5 * Created by Pat Schloss on 10/25/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
10 #include "command.hpp"
11 #include "clustercommand.h"
12 #include "collectcommand.h"
13 #include "collectsharedcommand.h"
14 #include "getgroupcommand.h"
15 #include "getlabelcommand.h"
16 #include "rarefactcommand.h"
17 #include "summarycommand.h"
18 #include "summarysharedcommand.h"
19 #include "rarefactsharedcommand.h"
20 #include "quitcommand.h"
21 #include "helpcommand.h"
22 #include "commandfactory.hpp"
23 #include "deconvolutecommand.h"
24 #include "parsimonycommand.h"
25 #include "unifracunweightedcommand.h"
26 #include "unifracweightedcommand.h"
27 #include "libshuffcommand.h"
28 #include "heatmapcommand.h"
29 #include "heatmapsimcommand.h"
30 #include "filterseqscommand.h"
31 #include "venncommand.h"
32 #include "nocommands.h"
33 #include "binsequencecommand.h"
34 #include "getoturepcommand.h"
35 #include "treegroupscommand.h"
36 #include "distancecommand.h"
37 #include "aligncommand.h"
38 #include "matrixoutputcommand.h"
39 #include "getsabundcommand.h"
40 #include "getrabundcommand.h"
41 #include "seqsummarycommand.h"
42 #include "screenseqscommand.h"
43 #include "reversecommand.h"
44 #include "trimseqscommand.h"
45 #include "mergefilecommand.h"
46 #include "listseqscommand.h"
47 #include "getseqscommand.h"
48 #include "removeseqscommand.h"
49 #include "systemcommand.h"
50 #include "secondarystructurecommand.h"
51 #include "getsharedotucommand.h"
52 #include "getlistcountcommand.h"
53 #include "hclustercommand.h"
54 #include "classifyseqscommand.h"
55 #include "phylotypecommand.h"
56 #include "mgclustercommand.h"
57 #include "preclustercommand.h"
58 #include "pcoacommand.h"
59 #include "otuhierarchycommand.h"
60 #include "setdircommand.h"
61 #include "parselistscommand.h"
62 #include "chimeraccodecommand.h"
63 #include "chimeracheckcommand.h"
64 #include "chimeraslayercommand.h"
65 #include "chimerapintailcommand.h"
66 #include "chimerabellerophoncommand.h"
67 #include "chimerauchimecommand.h"
68 #include "setlogfilecommand.h"
69 #include "phylodiversitycommand.h"
70 #include "makegroupcommand.h"
71 #include "chopseqscommand.h"
72 #include "clearcutcommand.h"
73 #include "catchallcommand.h"
74 #include "splitabundcommand.h"
75 #include "clustersplitcommand.h"
76 #include "classifyotucommand.h"
77 #include "degapseqscommand.h"
78 #include "getrelabundcommand.h"
79 #include "sensspeccommand.h"
80 #include "sffinfocommand.h"
81 #include "seqerrorcommand.h"
82 #include "normalizesharedcommand.h"
83 #include "metastatscommand.h"
84 #include "splitgroupscommand.h"
85 #include "clusterfragmentscommand.h"
86 #include "getlineagecommand.h"
87 #include "removelineagecommand.h"
88 #include "parsefastaqcommand.h"
89 #include "pipelinepdscommand.h"
90 #include "deuniqueseqscommand.h"
91 #include "pairwiseseqscommand.h"
92 #include "clusterdoturcommand.h"
93 #include "subsamplecommand.h"
94 #include "removegroupscommand.h"
95 #include "getgroupscommand.h"
96 #include "getotuscommand.h"
97 #include "removeotuscommand.h"
98 #include "indicatorcommand.h"
99 #include "consensusseqscommand.h"
100 #include "trimflowscommand.h"
101 #include "corraxescommand.h"
102 #include "shhhercommand.h"
103 #include "pcacommand.h"
104 #include "nmdscommand.h"
105 #include "removerarecommand.h"
106 #include "mergegroupscommand.h"
107 #include "amovacommand.h"
108 #include "homovacommand.h"
109 #include "mantelcommand.h"
110 #include "makefastqcommand.h"
111 #include "anosimcommand.h"
112 #include "getcurrentcommand.h"
113 #include "setcurrentcommand.h"
114 #include "sharedcommand.h"
115 #include "getcommandinfocommand.h"
116 #include "deuniquetreecommand.h"
117 #include "countseqscommand.h"
118 #include "countgroupscommand.h"
119 #include "clearmemorycommand.h"
120 #include "summarytaxcommand.h"
121 #include "chimeraperseuscommand.h"
122 #include "shhhseqscommand.h"
123 #include "summaryqualcommand.h"
124 #include "otuassociationcommand.h"
125 #include "sortseqscommand.h"
126 #include "classifytreecommand.h"
127 #include "cooccurrencecommand.h"
128 #include "pcrseqscommand.h"
129 #include "createdatabasecommand.h"
130 #include "makebiomcommand.h"
131 #include "getcoremicrobiomecommand.h"
132 #include "listotulabelscommand.h"
133 #include "getotulabelscommand.h"
134 #include "removeotulabelscommand.h"
135 #include "makecontigscommand.h"
136 #include "loadlogfilecommand.h"
137 #include "sffmultiplecommand.h"
138 #include "classifyrfsharedcommand.h"
139 #include "filtersharedcommand.h"
140 #include "primerdesigncommand.h"
141 #include "getdistscommand.h"
142 #include "removedistscommand.h"
143 #include "mergetaxsummarycommand.h"
144 #include "getmetacommunitycommand.h"
145 #include "sparcccommand.h"
146 #include "makelookupcommand.h"
147 #include "renameseqscommand.h"
148 #include "makelefsecommand.h"
149 #include "lefsecommand.h"
150 #include "kruskalwalliscommand.h"
152 /*******************************************************/
154 /******************************************************/
155 CommandFactory* CommandFactory::getInstance() {
156 if( _uniqueInstance == 0) {
157 _uniqueInstance = new CommandFactory();
159 return _uniqueInstance;
161 /***********************************************************/
163 /***********************************************************/
164 //note: This class is resposible for knowing which commands are mpiEnabled,
165 //If a command is not enabled only process 0 will execute the command.
166 //This avoids redundant outputs on pieces of code we have not paralellized.
167 //If you add mpi code to a existing command you need to modify the list below or the code will hang on MPI blocking commands like FIle_open.
168 //example: commands["dist.seqs"] = "MPIEnabled";
170 CommandFactory::CommandFactory(){
172 m = MothurOut::getInstance();
174 command = new NoCommand(s);
175 shellcommand = new NoCommand(s);
176 pipecommand = new NoCommand(s);
178 outputDir = ""; inputDir = "";
182 //initialize list of valid commands
183 commands["make.shared"] = "make.shared";
184 commands["bin.seqs"] = "bin.seqs";
185 commands["get.oturep"] = "get.oturep";
186 commands["cluster"] = "cluster";
187 commands["unique.seqs"] = "unique.seqs";
188 commands["dist.shared"] = "dist.shared";
189 commands["collect.single"] = "collect.single";
190 commands["collect.shared"] = "collect.shared";
191 commands["rarefaction.single"] = "rarefaction.single";
192 commands["rarefaction.shared"] = "rarefaction.shared";
193 commands["summary.single"] = "summary.single";
194 commands["summary.shared"] = "summary.shared";
195 commands["parsimony"] = "parsimony";
196 commands["unifrac.weighted"] = "unifrac.weighted";
197 commands["unifrac.unweighted"] = "unifrac.unweighted";
198 commands["libshuff"] = "libshuff";
199 commands["tree.shared"] = "tree.shared";
200 commands["heatmap.bin"] = "heatmap.bin";
201 commands["heatmap.sim"] = "heatmap.sim";
202 commands["venn"] = "venn";
203 commands["get.group"] = "get.group";
204 commands["get.label"] = "get.label";
205 commands["get.sabund"] = "get.sabund";
206 commands["get.rabund"] = "get.rabund";
207 commands["help"] = "help";
208 commands["reverse.seqs"] = "reverse.seqs";
209 commands["trim.seqs"] = "trim.seqs";
210 commands["trim.flows"] = "trim.flows";
211 commands["list.seqs"] = "list.seqs";
212 commands["get.seqs"] = "get.seqs";
213 commands["remove.seqs"] = "remove.seqs";
214 commands["system"] = "system";
215 commands["align.check"] = "align.check";
216 commands["get.sharedseqs"] = "get.sharedseqs";
217 commands["get.otulist"] = "get.otulist";
218 commands["hcluster"] = "hcluster";
219 commands["phylotype"] = "phylotype";
220 commands["mgcluster"] = "mgcluster";
221 commands["pre.cluster"] = "pre.cluster";
222 commands["pcoa"] = "pcoa";
223 commands["otu.hierarchy"] = "otu.hierarchy";
224 commands["set.dir"] = "MPIEnabled";
225 commands["merge.files"] = "merge.files";
226 commands["parse.list"] = "parse.list";
227 commands["set.logfile"] = "set.logfile";
228 commands["phylo.diversity"] = "phylo.diversity";
229 commands["make.group"] = "make.group";
230 commands["chop.seqs"] = "chop.seqs";
231 commands["clearcut"] = "clearcut";
232 commands["catchall"] = "catchall";
233 commands["split.abund"] = "split.abund";
234 commands["classify.otu"] = "classify.otu";
235 commands["degap.seqs"] = "degap.seqs";
236 commands["get.relabund"] = "get.relabund";
237 commands["sffinfo"] = "sffinfo";
238 commands["normalize.shared"] = "normalize.shared";
239 commands["metastats"] = "metastats";
240 commands["split.groups"] = "split.groups";
241 commands["cluster.fragments"] = "cluster.fragments";
242 commands["get.lineage"] = "get.lineage";
243 commands["remove.lineage"] = "remove.lineage";
244 commands["fastq.info"] = "fastq.info";
245 commands["deunique.seqs"] = "deunique.seqs";
246 commands["cluster.classic"] = "cluster.classic";
247 commands["sub.sample"] = "sub.sample";
248 commands["remove.groups"] = "remove.groups";
249 commands["get.groups"] = "get.groups";
250 commands["get.otus"] = "get.otus";
251 commands["remove.otus"] = "remove.otus";
252 commands["indicator"] = "indicator";
253 commands["consensus.seqs"] = "consensus.seqs";
254 commands["corr.axes"] = "corr.axes";
255 commands["pca"] = "pca";
256 commands["nmds"] = "nmds";
257 commands["remove.rare"] = "remove.rare";
258 commands["amova"] = "amova";
259 commands["homova"] = "homova";
260 commands["mantel"] = "mantel";
261 commands["anosim"] = "anosim";
262 commands["make.fastq"] = "make.fastq";
263 commands["merge.groups"] = "merge.groups";
264 commands["get.current"] = "MPIEnabled";
265 commands["set.current"] = "MPIEnabled";
266 commands["get.commandinfo"] = "get.commandinfo";
267 commands["deunique.tree"] = "deunique.tree";
268 commands["count.seqs"] = "count.seqs";
269 commands["count.groups"] = "count.groups";
270 commands["clear.memory"] = "clear.memory";
271 commands["pairwise.seqs"] = "MPIEnabled";
272 commands["pipeline.pds"] = "MPIEnabled";
273 commands["classify.seqs"] = "MPIEnabled";
274 commands["dist.seqs"] = "MPIEnabled";
275 commands["filter.seqs"] = "MPIEnabled";
276 commands["align.seqs"] = "MPIEnabled";
277 commands["chimera.ccode"] = "MPIEnabled";
278 commands["chimera.check"] = "MPIEnabled";
279 commands["chimera.slayer"] = "MPIEnabled";
280 commands["chimera.uchime"] = "chimera.uchime";
281 commands["chimera.perseus"] = "chimera.perseus";
282 commands["chimera.pintail"] = "MPIEnabled";
283 commands["chimera.bellerophon"] = "MPIEnabled";
284 commands["screen.seqs"] = "MPIEnabled";
285 commands["summary.seqs"] = "MPIEnabled";
286 commands["cluster.split"] = "MPIEnabled";
287 commands["shhh.flows"] = "MPIEnabled";
288 commands["sens.spec"] = "sens.spec";
289 commands["seq.error"] = "seq.error";
290 commands["summary.tax"] = "summary.tax";
291 commands["summary.qual"] = "summary.qual";
292 commands["shhh.seqs"] = "shhh.seqs";
293 commands["otu.association"] = "otu.association";
294 commands["sort.seqs"] = "sort.seqs";
295 commands["classify.tree"] = "classify.tree";
296 commands["cooccurrence"] = "cooccurrence";
297 commands["pcr.seqs"] = "pcr.seqs";
298 commands["create.database"] = "create.database";
299 commands["make.biom"] = "make.biom";
300 commands["get.coremicrobiome"] = "get.coremicrobiome";
301 commands["list.otulabels"] = "list.otulabels";
302 commands["get.otulabels"] = "get.otulabels";
303 commands["remove.otulabels"] = "remove.otulabels";
304 commands["make.contigs"] = "make.contigs";
305 commands["load.logfile"] = "load.logfile";
306 commands["make.table"] = "make.table";
307 commands["sff.multiple"] = "sff.multiple";
308 commands["quit"] = "MPIEnabled";
309 commands["classify.rf"] = "classify.rf";
310 commands["filter.shared"] = "filter.shared";
311 commands["primer.design"] = "primer.design";
312 commands["get.dists"] = "get.dists";
313 commands["remove.dists"] = "remove.dists";
314 commands["merge.taxsummary"] = "merge.taxsummary";
315 commands["get.communitytype"] = "get.communitytype";
316 commands["sparcc"] = "sparcc";
317 commands["make.lookup"] = "make.lookup";
318 commands["rename.seqs"] = "rename.seqs";
319 commands["make.lefse"] = "make.lefse";
320 commands["lefse"] = "lefse";
321 commands["kruskal.wallis"] = "kruskal.wallis";
325 /***********************************************************/
327 /***********************************************************/
328 bool CommandFactory::MPIEnabled(string commandName) {
330 it = commands.find(commandName);
331 if (it != commands.end()) {
332 if (it->second == "MPIEnabled") { return true; }
336 /***********************************************************/
338 /***********************************************************/
339 CommandFactory::~CommandFactory(){
345 /***********************************************************/
347 /***********************************************************/
348 int CommandFactory::checkForRedirects(string optionString) {
351 int pos = optionString.find("outputdir");
352 if (pos != string::npos) { //user has set outputdir in command option string
353 string outputOption = "";
354 bool foundEquals = false;
355 for(int i=pos;i<optionString.length();i++){
356 if(optionString[i] == ',') { break; }
357 else if(optionString[i] == '=') { foundEquals = true; }
358 if (foundEquals) { outputOption += optionString[i]; }
360 if(m->dirCheck(outputOption)){
361 setOutputDirectory(outputOption);
362 m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
366 pos = optionString.find("inputdir");
367 if (pos != string::npos) { //user has set inputdir in command option string
368 string intputOption = "";
369 bool foundEquals = false;
370 for(int i=pos;i<optionString.length();i++){
371 if(optionString[i] == ',') { break; }
372 else if(optionString[i] == '=') { foundEquals = true; }
373 if (foundEquals) { intputOption += optionString[i]; }
375 if(m->dirCheck(intputOption)){
376 setInputDirectory(intputOption);
377 m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
383 catch(exception& e) {
384 m->errorOut(e, "CommandFactory", "getCommand");
388 /***********************************************************/
390 /***********************************************************/
391 //This function calls the appropriate command fucntions based on user input.
392 Command* CommandFactory::getCommand(string commandName, string optionString){
395 delete command; //delete the old command
397 checkForRedirects(optionString);
399 //user has opted to redirect output from dir where input files are located to some other place
400 if (outputDir != "") {
401 if (optionString != "") { optionString += ", outputdir=" + outputDir; }
402 else { optionString += "outputdir=" + outputDir; }
405 //user has opted to redirect input from dir where mothur.exe is located to some other place
406 if (inputDir != "") {
407 if (optionString != "") { optionString += ", inputdir=" + inputDir; }
408 else { optionString += "inputdir=" + inputDir; }
411 if(commandName == "cluster") { command = new ClusterCommand(optionString); }
412 else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
413 else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
414 else if(commandName == "help") { command = new HelpCommand(optionString); }
415 else if(commandName == "quit") { command = new QuitCommand(optionString); }
416 else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
417 else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
418 else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
419 else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
420 else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
421 else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
422 else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
423 else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
424 else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
425 else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
426 else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
427 else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
428 else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
429 else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
430 else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
431 else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
432 else if(commandName == "venn") { command = new VennCommand(optionString); }
433 else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
434 else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
435 else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
436 else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
437 else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
438 else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
439 else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
440 else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
441 else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
442 else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
443 else if(commandName == "trim.flows") { command = new TrimFlowsCommand(optionString); }
444 else if(commandName == "shhh.flows") { command = new ShhherCommand(optionString); }
445 else if(commandName == "list.seqs") { command = new ListSeqsCommand(optionString); }
446 else if(commandName == "get.seqs") { command = new GetSeqsCommand(optionString); }
447 else if(commandName == "remove.seqs") { command = new RemoveSeqsCommand(optionString); }
448 else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
449 else if(commandName == "system") { command = new SystemCommand(optionString); }
450 else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
451 else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
452 else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
453 else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
454 else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(optionString); }
455 else if(commandName == "chimera.ccode") { command = new ChimeraCcodeCommand(optionString); }
456 else if(commandName == "chimera.check") { command = new ChimeraCheckCommand(optionString); }
457 else if(commandName == "chimera.slayer") { command = new ChimeraSlayerCommand(optionString); }
458 else if(commandName == "chimera.uchime") { command = new ChimeraUchimeCommand(optionString); }
459 else if(commandName == "chimera.pintail") { command = new ChimeraPintailCommand(optionString); }
460 else if(commandName == "chimera.bellerophon") { command = new ChimeraBellerophonCommand(optionString); }
461 else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
462 else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
463 else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
464 else if(commandName == "pcoa") { command = new PCOACommand(optionString); }
465 else if(commandName == "pca") { command = new PCACommand(optionString); }
466 else if(commandName == "nmds") { command = new NMDSCommand(optionString); }
467 else if(commandName == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
468 else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
469 else if(commandName == "set.logfile") { command = new SetLogFileCommand(optionString); }
470 else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
471 else if(commandName == "phylo.diversity") { command = new PhyloDiversityCommand(optionString); }
472 else if(commandName == "make.group") { command = new MakeGroupCommand(optionString); }
473 else if(commandName == "chop.seqs") { command = new ChopSeqsCommand(optionString); }
474 else if(commandName == "clearcut") { command = new ClearcutCommand(optionString); }
475 else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
476 else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
477 else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
478 else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(optionString); }
479 else if(commandName == "degap.seqs") { command = new DegapSeqsCommand(optionString); }
480 else if(commandName == "get.relabund") { command = new GetRelAbundCommand(optionString); }
481 else if(commandName == "sens.spec") { command = new SensSpecCommand(optionString); }
482 else if(commandName == "seq.error") { command = new SeqErrorCommand(optionString); }
483 else if(commandName == "sffinfo") { command = new SffInfoCommand(optionString); }
484 else if(commandName == "normalize.shared") { command = new NormalizeSharedCommand(optionString); }
485 else if(commandName == "metastats") { command = new MetaStatsCommand(optionString); }
486 else if(commandName == "split.groups") { command = new SplitGroupCommand(optionString); }
487 else if(commandName == "cluster.fragments") { command = new ClusterFragmentsCommand(optionString); }
488 else if(commandName == "get.lineage") { command = new GetLineageCommand(optionString); }
489 else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
490 else if(commandName == "get.groups") { command = new GetGroupsCommand(optionString); }
491 else if(commandName == "remove.groups") { command = new RemoveGroupsCommand(optionString); }
492 else if(commandName == "get.otus") { command = new GetOtusCommand(optionString); }
493 else if(commandName == "remove.otus") { command = new RemoveOtusCommand(optionString); }
494 else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
495 else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
496 else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
497 else if(commandName == "pairwise.seqs") { command = new PairwiseSeqsCommand(optionString); }
498 else if(commandName == "cluster.classic") { command = new ClusterDoturCommand(optionString); }
499 else if(commandName == "sub.sample") { command = new SubSampleCommand(optionString); }
500 else if(commandName == "indicator") { command = new IndicatorCommand(optionString); }
501 else if(commandName == "consensus.seqs") { command = new ConsensusSeqsCommand(optionString); }
502 else if(commandName == "corr.axes") { command = new CorrAxesCommand(optionString); }
503 else if(commandName == "remove.rare") { command = new RemoveRareCommand(optionString); }
504 else if(commandName == "merge.groups") { command = new MergeGroupsCommand(optionString); }
505 else if(commandName == "amova") { command = new AmovaCommand(optionString); }
506 else if(commandName == "homova") { command = new HomovaCommand(optionString); }
507 else if(commandName == "mantel") { command = new MantelCommand(optionString); }
508 else if(commandName == "make.fastq") { command = new MakeFastQCommand(optionString); }
509 else if(commandName == "get.current") { command = new GetCurrentCommand(optionString); }
510 else if(commandName == "set.current") { command = new SetCurrentCommand(optionString); }
511 else if(commandName == "anosim") { command = new AnosimCommand(optionString); }
512 else if(commandName == "make.shared") { command = new SharedCommand(optionString); }
513 else if(commandName == "get.commandinfo") { command = new GetCommandInfoCommand(optionString); }
514 else if(commandName == "deunique.tree") { command = new DeuniqueTreeCommand(optionString); }
515 else if((commandName == "count.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(optionString); }
516 else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); }
517 else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); }
518 else if(commandName == "summary.tax") { command = new SummaryTaxCommand(optionString); }
519 else if(commandName == "summary.qual") { command = new SummaryQualCommand(optionString); }
520 else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); }
521 else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); }
522 else if(commandName == "otu.association") { command = new OTUAssociationCommand(optionString); }
523 else if(commandName == "sort.seqs") { command = new SortSeqsCommand(optionString); }
524 else if(commandName == "classify.tree") { command = new ClassifyTreeCommand(optionString); }
525 else if(commandName == "cooccurrence") { command = new CooccurrenceCommand(optionString); }
526 else if(commandName == "pcr.seqs") { command = new PcrSeqsCommand(optionString); }
527 else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
528 else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); }
529 else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); }
530 else if(commandName == "list.otulabels") { command = new ListOtuLabelsCommand(optionString); }
531 else if(commandName == "get.otulabels") { command = new GetOtuLabelsCommand(optionString); }
532 else if(commandName == "remove.otulabels") { command = new RemoveOtuLabelsCommand(optionString); }
533 else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
534 else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); }
535 else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
536 else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
537 else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
538 else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
539 else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
540 else if(commandName == "remove.dists") { command = new RemoveDistsCommand(optionString); }
541 else if(commandName == "merge.taxsummary") { command = new MergeTaxSummaryCommand(optionString); }
542 else if(commandName == "get.communitytype") { command = new GetMetaCommunityCommand(optionString); }
543 else if(commandName == "sparcc") { command = new SparccCommand(optionString); }
544 else if(commandName == "make.lookup") { command = new MakeLookupCommand(optionString); }
545 else if(commandName == "rename.seqs") { command = new RenameSeqsCommand(optionString); }
546 else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
547 else if(commandName == "lefse") { command = new LefseCommand(optionString); }
548 else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
549 else { command = new NoCommand(optionString); }
553 catch(exception& e) {
554 m->errorOut(e, "CommandFactory", "getCommand");
558 /***********************************************************/
560 /***********************************************************/
561 //This function calls the appropriate command fucntions based on user input.
562 Command* CommandFactory::getCommand(string commandName, string optionString, string mode){
564 delete pipecommand; //delete the old command
566 checkForRedirects(optionString);
568 //user has opted to redirect output from dir where input files are located to some other place
569 if (outputDir != "") {
570 if (optionString != "") { optionString += ", outputdir=" + outputDir; }
571 else { optionString += "outputdir=" + outputDir; }
574 //user has opted to redirect input from dir where mothur.exe is located to some other place
575 if (inputDir != "") {
576 if (optionString != "") { optionString += ", inputdir=" + inputDir; }
577 else { optionString += "inputdir=" + inputDir; }
580 if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); }
581 else if(commandName == "unique.seqs") { pipecommand = new DeconvoluteCommand(optionString); }
582 else if(commandName == "parsimony") { pipecommand = new ParsimonyCommand(optionString); }
583 else if(commandName == "help") { pipecommand = new HelpCommand(optionString); }
584 else if(commandName == "quit") { pipecommand = new QuitCommand(optionString); }
585 else if(commandName == "collect.single") { pipecommand = new CollectCommand(optionString); }
586 else if(commandName == "collect.shared") { pipecommand = new CollectSharedCommand(optionString); }
587 else if(commandName == "rarefaction.single") { pipecommand = new RareFactCommand(optionString); }
588 else if(commandName == "rarefaction.shared") { pipecommand = new RareFactSharedCommand(optionString); }
589 else if(commandName == "summary.single") { pipecommand = new SummaryCommand(optionString); }
590 else if(commandName == "summary.shared") { pipecommand = new SummarySharedCommand(optionString); }
591 else if(commandName == "unifrac.weighted") { pipecommand = new UnifracWeightedCommand(optionString); }
592 else if(commandName == "unifrac.unweighted") { pipecommand = new UnifracUnweightedCommand(optionString); }
593 else if(commandName == "get.group") { pipecommand = new GetgroupCommand(optionString); }
594 else if(commandName == "get.label") { pipecommand = new GetlabelCommand(optionString); }
595 else if(commandName == "get.sabund") { pipecommand = new GetSAbundCommand(optionString); }
596 else if(commandName == "get.rabund") { pipecommand = new GetRAbundCommand(optionString); }
597 else if(commandName == "libshuff") { pipecommand = new LibShuffCommand(optionString); }
598 else if(commandName == "heatmap.bin") { pipecommand = new HeatMapCommand(optionString); }
599 else if(commandName == "heatmap.sim") { pipecommand = new HeatMapSimCommand(optionString); }
600 else if(commandName == "filter.seqs") { pipecommand = new FilterSeqsCommand(optionString); }
601 else if(commandName == "venn") { pipecommand = new VennCommand(optionString); }
602 else if(commandName == "bin.seqs") { pipecommand = new BinSeqCommand(optionString); }
603 else if(commandName == "get.oturep") { pipecommand = new GetOTURepCommand(optionString); }
604 else if(commandName == "tree.shared") { pipecommand = new TreeGroupCommand(optionString); }
605 else if(commandName == "dist.shared") { pipecommand = new MatrixOutputCommand(optionString); }
606 else if(commandName == "dist.seqs") { pipecommand = new DistanceCommand(optionString); }
607 else if(commandName == "align.seqs") { pipecommand = new AlignCommand(optionString); }
608 else if(commandName == "summary.seqs") { pipecommand = new SeqSummaryCommand(optionString); }
609 else if(commandName == "screen.seqs") { pipecommand = new ScreenSeqsCommand(optionString); }
610 else if(commandName == "reverse.seqs") { pipecommand = new ReverseSeqsCommand(optionString); }
611 else if(commandName == "trim.seqs") { pipecommand = new TrimSeqsCommand(optionString); }
612 else if(commandName == "trim.flows") { pipecommand = new TrimFlowsCommand(optionString); }
613 else if(commandName == "shhh.flows") { pipecommand = new ShhherCommand(optionString); }
614 else if(commandName == "list.seqs") { pipecommand = new ListSeqsCommand(optionString); }
615 else if(commandName == "get.seqs") { pipecommand = new GetSeqsCommand(optionString); }
616 else if(commandName == "remove.seqs") { pipecommand = new RemoveSeqsCommand(optionString); }
617 else if(commandName == "merge.files") { pipecommand = new MergeFileCommand(optionString); }
618 else if(commandName == "system") { pipecommand = new SystemCommand(optionString); }
619 else if(commandName == "align.check") { pipecommand = new AlignCheckCommand(optionString); }
620 else if(commandName == "get.sharedseqs") { pipecommand = new GetSharedOTUCommand(optionString); }
621 else if(commandName == "get.otulist") { pipecommand = new GetListCountCommand(optionString); }
622 else if(commandName == "hcluster") { pipecommand = new HClusterCommand(optionString); }
623 else if(commandName == "classify.seqs") { pipecommand = new ClassifySeqsCommand(optionString); }
624 else if(commandName == "chimera.ccode") { pipecommand = new ChimeraCcodeCommand(optionString); }
625 else if(commandName == "chimera.check") { pipecommand = new ChimeraCheckCommand(optionString); }
626 else if(commandName == "chimera.uchime") { pipecommand = new ChimeraUchimeCommand(optionString); }
627 else if(commandName == "chimera.slayer") { pipecommand = new ChimeraSlayerCommand(optionString); }
628 else if(commandName == "chimera.pintail") { pipecommand = new ChimeraPintailCommand(optionString); }
629 else if(commandName == "chimera.bellerophon") { pipecommand = new ChimeraBellerophonCommand(optionString); }
630 else if(commandName == "phylotype") { pipecommand = new PhylotypeCommand(optionString); }
631 else if(commandName == "mgcluster") { pipecommand = new MGClusterCommand(optionString); }
632 else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
633 else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
634 else if(commandName == "pca") { pipecommand = new PCACommand(optionString); }
635 else if(commandName == "nmds") { pipecommand = new NMDSCommand(optionString); }
636 else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
637 else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
638 else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
639 else if(commandName == "parse.list") { pipecommand = new ParseListCommand(optionString); }
640 else if(commandName == "phylo.diversity") { pipecommand = new PhyloDiversityCommand(optionString); }
641 else if(commandName == "make.group") { pipecommand = new MakeGroupCommand(optionString); }
642 else if(commandName == "chop.seqs") { pipecommand = new ChopSeqsCommand(optionString); }
643 else if(commandName == "clearcut") { pipecommand = new ClearcutCommand(optionString); }
644 else if(commandName == "catchall") { pipecommand = new CatchAllCommand(optionString); }
645 else if(commandName == "split.abund") { pipecommand = new SplitAbundCommand(optionString); }
646 else if(commandName == "cluster.split") { pipecommand = new ClusterSplitCommand(optionString); }
647 else if(commandName == "classify.otu") { pipecommand = new ClassifyOtuCommand(optionString); }
648 else if(commandName == "degap.seqs") { pipecommand = new DegapSeqsCommand(optionString); }
649 else if(commandName == "get.relabund") { pipecommand = new GetRelAbundCommand(optionString); }
650 else if(commandName == "sens.spec") { pipecommand = new SensSpecCommand(optionString); }
651 else if(commandName == "seq.error") { pipecommand = new SeqErrorCommand(optionString); }
652 else if(commandName == "sffinfo") { pipecommand = new SffInfoCommand(optionString); }
653 else if(commandName == "normalize.shared") { pipecommand = new NormalizeSharedCommand(optionString); }
654 else if(commandName == "metastats") { pipecommand = new MetaStatsCommand(optionString); }
655 else if(commandName == "split.groups") { pipecommand = new SplitGroupCommand(optionString); }
656 else if(commandName == "cluster.fragments") { pipecommand = new ClusterFragmentsCommand(optionString); }
657 else if(commandName == "get.lineage") { pipecommand = new GetLineageCommand(optionString); }
658 else if(commandName == "get.groups") { pipecommand = new GetGroupsCommand(optionString); }
659 else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
660 else if(commandName == "remove.groups") { pipecommand = new RemoveGroupsCommand(optionString); }
661 else if(commandName == "get.otus") { pipecommand = new GetOtusCommand(optionString); }
662 else if(commandName == "remove.otus") { pipecommand = new RemoveOtusCommand(optionString); }
663 else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
664 else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
665 else if(commandName == "pairwise.seqs") { pipecommand = new PairwiseSeqsCommand(optionString); }
666 else if(commandName == "cluster.classic") { pipecommand = new ClusterDoturCommand(optionString); }
667 else if(commandName == "sub.sample") { pipecommand = new SubSampleCommand(optionString); }
668 else if(commandName == "indicator") { pipecommand = new IndicatorCommand(optionString); }
669 else if(commandName == "consensus.seqs") { pipecommand = new ConsensusSeqsCommand(optionString); }
670 else if(commandName == "corr.axes") { pipecommand = new CorrAxesCommand(optionString); }
671 else if(commandName == "remove.rare") { pipecommand = new RemoveRareCommand(optionString); }
672 else if(commandName == "merge.groups") { pipecommand = new MergeGroupsCommand(optionString); }
673 else if(commandName == "amova") { pipecommand = new AmovaCommand(optionString); }
674 else if(commandName == "homova") { pipecommand = new HomovaCommand(optionString); }
675 else if(commandName == "mantel") { pipecommand = new MantelCommand(optionString); }
676 else if(commandName == "anosim") { pipecommand = new AnosimCommand(optionString); }
677 else if(commandName == "make.fastq") { pipecommand = new MakeFastQCommand(optionString); }
678 else if(commandName == "get.current") { pipecommand = new GetCurrentCommand(optionString); }
679 else if(commandName == "set.current") { pipecommand = new SetCurrentCommand(optionString); }
680 else if(commandName == "make.shared") { pipecommand = new SharedCommand(optionString); }
681 else if(commandName == "get.commandinfo") { pipecommand = new GetCommandInfoCommand(optionString); }
682 else if(commandName == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(optionString); }
683 else if((commandName == "count.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(optionString); }
684 else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
685 else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
686 else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(optionString); }
687 else if(commandName == "summary.qual") { pipecommand = new SummaryQualCommand(optionString); }
688 else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
689 else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
690 else if(commandName == "otu.association") { pipecommand = new OTUAssociationCommand(optionString); }
691 else if(commandName == "sort.seqs") { pipecommand = new SortSeqsCommand(optionString); }
692 else if(commandName == "classify.tree") { pipecommand = new ClassifyTreeCommand(optionString); }
693 else if(commandName == "cooccurrence") { pipecommand = new CooccurrenceCommand(optionString); }
694 else if(commandName == "pcr.seqs") { pipecommand = new PcrSeqsCommand(optionString); }
695 else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); }
696 else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); }
697 else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
698 else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); }
699 else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); }
700 else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); }
701 else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
702 else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); }
703 else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
704 else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
705 else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
706 else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
707 else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
708 else if(commandName == "remove.dists") { pipecommand = new RemoveDistsCommand(optionString); }
709 else if(commandName == "merge.taxsummary") { pipecommand = new MergeTaxSummaryCommand(optionString); }
710 else if(commandName == "get.communitytype") { pipecommand = new GetMetaCommunityCommand(optionString); }
711 else if(commandName == "sparcc") { pipecommand = new SparccCommand(optionString); }
712 else if(commandName == "make.lookup") { pipecommand = new MakeLookupCommand(optionString); }
713 else if(commandName == "rename.seqs") { pipecommand = new RenameSeqsCommand(optionString); }
714 else if(commandName == "make.lefse") { pipecommand = new MakeLefseCommand(optionString); }
715 else if(commandName == "lefse") { pipecommand = new LefseCommand(optionString); }
716 else if(commandName == "kruskal.wallis") { pipecommand = new KruskalWallisCommand(optionString); }
717 else { pipecommand = new NoCommand(optionString); }
721 catch(exception& e) {
722 m->errorOut(e, "CommandFactory", "getCommand");
726 /***********************************************************/
728 /***********************************************************/
729 //This function calls the appropriate command fucntions based on user input, this is used by the pipeline command to check a users piepline for errors before running
730 Command* CommandFactory::getCommand(string commandName){
732 delete shellcommand; //delete the old command
734 if(commandName == "cluster") { shellcommand = new ClusterCommand(); }
735 else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); }
736 else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); }
737 else if(commandName == "help") { shellcommand = new HelpCommand(); }
738 else if(commandName == "quit") { shellcommand = new QuitCommand(); }
739 else if(commandName == "collect.single") { shellcommand = new CollectCommand(); }
740 else if(commandName == "collect.shared") { shellcommand = new CollectSharedCommand(); }
741 else if(commandName == "rarefaction.single") { shellcommand = new RareFactCommand(); }
742 else if(commandName == "rarefaction.shared") { shellcommand = new RareFactSharedCommand(); }
743 else if(commandName == "summary.single") { shellcommand = new SummaryCommand(); }
744 else if(commandName == "summary.shared") { shellcommand = new SummarySharedCommand(); }
745 else if(commandName == "unifrac.weighted") { shellcommand = new UnifracWeightedCommand(); }
746 else if(commandName == "unifrac.unweighted") { shellcommand = new UnifracUnweightedCommand(); }
747 else if(commandName == "get.group") { shellcommand = new GetgroupCommand(); }
748 else if(commandName == "get.label") { shellcommand = new GetlabelCommand(); }
749 else if(commandName == "get.sabund") { shellcommand = new GetSAbundCommand(); }
750 else if(commandName == "get.rabund") { shellcommand = new GetRAbundCommand(); }
751 else if(commandName == "libshuff") { shellcommand = new LibShuffCommand(); }
752 else if(commandName == "heatmap.bin") { shellcommand = new HeatMapCommand(); }
753 else if(commandName == "heatmap.sim") { shellcommand = new HeatMapSimCommand(); }
754 else if(commandName == "filter.seqs") { shellcommand = new FilterSeqsCommand(); }
755 else if(commandName == "venn") { shellcommand = new VennCommand(); }
756 else if(commandName == "bin.seqs") { shellcommand = new BinSeqCommand(); }
757 else if(commandName == "get.oturep") { shellcommand = new GetOTURepCommand(); }
758 else if(commandName == "tree.shared") { shellcommand = new TreeGroupCommand(); }
759 else if(commandName == "dist.shared") { shellcommand = new MatrixOutputCommand(); }
760 else if(commandName == "dist.seqs") { shellcommand = new DistanceCommand(); }
761 else if(commandName == "align.seqs") { shellcommand = new AlignCommand(); }
762 else if(commandName == "summary.seqs") { shellcommand = new SeqSummaryCommand(); }
763 else if(commandName == "screen.seqs") { shellcommand = new ScreenSeqsCommand(); }
764 else if(commandName == "reverse.seqs") { shellcommand = new ReverseSeqsCommand(); }
765 else if(commandName == "trim.seqs") { shellcommand = new TrimSeqsCommand(); }
766 else if(commandName == "trim.flows") { shellcommand = new TrimFlowsCommand(); }
767 else if(commandName == "shhh.flows") { shellcommand = new ShhherCommand(); }
768 else if(commandName == "list.seqs") { shellcommand = new ListSeqsCommand(); }
769 else if(commandName == "get.seqs") { shellcommand = new GetSeqsCommand(); }
770 else if(commandName == "remove.seqs") { shellcommand = new RemoveSeqsCommand(); }
771 else if(commandName == "merge.files") { shellcommand = new MergeFileCommand(); }
772 else if(commandName == "system") { shellcommand = new SystemCommand(); }
773 else if(commandName == "align.check") { shellcommand = new AlignCheckCommand(); }
774 else if(commandName == "get.sharedseqs") { shellcommand = new GetSharedOTUCommand(); }
775 else if(commandName == "get.otulist") { shellcommand = new GetListCountCommand(); }
776 else if(commandName == "hcluster") { shellcommand = new HClusterCommand(); }
777 else if(commandName == "classify.seqs") { shellcommand = new ClassifySeqsCommand(); }
778 else if(commandName == "chimera.ccode") { shellcommand = new ChimeraCcodeCommand(); }
779 else if(commandName == "chimera.check") { shellcommand = new ChimeraCheckCommand(); }
780 else if(commandName == "chimera.slayer") { shellcommand = new ChimeraSlayerCommand(); }
781 else if(commandName == "chimera.uchime") { shellcommand = new ChimeraUchimeCommand(); }
782 else if(commandName == "chimera.pintail") { shellcommand = new ChimeraPintailCommand(); }
783 else if(commandName == "chimera.bellerophon") { shellcommand = new ChimeraBellerophonCommand(); }
784 else if(commandName == "phylotype") { shellcommand = new PhylotypeCommand(); }
785 else if(commandName == "mgcluster") { shellcommand = new MGClusterCommand(); }
786 else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
787 else if(commandName == "pcoa") { shellcommand = new PCOACommand(); }
788 else if(commandName == "pca") { shellcommand = new PCACommand(); }
789 else if(commandName == "nmds") { shellcommand = new NMDSCommand(); }
790 else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
791 else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
792 else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }
793 else if(commandName == "parse.list") { shellcommand = new ParseListCommand(); }
794 else if(commandName == "phylo.diversity") { shellcommand = new PhyloDiversityCommand(); }
795 else if(commandName == "make.group") { shellcommand = new MakeGroupCommand(); }
796 else if(commandName == "chop.seqs") { shellcommand = new ChopSeqsCommand(); }
797 else if(commandName == "clearcut") { shellcommand = new ClearcutCommand(); }
798 else if(commandName == "catchall") { shellcommand = new CatchAllCommand(); }
799 else if(commandName == "split.abund") { shellcommand = new SplitAbundCommand(); }
800 else if(commandName == "cluster.split") { shellcommand = new ClusterSplitCommand(); }
801 else if(commandName == "classify.otu") { shellcommand = new ClassifyOtuCommand(); }
802 else if(commandName == "degap.seqs") { shellcommand = new DegapSeqsCommand(); }
803 else if(commandName == "get.relabund") { shellcommand = new GetRelAbundCommand(); }
804 else if(commandName == "sens.spec") { shellcommand = new SensSpecCommand(); }
805 else if(commandName == "seq.error") { shellcommand = new SeqErrorCommand(); }
806 else if(commandName == "sffinfo") { shellcommand = new SffInfoCommand(); }
807 else if(commandName == "normalize.shared") { shellcommand = new NormalizeSharedCommand(); }
808 else if(commandName == "metastats") { shellcommand = new MetaStatsCommand(); }
809 else if(commandName == "split.groups") { shellcommand = new SplitGroupCommand(); }
810 else if(commandName == "cluster.fragments") { shellcommand = new ClusterFragmentsCommand(); }
811 else if(commandName == "get.lineage") { shellcommand = new GetLineageCommand(); }
812 else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
813 else if(commandName == "get.groups") { shellcommand = new GetGroupsCommand(); }
814 else if(commandName == "remove.groups") { shellcommand = new RemoveGroupsCommand(); }
815 else if(commandName == "get.otus") { shellcommand = new GetOtusCommand(); }
816 else if(commandName == "remove.otus") { shellcommand = new RemoveOtusCommand(); }
817 else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
818 else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
819 else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); }
820 else if(commandName == "cluster.classic") { shellcommand = new ClusterDoturCommand(); }
821 else if(commandName == "sub.sample") { shellcommand = new SubSampleCommand(); }
822 else if(commandName == "indicator") { shellcommand = new IndicatorCommand(); }
823 else if(commandName == "consensus.seqs") { shellcommand = new ConsensusSeqsCommand(); }
824 else if(commandName == "corr.axes") { shellcommand = new CorrAxesCommand(); }
825 else if(commandName == "remove.rare") { shellcommand = new RemoveRareCommand(); }
826 else if(commandName == "merge.groups") { shellcommand = new MergeGroupsCommand(); }
827 else if(commandName == "amova") { shellcommand = new AmovaCommand(); }
828 else if(commandName == "homova") { shellcommand = new HomovaCommand(); }
829 else if(commandName == "mantel") { shellcommand = new MantelCommand(); }
830 else if(commandName == "anosim") { shellcommand = new AnosimCommand(); }
831 else if(commandName == "make.fastq") { shellcommand = new MakeFastQCommand(); }
832 else if(commandName == "get.current") { shellcommand = new GetCurrentCommand(); }
833 else if(commandName == "set.current") { shellcommand = new SetCurrentCommand(); }
834 else if(commandName == "make.shared") { shellcommand = new SharedCommand(); }
835 else if(commandName == "get.commandinfo") { shellcommand = new GetCommandInfoCommand(); }
836 else if(commandName == "deunique.tree") { shellcommand = new DeuniqueTreeCommand(); }
837 else if((commandName == "count.seqs") || (commandName == "make.table")) { shellcommand = new CountSeqsCommand(); }
838 else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); }
839 else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
840 else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); }
841 else if(commandName == "summary.qual") { shellcommand = new SummaryQualCommand(); }
842 else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); }
843 else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); }
844 else if(commandName == "otu.association") { shellcommand = new OTUAssociationCommand(); }
845 else if(commandName == "sort.seqs") { shellcommand = new SortSeqsCommand(); }
846 else if(commandName == "classify.tree") { shellcommand = new ClassifyTreeCommand(); }
847 else if(commandName == "cooccurrence") { shellcommand = new CooccurrenceCommand(); }
848 else if(commandName == "pcr.seqs") { shellcommand = new PcrSeqsCommand(); }
849 else if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); }
850 else if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); }
851 else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
852 else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); }
853 else if(commandName == "get.otulabels") { shellcommand = new GetOtuLabelsCommand(); }
854 else if(commandName == "remove.otulabels") { shellcommand = new RemoveOtuLabelsCommand(); }
855 else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
856 else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); }
857 else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
858 else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
859 else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
860 else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
861 else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
862 else if(commandName == "remove.dists") { shellcommand = new RemoveDistsCommand(); }
863 else if(commandName == "merge.taxsummary") { shellcommand = new MergeTaxSummaryCommand(); }
864 else if(commandName == "get.communitytype") { shellcommand = new GetMetaCommunityCommand(); }
865 else if(commandName == "sparcc") { shellcommand = new SparccCommand(); }
866 else if(commandName == "make.lookup") { shellcommand = new MakeLookupCommand(); }
867 else if(commandName == "rename.seqs") { shellcommand = new RenameSeqsCommand(); }
868 else if(commandName == "make.lefse") { shellcommand = new MakeLefseCommand(); }
869 else if(commandName == "lefse") { shellcommand = new LefseCommand(); }
870 else if(commandName == "kruskal.wallis") { shellcommand = new KruskalWallisCommand(); }
871 else { shellcommand = new NoCommand(); }
875 catch(exception& e) {
876 m->errorOut(e, "CommandFactory", "getCommand");
880 /***********************************************************
881 //This function is used to interrupt a command
882 Command* CommandFactory::getCommand(){
884 delete command; //delete the old command
887 command = new NoCommand(s);
891 catch(exception& e) {
892 m->errorOut(e, "CommandFactory", "getCommand");
896 ***********************************************************************/
897 bool CommandFactory::isValidCommand(string command) {
900 //is the command in the map
901 if ((commands.find(command)) != (commands.end())) {
904 m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
905 for (it = commands.begin(); it != commands.end(); it++) {
906 m->mothurOut(it->first + ", ");
908 m->mothurOutEndLine();
913 catch(exception& e) {
914 m->errorOut(e, "CommandFactory", "isValidCommand");
918 /***********************************************************************/
919 bool CommandFactory::isValidCommand(string command, string noError) {
922 //is the command in the map
923 if ((commands.find(command)) != (commands.end())) {
930 catch(exception& e) {
931 m->errorOut(e, "CommandFactory", "isValidCommand");
935 /***********************************************************************/
936 void CommandFactory::printCommands(ostream& out) {
938 out << "Valid commands are: ";
939 for (it = commands.begin(); it != commands.end(); it++) {
940 out << it->first << ",";
944 catch(exception& e) {
945 m->errorOut(e, "CommandFactory", "printCommands");
949 /***********************************************************************/
950 void CommandFactory::printCommandsCategories(ostream& out) {
952 map<string, string> commands = getListCommands();
953 map<string, string>::iterator it;
955 map<string, string> categories;
956 map<string, string>::iterator itCat;
957 //loop through each command outputting info
958 for (it = commands.begin(); it != commands.end(); it++) {
960 Command* thisCommand = getCommand(it->first);
962 //don't add hidden commands
963 if (thisCommand->getCommandCategory() != "Hidden") {
964 itCat = categories.find(thisCommand->getCommandCategory());
965 if (itCat == categories.end()) {
966 categories[thisCommand->getCommandCategory()] = thisCommand->getCommandName();
968 categories[thisCommand->getCommandCategory()] += ", " + thisCommand->getCommandName();
973 for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
974 out << itCat->first << " commmands include: " << itCat->second << endl;
978 catch(exception& e) {
979 m->errorOut(e, "CommandFactory", "printCommandsCategories");
984 /***********************************************************************/