataArray->Estimators[i] == "spearman") {
201 sumCalculators.push_back(new Spearman());
202 }else if (pDataArray->Estimators[i] == "structkulczynski") {
203 sumCalculators.push_back(new StructKulczynski());
204 }else if (pDataArray->Estimators[i] == "speciesprofile") {
205 sumCalculators.push_back(new SpeciesProfile());
206 }else if (pDataArray->Estimators[i] == "hamming") {
207 sumCalculators.push_back(new Hamming());
208 }else if (pDataArray->Estimators[i] == "structchi2") {
209 sumCalculators.push_back(new StructChi2());
210 }else if (pDataArray->Estimators[i] == "gower") {
211 sumCalculators.push_back(new Gower());
212 }else if (pDataArray->Estimators[i] == "memchi2") {
213 sumCalculators.push_back(new MemChi2());
214 }else if (pDataArray->Estimators[i] == "memchord") {
215 sumCalculators.push_back(new MemChord());
216 }else if (pDataArray->Estimators[i] == "memeuclidean") {
217 sumCalculators.push_back(new MemEuclidean());
218 }else if (pDataArray->Estimators[i] == "mempearson") {
219 sumCalculators.push_back(new MemPearson());
220 }else if (pDataArray->Estimators[i] == "jsd") {
221 sumCalculators.push_back(new JSD());
226 pDataArray->calcDists.resize(sumCalculators.size());
228 ofstream outputFileHandle;
229 pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle);
231 vector<SharedRAbundVector*> subset;
232 for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
234 for (int l = 0; l < k; l++) {
236 outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';
238 subset.clear(); //clear out old pair of sharedrabunds
239 //add new pair of sharedrabunds
240 subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
242 //sort groups to be alphanumeric
243 if (pDataArray->thisLookup[k]->getGroup() > pDataArray->thisLookup[l]->getGroup()) {
244 outputFileHandle << (pDataArray->thisLookup[l]->getGroup() +'\t' + pDataArray->thisLookup[k]->getGroup()) << '\t'; //print out groups
246 outputFileHandle << (pDataArray->thisLookup[k]->getGroup() +'\t' + pDataArray->thisLookup[l]->getGroup()) << '\t'; //print out groups
249 for(int i=0;i<sumCalculators.size();i++) {
251 //if this calc needs all groups to calculate the pair load all groups
252 if (sumCalculators[i]->getNeedsAll()) {
253 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
254 for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
255 if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
259 vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
261 if (pDataArray->m->control_pressed) { for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } outputFileHandle.close(); return 1; }
263 outputFileHandle << '\t';
264 sumCalculators[i]->print(outputFileHandle);
266 seqDist temp(l, k, tempdata[0]);
267 pDataArray->calcDists[i].push_back(temp);
269 outputFileHandle << endl;
273 outputFileHandle.close();
274 for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
279 catch(exception& e) {
280 pDataArray->m->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction");