2 * matrixoutputcommand.cpp
5 * Created by Sarah Westcott on 5/20/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "matrixoutputcommand.h"
11 #include "subsample.h"
13 //**********************************************************************************************************************
14 vector<string> MatrixOutputCommand::setParameters(){
16 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","phylip",false,true,true); parameters.push_back(pshared);
17 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
18 CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
19 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
20 CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
21 CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
22 CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
23 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
24 CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
25 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
26 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
28 vector<string> myArray;
29 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
33 m->errorOut(e, "MatrixOutputCommand", "setParameters");
37 //**********************************************************************************************************************
38 string MatrixOutputCommand::getHelpString(){
40 string helpString = "";
41 ValidCalculators validCalculator;
42 helpString += "The dist.shared command parameters are shared, groups, calc, output, processors, subsample, iters, mode, and label. shared is a required, unless you have a valid current file.\n";
43 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
44 helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
45 helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
46 helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
47 helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
48 helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
49 helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
50 helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
51 helpString += "The default value for groups is all the groups in your groupfile.\n";
52 helpString += "The default value for calc is jclass and thetayc.\n";
53 helpString += validCalculator.printCalc("matrix");
54 helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
55 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
59 m->errorOut(e, "MatrixOutputCommand", "getHelpString");
63 //**********************************************************************************************************************
64 string MatrixOutputCommand::getOutputPattern(string type) {
68 if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],dist-[filename],[calc],[distance],[outputtag],[tag2],dist"; }
69 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
74 m->errorOut(e, "MatrixOutputCommand", "getOutputPattern");
78 //**********************************************************************************************************************
79 MatrixOutputCommand::MatrixOutputCommand(){
81 abort = true; calledHelp = true;
83 vector<string> tempOutNames;
84 outputTypes["phylip"] = tempOutNames;
87 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
91 //**********************************************************************************************************************
93 MatrixOutputCommand::MatrixOutputCommand(string option) {
95 abort = false; calledHelp = false;
98 //allow user to run help
99 if(option == "help") { help(); abort = true; calledHelp = true; }
100 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
103 vector<string> myArray = setParameters();
105 OptionParser parser(option);
106 map<string,string> parameters = parser.getParameters();
107 map<string,string>::iterator it;
109 ValidParameters validParameter;
111 //check to make sure all parameters are valid for command
112 for (it = parameters.begin(); it != parameters.end(); it++) {
113 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
116 //initialize outputTypes
117 vector<string> tempOutNames;
118 outputTypes["phylip"] = tempOutNames;
120 //if the user changes the input directory command factory will send this info to us in the output parameter
121 string inputDir = validParameter.validFile(parameters, "inputdir", false);
122 if (inputDir == "not found"){ inputDir = ""; }
125 it = parameters.find("shared");
126 //user has given a template file
127 if(it != parameters.end()){
128 path = m->hasPath(it->second);
129 //if the user has not given a path then, add inputdir. else leave path alone.
130 if (path == "") { parameters["shared"] = inputDir + it->second; }
134 sharedfile = validParameter.validFile(parameters, "shared", true);
135 if (sharedfile == "not found") {
136 //if there is a current shared file, use it
137 sharedfile = m->getSharedFile();
138 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
139 else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
140 }else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
141 else { m->setSharedFile(sharedfile); }
143 //if the user changes the output directory command factory will send this info to us in the output parameter
144 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
146 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
149 //check for optional parameter and set defaults
150 // ...at some point should added some additional type checking...
151 label = validParameter.validFile(parameters, "label", false);
152 if (label == "not found") { label = ""; }
154 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
155 else { allLines = 1; }
158 output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
159 if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
161 mode = validParameter.validFile(parameters, "mode", false); if(mode == "not found"){ mode = "average"; }
162 if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
164 groups = validParameter.validFile(parameters, "groups", false);
165 if (groups == "not found") { groups = ""; }
167 m->splitAtDash(groups, Groups);
168 m->setGroups(Groups);
171 string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
172 m->setProcessors(temp);
173 m->mothurConvert(temp, processors);
175 calc = validParameter.validFile(parameters, "calc", false);
176 if (calc == "not found") { calc = "jclass-thetayc"; }
178 if (calc == "default") { calc = "jclass-thetayc"; }
180 m->splitAtDash(calc, Estimators);
181 if (m->inUsersGroups("citation", Estimators)) {
182 ValidCalculators validCalc; validCalc.printCitations(Estimators);
183 //remove citation from list of calcs
184 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
187 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
188 m->mothurConvert(temp, iters);
190 temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
191 if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
193 if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
194 else { subsample = false; }
197 if (subsample == false) { iters = 0; }
199 if (abort == false) {
201 ValidCalculators validCalculator;
204 for (i=0; i<Estimators.size(); i++) {
205 if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
206 if (Estimators[i] == "sharedsobs") {
207 matrixCalculators.push_back(new SharedSobsCS());
208 }else if (Estimators[i] == "sharedchao") {
209 matrixCalculators.push_back(new SharedChao1());
210 }else if (Estimators[i] == "sharedace") {
211 matrixCalculators.push_back(new SharedAce());
212 }else if (Estimators[i] == "jabund") {
213 matrixCalculators.push_back(new JAbund());
214 }else if (Estimators[i] == "sorabund") {
215 matrixCalculators.push_back(new SorAbund());
216 }else if (Estimators[i] == "jclass") {
217 matrixCalculators.push_back(new Jclass());
218 }else if (Estimators[i] == "sorclass") {
219 matrixCalculators.push_back(new SorClass());
220 }else if (Estimators[i] == "jest") {
221 matrixCalculators.push_back(new Jest());
222 }else if (Estimators[i] == "sorest") {
223 matrixCalculators.push_back(new SorEst());
224 }else if (Estimators[i] == "thetayc") {
225 matrixCalculators.push_back(new ThetaYC());
226 }else if (Estimators[i] == "thetan") {
227 matrixCalculators.push_back(new ThetaN());
228 }else if (Estimators[i] == "kstest") {
229 matrixCalculators.push_back(new KSTest());
230 }else if (Estimators[i] == "sharednseqs") {
231 matrixCalculators.push_back(new SharedNSeqs());
232 }else if (Estimators[i] == "ochiai") {
233 matrixCalculators.push_back(new Ochiai());
234 }else if (Estimators[i] == "anderberg") {
235 matrixCalculators.push_back(new Anderberg());
236 }else if (Estimators[i] == "kulczynski") {
237 matrixCalculators.push_back(new Kulczynski());
238 }else if (Estimators[i] == "kulczynskicody") {
239 matrixCalculators.push_back(new KulczynskiCody());
240 }else if (Estimators[i] == "lennon") {
241 matrixCalculators.push_back(new Lennon());
242 }else if (Estimators[i] == "morisitahorn") {
243 matrixCalculators.push_back(new MorHorn());
244 }else if (Estimators[i] == "braycurtis") {
245 matrixCalculators.push_back(new BrayCurtis());
246 }else if (Estimators[i] == "whittaker") {
247 matrixCalculators.push_back(new Whittaker());
248 }else if (Estimators[i] == "odum") {
249 matrixCalculators.push_back(new Odum());
250 }else if (Estimators[i] == "canberra") {
251 matrixCalculators.push_back(new Canberra());
252 }else if (Estimators[i] == "structeuclidean") {
253 matrixCalculators.push_back(new StructEuclidean());
254 }else if (Estimators[i] == "structchord") {
255 matrixCalculators.push_back(new StructChord());
256 }else if (Estimators[i] == "hellinger") {
257 matrixCalculators.push_back(new Hellinger());
258 }else if (Estimators[i] == "manhattan") {
259 matrixCalculators.push_back(new Manhattan());
260 }else if (Estimators[i] == "structpearson") {
261 matrixCalculators.push_back(new StructPearson());
262 }else if (Estimators[i] == "soergel") {
263 matrixCalculators.push_back(new Soergel());
264 }else if (Estimators[i] == "spearman") {
265 matrixCalculators.push_back(new Spearman());
266 }else if (Estimators[i] == "structkulczynski") {
267 matrixCalculators.push_back(new StructKulczynski());
268 }else if (Estimators[i] == "speciesprofile") {
269 matrixCalculators.push_back(new SpeciesProfile());
270 }else if (Estimators[i] == "hamming") {
271 matrixCalculators.push_back(new Hamming());
272 }else if (Estimators[i] == "structchi2") {
273 matrixCalculators.push_back(new StructChi2());
274 }else if (Estimators[i] == "gower") {
275 matrixCalculators.push_back(new Gower());
276 }else if (Estimators[i] == "memchi2") {
277 matrixCalculators.push_back(new MemChi2());
278 }else if (Estimators[i] == "memchord") {
279 matrixCalculators.push_back(new MemChord());
280 }else if (Estimators[i] == "memeuclidean") {
281 matrixCalculators.push_back(new MemEuclidean());
282 }else if (Estimators[i] == "mempearson") {
283 matrixCalculators.push_back(new MemPearson());
292 catch(exception& e) {
293 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
298 //**********************************************************************************************************************
300 MatrixOutputCommand::~MatrixOutputCommand(){}
302 //**********************************************************************************************************************
304 int MatrixOutputCommand::execute(){
307 if (abort == true) { if (calledHelp) { return 0; } return 2; }
309 //if the users entered no valid calculators don't execute command
310 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
312 input = new InputData(sharedfile, "sharedfile");
313 lookup = input->getSharedRAbundVectors();
314 string lastLabel = lookup[0]->getLabel();
316 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
317 set<string> processedLabels;
318 set<string> userLabels = labels;
320 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0;}
323 if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
324 subsampleSize = lookup[0]->getNumSeqs();
325 for (int i = 1; i < lookup.size(); i++) {
326 int thisSize = lookup[i]->getNumSeqs();
328 if (thisSize < subsampleSize) { subsampleSize = thisSize; }
333 vector<SharedRAbundVector*> temp;
334 for (int i = 0; i < lookup.size(); i++) {
335 if (lookup[i]->getNumSeqs() < subsampleSize) {
336 m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
339 Groups.push_back(lookup[i]->getGroup());
340 temp.push_back(lookup[i]);
344 m->setGroups(Groups);
347 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
350 numGroups = lookup.size();
351 lines.resize(processors);
352 for (int i = 0; i < processors; i++) {
353 lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
354 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
357 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
359 //as long as you are not at the end of the file or done wih the lines you want
360 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
362 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
364 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
365 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
368 processedLabels.insert(lookup[0]->getLabel());
369 userLabels.erase(lookup[0]->getLabel());
372 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
373 string saveLabel = lookup[0]->getLabel();
375 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
376 lookup = input->getSharedRAbundVectors(lastLabel);
378 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
381 processedLabels.insert(lookup[0]->getLabel());
382 userLabels.erase(lookup[0]->getLabel());
384 //restore real lastlabel to save below
385 lookup[0]->setLabel(saveLabel);
388 lastLabel = lookup[0]->getLabel();
390 //get next line to process
391 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
392 lookup = input->getSharedRAbundVectors();
395 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
397 //output error messages about any remaining user labels
398 set<string>::iterator it;
399 bool needToRun = false;
400 for (it = userLabels.begin(); it != userLabels.end(); it++) {
401 m->mothurOut("Your file does not include the label " + *it);
402 if (processedLabels.count(lastLabel) != 1) {
403 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
406 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
410 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
412 //run last label if you need to
413 if (needToRun == true) {
414 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
415 lookup = input->getSharedRAbundVectors(lastLabel);
417 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
419 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
422 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
424 //reset groups parameter
427 //set phylip file as new current phylipfile
429 itTypes = outputTypes.find("phylip");
430 if (itTypes != outputTypes.end()) {
431 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
434 m->mothurOutEndLine();
435 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
436 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
437 m->mothurOutEndLine();
442 catch(exception& e) {
443 m->errorOut(e, "MatrixOutputCommand", "execute");
447 /***********************************************************/
448 void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
451 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
454 out << simMatrix.size() << endl;
456 if (output == "lt") {
457 for (int b = 0; b < simMatrix.size(); b++) {
458 out << lookup[b]->getGroup() << '\t';
459 for (int n = 0; n < b; n++) {
460 out << simMatrix[b][n] << '\t';
465 for (int b = 0; b < simMatrix.size(); b++) {
466 out << lookup[b]->getGroup() << '\t';
467 for (int n = 0; n < simMatrix[b].size(); n++) {
468 out << simMatrix[b][n] << '\t';
474 catch(exception& e) {
475 m->errorOut(e, "MatrixOutputCommand", "printSims");
479 /***********************************************************/
480 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
482 vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
483 vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size());
485 for (int thisIter = 0; thisIter < iters+1; thisIter++) {
486 map<string, string> variables;
487 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
488 variables["[distance]"] = thisLookup[0]->getLabel();
489 variables["[tag2]"] = "";
491 vector<SharedRAbundVector*> thisItersLookup = thisLookup;
493 if (subsample && (thisIter != 0)) {
495 vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
497 //make copy of lookup so we don't get access violations
498 vector<SharedRAbundVector*> newLookup;
499 for (int k = 0; k < thisItersLookup.size(); k++) {
500 SharedRAbundVector* temp = new SharedRAbundVector();
501 temp->setLabel(thisItersLookup[k]->getLabel());
502 temp->setGroup(thisItersLookup[k]->getGroup());
503 newLookup.push_back(temp);
507 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
508 if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
509 for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
512 tempLabels = sample.getSample(newLookup, subsampleSize);
513 thisItersLookup = newLookup;
517 driver(thisItersLookup, 0, numGroups, calcDists);
520 vector<int> processIDS;
522 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
523 //loop through and create all the processes you want
524 while (process != processors) {
528 processIDS.push_back(pid);
532 driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
534 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
536 m->openOutputFile(tempdistFileName, outtemp);
538 for (int i = 0; i < calcDists.size(); i++) {
539 outtemp << calcDists[i].size() << endl;
541 for (int j = 0; j < calcDists[i].size(); j++) {
542 outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
549 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
550 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
555 //parent do your part
556 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
558 //force parent to wait until all the processes are done
559 for (int i = 0; i < processIDS.size(); i++) {
560 int temp = processIDS[i];
564 for (int i = 0; i < processIDS.size(); i++) {
565 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) + ".dist";
567 m->openInputFile(tempdistFileName, intemp);
569 for (int k = 0; k < calcDists.size(); k++) {
571 intemp >> size; m->gobble(intemp);
573 for (int j = 0; j < size; j++) {
578 intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
580 seqDist tempDist(seq1, seq2, dist);
581 calcDists[k].push_back(tempDist);
585 m->mothurRemove(tempdistFileName);
588 //////////////////////////////////////////////////////////////////////////////////////////////////////
589 //Windows version shared memory, so be careful when passing variables through the distSharedData struct.
590 //Above fork() will clone, so memory is separate, but that's not the case with windows,
591 //Taking advantage of shared memory to pass results vectors.
592 //////////////////////////////////////////////////////////////////////////////////////////////////////
594 vector<distSharedData*> pDataArray;
595 DWORD dwThreadIdArray[processors-1];
596 HANDLE hThreadArray[processors-1];
598 //Create processor worker threads.
599 for( int i=1; i<processors; i++ ){
601 //make copy of lookup so we don't get access violations
602 vector<SharedRAbundVector*> newLookup;
603 for (int k = 0; k < thisItersLookup.size(); k++) {
604 SharedRAbundVector* temp = new SharedRAbundVector();
605 temp->setLabel(thisItersLookup[k]->getLabel());
606 temp->setGroup(thisItersLookup[k]->getGroup());
607 newLookup.push_back(temp);
611 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
612 if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
613 for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
616 // Allocate memory for thread data.
617 distSharedData* tempSum = new distSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
618 pDataArray.push_back(tempSum);
619 processIDS.push_back(i);
621 hThreadArray[i-1] = CreateThread(NULL, 0, MyDistSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
624 //parent do your part
625 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
627 //Wait until all threads have terminated.
628 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
630 //Close all thread handles and free memory allocations.
631 for(int i=0; i < pDataArray.size(); i++){
632 for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
634 for (int k = 0; k < calcDists.size(); k++) {
635 int size = pDataArray[i]->calcDists[k].size();
636 for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); }
639 CloseHandle(hThreadArray[i]);
640 delete pDataArray[i];
646 if (subsample && (thisIter != 0)) {
647 if((thisIter) % 100 == 0){ m->mothurOut(toString(thisIter)); m->mothurOutEndLine(); }
648 calcDistsTotals.push_back(calcDists);
649 for (int i = 0; i < calcDists.size(); i++) {
650 for (int j = 0; j < calcDists[i].size(); j++) {
651 if (m->debug) { m->mothurOut("[DEBUG]: Results: iter = " + toString(thisIter) + ", " + thisLookup[calcDists[i][j].seq1]->getGroup() + " - " + thisLookup[calcDists[i][j].seq2]->getGroup() + " distance = " + toString(calcDists[i][j].dist) + ".\n"); }
655 for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
656 thisItersLookup.clear();
657 }else { //print results for whole dataset
658 for (int i = 0; i < calcDists.size(); i++) {
659 if (m->control_pressed) { break; }
662 vector< vector<double> > matrix; //square matrix to represent the distance
663 matrix.resize(thisLookup.size());
664 for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
666 for (int j = 0; j < calcDists[i].size(); j++) {
667 int row = calcDists[i][j].seq1;
668 int column = calcDists[i][j].seq2;
669 double dist = calcDists[i][j].dist;
671 matrix[row][column] = dist;
672 matrix[column][row] = dist;
675 variables["[outputtag]"] = output;
676 variables["[calc]"] = matrixCalculators[i]->getName();
677 string distFileName = getOutputFileName("phylip",variables);
678 outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
681 m->openOutputFile(distFileName, outDist);
682 outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
684 printSims(outDist, matrix);
689 for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
693 //we need to find the average distance and standard deviation for each groups distance
695 vector< vector<seqDist> > calcAverages; calcAverages.resize(matrixCalculators.size());
696 for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
697 calcAverages[i].resize(calcDistsTotals[0][i].size());
699 for (int j = 0; j < calcAverages[i].size(); j++) {
700 calcAverages[i][j].seq1 = calcDistsTotals[0][i][j].seq1;
701 calcAverages[i][j].seq2 = calcDistsTotals[0][i][j].seq2;
702 calcAverages[i][j].dist = 0.0;
705 if (mode == "average") {
706 for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
707 for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
708 for (int j = 0; j < calcAverages[i].size(); j++) {
709 calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
710 if (m->debug) { m->mothurOut("[DEBUG]: Totaling for average calc: iter = " + toString(thisIter) + ", " + thisLookup[calcDistsTotals[thisIter][i][j].seq1]->getGroup() + " - " + thisLookup[calcDistsTotals[thisIter][i][j].seq2]->getGroup() + " distance = " + toString(calcDistsTotals[thisIter][i][j].dist) + ". New total = " + toString(calcAverages[i][j].dist) + ".\n"); }
715 for (int i = 0; i < calcAverages.size(); i++) { //finds average.
716 for (int j = 0; j < calcAverages[i].size(); j++) {
717 calcAverages[i][j].dist /= (float) iters;
720 }else { //find median
721 for (int i = 0; i < calcAverages.size(); i++) { //for each calc
722 for (int j = 0; j < calcAverages[i].size(); j++) { //for each comparison
723 vector<double> dists;
724 for (int thisIter = 0; thisIter < iters; thisIter++) { //for each subsample
725 dists.push_back(calcDistsTotals[thisIter][i][j].dist);
727 sort(dists.begin(), dists.end());
728 calcAverages[i][j].dist = dists[(iters/2)];
732 //find standard deviation
733 vector< vector<seqDist> > stdDev; stdDev.resize(matrixCalculators.size());
734 for (int i = 0; i < stdDev.size(); i++) { //initialize sums to zero.
735 stdDev[i].resize(calcDistsTotals[0][i].size());
737 for (int j = 0; j < stdDev[i].size(); j++) {
738 stdDev[i][j].seq1 = calcDistsTotals[0][i][j].seq1;
739 stdDev[i][j].seq2 = calcDistsTotals[0][i][j].seq2;
740 stdDev[i][j].dist = 0.0;
744 for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
745 for (int i = 0; i < stdDev.size(); i++) {
746 for (int j = 0; j < stdDev[i].size(); j++) {
747 stdDev[i][j].dist += ((calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist) * (calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist));
752 for (int i = 0; i < stdDev.size(); i++) { //finds average.
753 for (int j = 0; j < stdDev[i].size(); j++) {
754 stdDev[i][j].dist /= (float) iters;
755 stdDev[i][j].dist = sqrt(stdDev[i][j].dist);
760 for (int i = 0; i < calcDists.size(); i++) {
761 vector< vector<double> > matrix; //square matrix to represent the distance
762 matrix.resize(thisLookup.size());
763 for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
765 vector< vector<double> > stdmatrix; //square matrix to represent the stdDev
766 stdmatrix.resize(thisLookup.size());
767 for (int k = 0; k < thisLookup.size(); k++) { stdmatrix[k].resize(thisLookup.size(), 0.0); }
770 for (int j = 0; j < calcAverages[i].size(); j++) {
771 int row = calcAverages[i][j].seq1;
772 int column = calcAverages[i][j].seq2;
773 float dist = calcAverages[i][j].dist;
774 float stdDist = stdDev[i][j].dist;
776 matrix[row][column] = dist;
777 matrix[column][row] = dist;
778 stdmatrix[row][column] = stdDist;
779 stdmatrix[column][row] = stdDist;
782 map<string, string> variables;
783 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
784 variables["[distance]"] = thisLookup[0]->getLabel();
785 variables["[outputtag]"] = output;
786 variables["[tag2]"] = "ave";
787 variables["[calc]"] = matrixCalculators[i]->getName();
788 string distFileName = getOutputFileName("phylip",variables);
789 outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
791 m->openOutputFile(distFileName, outAve);
792 outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
794 printSims(outAve, matrix);
798 variables["[tag2]"] = "std";
799 distFileName = getOutputFileName("phylip",variables);
800 outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
802 m->openOutputFile(distFileName, outSTD);
803 outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
805 printSims(outSTD, stdmatrix);
814 catch(exception& e) {
815 m->errorOut(e, "MatrixOutputCommand", "process");
819 /**************************************************************************************************/
820 int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
822 vector<SharedRAbundVector*> subset;
824 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
826 for (int l = 0; l < k; l++) {
828 if (k != l) { //we dont need to similiarity of a groups to itself
829 subset.clear(); //clear out old pair of sharedrabunds
830 //add new pair of sharedrabunds
831 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
833 for(int i=0;i<matrixCalculators.size();i++) {
835 //if this calc needs all groups to calculate the pair load all groups
836 if (matrixCalculators[i]->getNeedsAll()) {
837 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
838 for (int w = 0; w < thisLookup.size(); w++) {
839 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
843 vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
845 if (m->control_pressed) { return 1; }
847 seqDist temp(l, k, tempdata[0]);
848 calcDists[i].push_back(temp);
856 catch(exception& e) {
857 m->errorOut(e, "MatrixOutputCommand", "driver");
861 /***********************************************************/