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",false,false); parameters.push_back(plist);
24 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); 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 pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
31 CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
32 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
33 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
35 vector<string> myArray;
36 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
40 m->errorOut(e, "VennCommand", "setParameters");
44 //**********************************************************************************************************************
45 string VennCommand::getHelpString(){
47 string helpString = "";
48 helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
49 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";
50 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";
51 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
52 helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
53 helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
54 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";
55 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";
56 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";
57 helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
58 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";
59 helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
60 helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
61 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
65 m->errorOut(e, "VennCommand", "getHelpString");
69 //**********************************************************************************************************************
71 string VennCommand::getOutputFileNameTag(string type, string inputName=""){
73 string outputFileName = "";
74 map<string, vector<string> >::iterator it;
76 //is this a type this command creates
77 it = outputTypes.find(type);
78 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
80 if (type == "svg") { outputFileName = "svg"; }
81 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
83 return outputFileName;
86 m->errorOut(e, "VennCommand", "getOutputFileNameTag");
91 //**********************************************************************************************************************
92 VennCommand::VennCommand(){
94 abort = true; calledHelp = true;
96 vector<string> tempOutNames;
97 outputTypes["svg"] = tempOutNames;
100 m->errorOut(e, "VennCommand", "VennCommand");
104 //**********************************************************************************************************************
106 VennCommand::VennCommand(string option) {
108 abort = false; calledHelp = false;
111 //allow user to run help
112 if(option == "help") { help(); abort = true; calledHelp = true; }
113 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
116 vector<string> myArray = setParameters();
118 OptionParser parser(option);
119 map<string,string> parameters = parser.getParameters();
120 map<string,string>::iterator it;
122 ValidParameters validParameter;
124 //check to make sure all parameters are valid for command
125 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
126 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
129 //if the user changes the input directory command factory will send this info to us in the output parameter
130 string inputDir = validParameter.validFile(parameters, "inputdir", false);
131 if (inputDir == "not found"){ inputDir = ""; }
134 it = parameters.find("shared");
135 //user has given a template file
136 if(it != parameters.end()){
137 path = m->hasPath(it->second);
138 //if the user has not given a path then, add inputdir. else leave path alone.
139 if (path == "") { parameters["shared"] = inputDir + it->second; }
142 it = parameters.find("list");
143 //user has given a template file
144 if(it != parameters.end()){
145 path = m->hasPath(it->second);
146 //if the user has not given a path then, add inputdir. else leave path alone.
147 if (path == "") { parameters["list"] = inputDir + it->second; }
151 //check for required parameters
152 listfile = validParameter.validFile(parameters, "list", true);
153 if (listfile == "not open") { listfile = ""; abort = true; }
154 else if (listfile == "not found") { listfile = ""; }
155 else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
157 sharedfile = validParameter.validFile(parameters, "shared", true);
158 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
159 else if (sharedfile == "not found") { sharedfile = ""; }
160 else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
162 if ((sharedfile == "") && (listfile == "")) {
163 //is there are current file available for any of these?
164 //give priority to shared, then list, then rabund, then sabund
165 //if there is a current shared file, use it
166 sharedfile = m->getSharedFile();
167 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
169 listfile = m->getListFile();
170 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
172 m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
178 //if the user changes the output directory command factory will send this info to us in the output parameter
179 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
181 //check for optional parameter and set defaults
182 // ...at some point should added some additional type checking...
183 label = validParameter.validFile(parameters, "label", false);
184 if (label == "not found") { label = ""; }
186 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
187 else { allLines = 1; }
190 groups = validParameter.validFile(parameters, "groups", false);
191 if (groups == "not found") { groups = ""; }
193 m->splitAtDash(groups, Groups);
194 m->setGroups(Groups);
197 calc = validParameter.validFile(parameters, "calc", false);
198 if (calc == "not found") {
199 if(format == "list") { calc = "sobs"; }
200 else { calc = "sharedsobs"; }
203 if (calc == "default") {
204 if(format == "list") { calc = "sobs"; }
205 else { calc = "sharedsobs"; }
208 m->splitAtDash(calc, Estimators);
209 if (m->inUsersGroups("citation", Estimators)) {
210 ValidCalculators validCalc; validCalc.printCitations(Estimators);
211 //remove citation from list of calcs
212 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
216 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
217 m->mothurConvert(temp, abund);
219 temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
220 nseqs = m->isTrue(temp);
222 temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
223 perm = m->isTrue(temp);
225 temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
226 m->mothurConvert(temp, fontsize);
231 catch(exception& e) {
232 m->errorOut(e, "VennCommand", "VennCommand");
236 //**********************************************************************************************************************
238 int VennCommand::execute(){
241 if (abort == true) { if (calledHelp) { return 0; } return 2; }
243 ValidCalculators validCalculator;
245 if (format == "list") {
246 for (int i=0; i<Estimators.size(); i++) {
247 if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
248 if (Estimators[i] == "sobs") {
249 vennCalculators.push_back(new Sobs());
250 }else if (Estimators[i] == "chao") {
251 vennCalculators.push_back(new Chao1());
252 }else if (Estimators[i] == "ace") {
255 vennCalculators.push_back(new Ace(abund));
260 for (int i=0; i<Estimators.size(); i++) {
261 if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
262 if (Estimators[i] == "sharedsobs") {
263 vennCalculators.push_back(new SharedSobsCS());
264 }else if (Estimators[i] == "sharedchao") {
265 vennCalculators.push_back(new SharedChao1());
266 }else if (Estimators[i] == "sharedace") {
267 vennCalculators.push_back(new SharedAce());
273 //if the users entered no valid calculators don't execute command
274 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; }
276 venn = new Venn(outputDir, nseqs, inputfile, fontsize);
277 input = new InputData(inputfile, format);
281 if (format == "sharedfile") {
282 lookup = input->getSharedRAbundVectors();
283 lastLabel = lookup[0]->getLabel();
285 if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
286 }else if (format == "list") {
287 sabund = input->getSAbundVector();
288 lastLabel = sabund->getLabel();
291 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
292 set<string> processedLabels;
293 set<string> userLabels = labels;
295 if (format != "list") {
297 //as long as you are not at the end of the file or done wih the lines you want
298 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
300 if (m->control_pressed) {
301 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
302 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
303 m->clearGroups(); delete venn; delete input;
304 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
308 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
309 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
310 processedLabels.insert(lookup[0]->getLabel());
311 userLabels.erase(lookup[0]->getLabel());
313 if ((lookup.size() > 4) && (!perm)){
314 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();
315 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
317 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
318 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
320 }else if ((lookup.size() > 4) && (perm)) {
321 set< set<int> >::iterator it3;
322 set<int>::iterator it2;
323 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
325 set<int> poss = *it3;
326 vector<SharedRAbundVector*> subset;
327 for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
329 vector<string> outfilenames = venn->getPic(subset, vennCalculators);
330 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
333 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
334 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
338 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
339 string saveLabel = lookup[0]->getLabel();
341 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
342 lookup = input->getSharedRAbundVectors(lastLabel);
344 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
345 processedLabels.insert(lookup[0]->getLabel());
346 userLabels.erase(lookup[0]->getLabel());
348 if ((lookup.size() > 4) && (!perm)){
349 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();
350 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
352 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
353 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
355 }else if ((lookup.size() > 4) && (perm)) {
356 set< set<int> >::iterator it3;
357 set<int>::iterator it2;
358 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
360 set<int> poss = *it3;
361 vector<SharedRAbundVector*> subset;
362 for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
364 vector<string> outfilenames = venn->getPic(subset, vennCalculators);
365 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
368 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
369 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
372 //restore real lastlabel to save below
373 lookup[0]->setLabel(saveLabel);
377 lastLabel = lookup[0]->getLabel();
379 //get next line to process
380 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
381 lookup = input->getSharedRAbundVectors();
384 if (m->control_pressed) {
385 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
386 m->clearGroups(); delete venn; delete input;
387 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
392 //output error messages about any remaining user labels
393 set<string>::iterator it;
394 bool needToRun = false;
395 for (it = userLabels.begin(); it != userLabels.end(); it++) {
396 m->mothurOut("Your file does not include the label " + *it);
397 if (processedLabels.count(lastLabel) != 1) {
398 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
401 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
405 //run last label if you need to
406 if (needToRun == true) {
407 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
408 lookup = input->getSharedRAbundVectors(lastLabel);
410 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
411 processedLabels.insert(lookup[0]->getLabel());
412 userLabels.erase(lookup[0]->getLabel());
414 if ((lookup.size() > 4) && (!perm)){
415 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();
416 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
418 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
419 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
421 }else if ((lookup.size() > 4) && (perm)) {
422 set< set<int> >::iterator it3;
423 set<int>::iterator it2;
424 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
426 set<int> poss = *it3;
427 vector<SharedRAbundVector*> subset;
428 for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
430 vector<string> outfilenames = venn->getPic(subset, vennCalculators);
431 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
434 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
435 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
438 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
442 //reset groups parameter
445 if (m->control_pressed) {
446 m->clearGroups(); delete venn; delete input;
447 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
448 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
455 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
457 if (m->control_pressed) {
458 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
459 delete sabund; delete venn; delete input;
460 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
464 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
466 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
467 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
468 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
471 processedLabels.insert(sabund->getLabel());
472 userLabels.erase(sabund->getLabel());
475 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
476 string saveLabel = sabund->getLabel();
479 sabund = input->getSAbundVector(lastLabel);
481 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
482 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
483 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
486 processedLabels.insert(sabund->getLabel());
487 userLabels.erase(sabund->getLabel());
489 //restore real lastlabel to save below
490 sabund->setLabel(saveLabel);
493 lastLabel = sabund->getLabel();
496 sabund = input->getSAbundVector();
499 if (m->control_pressed) {
500 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
501 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
502 delete venn; delete input;
506 //output error messages about any remaining user labels
507 set<string>::iterator it;
508 bool needToRun = false;
509 for (it = userLabels.begin(); it != userLabels.end(); it++) {
510 m->mothurOut("Your file does not include the label " + *it);
511 if (processedLabels.count(lastLabel) != 1) {
512 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
515 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
519 //run last label if you need to
520 if (needToRun == true) {
521 if (sabund != NULL) { delete sabund; }
522 sabund = input->getSAbundVector(lastLabel);
524 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
525 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
526 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
532 if (m->control_pressed) {
533 delete venn; delete input;
534 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
535 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
540 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
541 delete venn; delete input;
543 m->mothurOutEndLine();
544 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
545 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
546 m->mothurOutEndLine();
551 catch(exception& e) {
552 m->errorOut(e, "VennCommand", "execute");
556 //**********************************************************************************************************************
557 //returns a vector of sets containing the 4 group combinations
558 set< set<int> > VennCommand::findCombinations(int lookupSize){
560 set< set<int> > combos;
563 for (int i = 0; i < lookupSize; i++) { possibles.insert(i); }
565 getCombos(possibles, combos);
570 catch(exception& e) {
571 m->errorOut(e, "VennCommand", "findCombinations");
575 //**********************************************************************************************************************
576 //recusively finds combos of 4
577 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
580 if (possibles.size() == 4) { //done
581 if (combos.count(possibles) == 0) { //no dups
582 combos.insert(possibles);
584 }else { //we still have work to do
585 set<int>::iterator it;
586 set<int>::iterator it2;
587 for (it = possibles.begin(); it != possibles.end(); it++) {
589 set<int> newPossibles;
590 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) { //all possible combos of one length smaller
592 newPossibles.insert(*it2);
595 getCombos(newPossibles, combos);
601 catch(exception& e) {
602 m->errorOut(e, "VennCommand", "getCombos");
607 //**********************************************************************************************************************