5 * Created by Sarah Westcott on 3/30/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "venncommand.h"
14 //#include "jackknife.h"
15 #include "sharedsobscollectsummary.h"
16 #include "sharedchao1.h"
17 #include "sharedace.h"
20 //**********************************************************************************************************************
21 vector<string> VennCommand::setParameters(){
23 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
24 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
25 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
26 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
27 CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc);
28 CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
29 CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs);
30 CommandParameter psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus);
31 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
32 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute);
33 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
34 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
36 vector<string> myArray;
37 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
41 m->errorOut(e, "VennCommand", "setParameters");
45 //**********************************************************************************************************************
46 string VennCommand::getHelpString(){
48 string helpString = "";
49 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, sharedotus, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
50 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n";
51 helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n";
52 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
53 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
54 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
55 helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
56 helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n";
57 helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n";
58 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
59 helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n";
60 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
61 helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\n";
62 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
63 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
67 m->errorOut(e, "VennCommand", "getHelpString");
71 //**********************************************************************************************************************
72 string VennCommand::getOutputPattern(string type) {
76 if (type == "svg") { pattern = "[filename],svg"; }
77 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
82 m->errorOut(e, "VennCommand", "getOutputPattern");
87 //**********************************************************************************************************************
88 VennCommand::VennCommand(){
90 abort = true; calledHelp = true;
92 vector<string> tempOutNames;
93 outputTypes["svg"] = tempOutNames;
96 m->errorOut(e, "VennCommand", "VennCommand");
100 //**********************************************************************************************************************
102 VennCommand::VennCommand(string option) {
104 abort = false; calledHelp = false;
107 //allow user to run help
108 if(option == "help") { help(); abort = true; calledHelp = true; }
109 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
112 vector<string> myArray = setParameters();
114 OptionParser parser(option);
115 map<string,string> parameters = parser.getParameters();
116 map<string,string>::iterator it;
118 ValidParameters validParameter;
120 //check to make sure all parameters are valid for command
121 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
122 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
125 //if the user changes the input directory command factory will send this info to us in the output parameter
126 string inputDir = validParameter.validFile(parameters, "inputdir", false);
127 if (inputDir == "not found"){ inputDir = ""; }
130 it = parameters.find("shared");
131 //user has given a template file
132 if(it != parameters.end()){
133 path = m->hasPath(it->second);
134 //if the user has not given a path then, add inputdir. else leave path alone.
135 if (path == "") { parameters["shared"] = inputDir + it->second; }
138 it = parameters.find("list");
139 //user has given a template file
140 if(it != parameters.end()){
141 path = m->hasPath(it->second);
142 //if the user has not given a path then, add inputdir. else leave path alone.
143 if (path == "") { parameters["list"] = inputDir + it->second; }
147 //check for required parameters
148 listfile = validParameter.validFile(parameters, "list", true);
149 if (listfile == "not open") { listfile = ""; abort = true; }
150 else if (listfile == "not found") { listfile = ""; }
151 else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
153 sharedfile = validParameter.validFile(parameters, "shared", true);
154 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
155 else if (sharedfile == "not found") { sharedfile = ""; }
156 else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
158 if ((sharedfile == "") && (listfile == "")) {
159 //is there are current file available for any of these?
160 //give priority to shared, then list, then rabund, then sabund
161 //if there is a current shared file, use it
162 sharedfile = m->getSharedFile();
163 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
165 listfile = m->getListFile();
166 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
168 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
174 //if the user changes the output directory command factory will send this info to us in the output parameter
175 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
177 //check for optional parameter and set defaults
178 // ...at some point should added some additional type checking...
179 label = validParameter.validFile(parameters, "label", false);
180 if (label == "not found") { label = ""; }
182 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
183 else { allLines = 1; }
186 groups = validParameter.validFile(parameters, "groups", false);
187 if (groups == "not found") { groups = ""; }
189 m->splitAtDash(groups, Groups);
190 m->setGroups(Groups);
193 calc = validParameter.validFile(parameters, "calc", false);
194 if (calc == "not found") {
195 if(format == "list") { calc = "sobs"; }
196 else { calc = "sharedsobs"; }
199 if (calc == "default") {
200 if(format == "list") { calc = "sobs"; }
201 else { calc = "sharedsobs"; }
204 m->splitAtDash(calc, Estimators);
205 if (m->inUsersGroups("citation", Estimators)) {
206 ValidCalculators validCalc; validCalc.printCitations(Estimators);
207 //remove citation from list of calcs
208 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
212 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
213 m->mothurConvert(temp, abund);
215 temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
216 nseqs = m->isTrue(temp);
218 temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
219 perm = m->isTrue(temp);
221 temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; }
222 sharedOtus = m->isTrue(temp);
224 temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
225 m->mothurConvert(temp, fontsize);
230 catch(exception& e) {
231 m->errorOut(e, "VennCommand", "VennCommand");
235 //**********************************************************************************************************************
237 int VennCommand::execute(){
240 if (abort == true) { if (calledHelp) { return 0; } return 2; }
242 ValidCalculators validCalculator;
244 if (format == "list") {
245 for (int i=0; i<Estimators.size(); i++) {
246 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
247 if (Estimators[i] == "sobs") {
248 vennCalculators.push_back(new Sobs());
249 }else if (Estimators[i] == "chao") {
250 vennCalculators.push_back(new Chao1());
251 }else if (Estimators[i] == "ace") {
252 if(abund < 5) { abund = 10; }
253 vennCalculators.push_back(new Ace(abund));
258 for (int i=0; i<Estimators.size(); i++) {
259 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
260 if (Estimators[i] == "sharedsobs") {
261 vennCalculators.push_back(new SharedSobsCS());
262 }else if (Estimators[i] == "sharedchao") {
263 vennCalculators.push_back(new SharedChao1());
264 }else if (Estimators[i] == "sharedace") {
265 vennCalculators.push_back(new SharedAce());
271 //if the users entered no valid calculators don't execute command
272 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; }
274 venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus);
275 input = new InputData(inputfile, format);
279 if (format == "sharedfile") {
280 lookup = input->getSharedRAbundVectors();
281 lastLabel = lookup[0]->getLabel();
283 if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
284 }else if (format == "list") {
285 sabund = input->getSAbundVector();
286 lastLabel = sabund->getLabel();
289 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
290 set<string> processedLabels;
291 set<string> userLabels = labels;
293 if (format != "list") {
295 //as long as you are not at the end of the file or done wih the lines you want
296 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
298 if (m->control_pressed) {
299 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
300 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
301 m->clearGroups(); delete venn; delete input;
302 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
306 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
307 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
308 processedLabels.insert(lookup[0]->getLabel());
309 userLabels.erase(lookup[0]->getLabel());
311 if ((lookup.size() > 4) && (!perm)){
312 m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
313 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
315 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
316 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
318 }else if ((lookup.size() > 4) && (perm)) {
319 set< set<int> >::iterator it3;
320 set<int>::iterator it2;
321 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
323 set<int> poss = *it3;
324 vector<SharedRAbundVector*> subset;
325 for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
327 vector<string> outfilenames = venn->getPic(subset, vennCalculators);
328 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
331 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
332 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
336 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
337 string saveLabel = lookup[0]->getLabel();
339 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
340 lookup = input->getSharedRAbundVectors(lastLabel);
342 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
343 processedLabels.insert(lookup[0]->getLabel());
344 userLabels.erase(lookup[0]->getLabel());
346 if ((lookup.size() > 4) && (!perm)){
347 m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
348 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
350 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
351 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
353 }else if ((lookup.size() > 4) && (perm)) {
354 set< set<int> >::iterator it3;
355 set<int>::iterator it2;
356 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
358 set<int> poss = *it3;
359 vector<SharedRAbundVector*> subset;
360 for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
362 vector<string> outfilenames = venn->getPic(subset, vennCalculators);
363 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
366 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
367 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
370 //restore real lastlabel to save below
371 lookup[0]->setLabel(saveLabel);
375 lastLabel = lookup[0]->getLabel();
377 //get next line to process
378 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
379 lookup = input->getSharedRAbundVectors();
382 if (m->control_pressed) {
383 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
384 m->clearGroups(); delete venn; delete input;
385 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
390 //output error messages about any remaining user labels
391 set<string>::iterator it;
392 bool needToRun = false;
393 for (it = userLabels.begin(); it != userLabels.end(); it++) {
394 m->mothurOut("Your file does not include the label " + *it);
395 if (processedLabels.count(lastLabel) != 1) {
396 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
399 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
403 //run last label if you need to
404 if (needToRun == true) {
405 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
406 lookup = input->getSharedRAbundVectors(lastLabel);
408 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
409 processedLabels.insert(lookup[0]->getLabel());
410 userLabels.erase(lookup[0]->getLabel());
412 if ((lookup.size() > 4) && (!perm)){
413 m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
414 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
416 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
417 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
419 }else if ((lookup.size() > 4) && (perm)) {
420 set< set<int> >::iterator it3;
421 set<int>::iterator it2;
422 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
424 set<int> poss = *it3;
425 vector<SharedRAbundVector*> subset;
426 for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
428 vector<string> outfilenames = venn->getPic(subset, vennCalculators);
429 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
432 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
433 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
436 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
440 //reset groups parameter
443 if (m->control_pressed) {
444 m->clearGroups(); delete venn; delete input;
445 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
446 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
453 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
455 if (m->control_pressed) {
456 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
457 delete sabund; delete venn; delete input;
458 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
462 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
464 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
465 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
466 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
469 processedLabels.insert(sabund->getLabel());
470 userLabels.erase(sabund->getLabel());
473 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
474 string saveLabel = sabund->getLabel();
477 sabund = input->getSAbundVector(lastLabel);
479 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
480 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
481 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
484 processedLabels.insert(sabund->getLabel());
485 userLabels.erase(sabund->getLabel());
487 //restore real lastlabel to save below
488 sabund->setLabel(saveLabel);
491 lastLabel = sabund->getLabel();
494 sabund = input->getSAbundVector();
497 if (m->control_pressed) {
498 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
499 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
500 delete venn; delete input;
504 //output error messages about any remaining user labels
505 set<string>::iterator it;
506 bool needToRun = false;
507 for (it = userLabels.begin(); it != userLabels.end(); it++) {
508 m->mothurOut("Your file does not include the label " + *it);
509 if (processedLabels.count(lastLabel) != 1) {
510 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
513 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
517 //run last label if you need to
518 if (needToRun == true) {
519 if (sabund != NULL) { delete sabund; }
520 sabund = input->getSAbundVector(lastLabel);
522 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
523 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
524 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
530 if (m->control_pressed) {
531 delete venn; delete input;
532 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
533 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
538 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
539 delete venn; delete input;
541 m->mothurOutEndLine();
542 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
543 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
544 m->mothurOutEndLine();
549 catch(exception& e) {
550 m->errorOut(e, "VennCommand", "execute");
554 //**********************************************************************************************************************
555 //returns a vector of sets containing the 4 group combinations
556 set< set<int> > VennCommand::findCombinations(int lookupSize){
558 set< set<int> > combos;
561 for (int i = 0; i < lookupSize; i++) { possibles.insert(i); }
563 getCombos(possibles, combos);
568 catch(exception& e) {
569 m->errorOut(e, "VennCommand", "findCombinations");
573 //**********************************************************************************************************************
574 //recusively finds combos of 4
575 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
578 if (possibles.size() == 4) { //done
579 if (combos.count(possibles) == 0) { //no dups
580 combos.insert(possibles);
582 }else { //we still have work to do
583 set<int>::iterator it;
584 set<int>::iterator it2;
585 for (it = possibles.begin(); it != possibles.end(); it++) {
587 set<int> newPossibles;
588 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) { //all possible combos of one length smaller
590 newPossibles.insert(*it2);
593 getCombos(newPossibles, combos);
599 catch(exception& e) {
600 m->errorOut(e, "VennCommand", "getCombos");
605 //**********************************************************************************************************************