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"; }
70 string getHelpString();
71 string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
72 string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
75 void help() { m->mothurOut(getHelpString()); }
83 vector<linePair> lines;
84 vector<Calculator*> sumCalculators;
87 bool abort, allLines, mult, all, createPhylip;
88 set<string> labels; //holds labels to be used
89 string label, calc, groups, sharedfile;
90 vector<string> Estimators, Groups, outputNames;
91 vector<SharedRAbundVector*> lookup;
92 string format, outputDir;
93 int numGroups, processors;
94 int process(vector<SharedRAbundVector*>, string, string);
95 int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
99 /**************************************************************************************************/
100 //custom data structure for threads to use.
101 //main process handling the calcs that can do more than 2 groups
102 // This is passed by void pointer so it can be any data type
103 // that can be passed using a single void pointer (LPVOID).
104 struct summarySharedData {
105 vector<SharedRAbundVector*> thisLookup;
106 vector< vector<seqDist> > calcDists;
107 vector<string> Estimators;
108 unsigned long long start;
109 unsigned long long end;
113 summarySharedData(){}
114 summarySharedData(string sf, MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
123 /**************************************************************************************************/
124 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
126 static DWORD WINAPI MySummarySharedThreadFunction(LPVOID lpParam){
127 summarySharedData* pDataArray;
128 pDataArray = (summarySharedData*)lpParam;
132 vector<Calculator*> sumCalculators;
133 ValidCalculators validCalculator;
134 for (int i=0; i<pDataArray->Estimators.size(); i++) {
135 if (validCalculator.isValidCalculator("sharedsummary", pDataArray->Estimators[i]) == true) {
136 if (pDataArray->Estimators[i] == "sharedsobs") {
137 sumCalculators.push_back(new SharedSobsCS());
138 }else if (pDataArray->Estimators[i] == "sharedchao") {
139 sumCalculators.push_back(new SharedChao1());
140 }else if (pDataArray->Estimators[i] == "sharedace") {
141 sumCalculators.push_back(new SharedAce());
142 }else if (pDataArray->Estimators[i] == "jabund") {
143 sumCalculators.push_back(new JAbund());
144 }else if (pDataArray->Estimators[i] == "sorabund") {
145 sumCalculators.push_back(new SorAbund());
146 }else if (pDataArray->Estimators[i] == "jclass") {
147 sumCalculators.push_back(new Jclass());
148 }else if (pDataArray->Estimators[i] == "sorclass") {
149 sumCalculators.push_back(new SorClass());
150 }else if (pDataArray->Estimators[i] == "jest") {
151 sumCalculators.push_back(new Jest());
152 }else if (pDataArray->Estimators[i] == "sorest") {
153 sumCalculators.push_back(new SorEst());
154 }else if (pDataArray->Estimators[i] == "thetayc") {
155 sumCalculators.push_back(new ThetaYC());
156 }else if (pDataArray->Estimators[i] == "thetan") {
157 sumCalculators.push_back(new ThetaN());
158 }else if (pDataArray->Estimators[i] == "kstest") {
159 sumCalculators.push_back(new KSTest());
160 }else if (pDataArray->Estimators[i] == "sharednseqs") {
161 sumCalculators.push_back(new SharedNSeqs());
162 }else if (pDataArray->Estimators[i] == "ochiai") {
163 sumCalculators.push_back(new Ochiai());
164 }else if (pDataArray->Estimators[i] == "anderberg") {
165 sumCalculators.push_back(new Anderberg());
166 }else if (pDataArray->Estimators[i] == "kulczynski") {
167 sumCalculators.push_back(new Kulczynski());
168 }else if (pDataArray->Estimators[i] == "kulczynskicody") {
169 sumCalculators.push_back(new KulczynskiCody());
170 }else if (pDataArray->Estimators[i] == "lennon") {
171 sumCalculators.push_back(new Lennon());
172 }else if (pDataArray->Estimators[i] == "morisitahorn") {
173 sumCalculators.push_back(new MorHorn());
174 }else if (pDataArray->Estimators[i] == "braycurtis") {
175 sumCalculators.push_back(new BrayCurtis());
176 }else if (pDataArray->Estimators[i] == "whittaker") {
177 sumCalculators.push_back(new Whittaker());
178 }else if (pDataArray->Estimators[i] == "odum") {
179 sumCalculators.push_back(new Odum());
180 }else if (pDataArray->Estimators[i] == "canberra") {
181 sumCalculators.push_back(new Canberra());
182 }else if (pDataArray->Estimators[i] == "structeuclidean") {
183 sumCalculators.push_back(new StructEuclidean());
184 }else if (pDataArray->Estimators[i] == "structchord") {
185 sumCalculators.push_back(new StructChord());
186 }else if (pDataArray->Estimators[i] == "hellinger") {
187 sumCalculators.push_back(new Hellinger());
188 }else if (pDataArray->Estimators[i] == "manhattan") {
189 sumCalculators.push_back(new Manhattan());
190 }else if (pDataArray->Estimators[i] == "structpearson") {
191 sumCalculators.push_back(new StructPearson());
192 }else if (pDataArray->Estimators[i] == "soergel") {
193 sumCalculators.push_back(new Soergel());
194 }else if (pDataArray->Estimators[i] == "spearman") {
195 sumCalculators.push_back(new Spearman());
196 }else if (pDataArray->Estimators[i] == "structkulczynski") {
197 sumCalculators.push_back(new StructKulczynski());
198 }else if (pDataArray->Estimators[i] == "speciesprofile") {
199 sumCalculators.push_back(new SpeciesProfile());
200 }else if (pDataArray->Estimators[i] == "hamming") {
201 sumCalculators.push_back(new Hamming());
202 }else if (pDataArray->Estimators[i] == "structchi2") {
203 sumCalculators.push_back(new StructChi2());
204 }else if (pDataArray->Estimators[i] == "gower") {
205 sumCalculators.push_back(new Gower());
206 }else if (pDataArray->Estimators[i] == "memchi2") {
207 sumCalculators.push_back(new MemChi2());
208 }else if (pDataArray->Estimators[i] == "memchord") {
209 sumCalculators.push_back(new MemChord());
210 }else if (pDataArray->Estimators[i] == "memeuclidean") {
211 sumCalculators.push_back(new MemEuclidean());
212 }else if (pDataArray->Estimators[i] == "mempearson") {
213 sumCalculators.push_back(new MemPearson());
218 pDataArray->calcDists.resize(sumCalculators.size());
220 ofstream outputFileHandle;
221 pDataArray->m->openOutputFile(pDataArray->sumFile, outputFileHandle);
223 vector<SharedRAbundVector*> subset;
224 for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
226 for (int l = 0; l < k; l++) {
228 outputFileHandle << pDataArray->thisLookup[0]->getLabel() << '\t';
230 subset.clear(); //clear out old pair of sharedrabunds
231 //add new pair of sharedrabunds
232 subset.push_back(pDataArray->thisLookup[k]); subset.push_back(pDataArray->thisLookup[l]);
234 //sort groups to be alphanumeric
235 if (pDataArray->thisLookup[k]->getGroup() > pDataArray->thisLookup[l]->getGroup()) {
236 outputFileHandle << (pDataArray->thisLookup[l]->getGroup() +'\t' + pDataArray->thisLookup[k]->getGroup()) << '\t'; //print out groups
238 outputFileHandle << (pDataArray->thisLookup[k]->getGroup() +'\t' + pDataArray->thisLookup[l]->getGroup()) << '\t'; //print out groups
241 for(int i=0;i<sumCalculators.size();i++) {
243 //if this calc needs all groups to calculate the pair load all groups
244 if (sumCalculators[i]->getNeedsAll()) {
245 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
246 for (int w = 0; w < pDataArray->thisLookup.size(); w++) {
247 if ((w != k) && (w != l)) { subset.push_back(pDataArray->thisLookup[w]); }
251 vector<double> tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs
253 if (pDataArray->m->control_pressed) { for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } outputFileHandle.close(); return 1; }
255 outputFileHandle << '\t';
256 sumCalculators[i]->print(outputFileHandle);
258 seqDist temp(l, k, tempdata[0]);
259 pDataArray->calcDists[i].push_back(temp);
261 outputFileHandle << endl;
265 outputFileHandle.close();
266 for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
271 catch(exception& e) {
272 pDataArray->m->errorOut(e, "SummarySharedCommand", "MySummarySharedThreadFunction");