5 * Created by Pat Schloss on 10/25/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
10 #include "command.hpp"
11 #include "readdistcommand.h"
12 #include "readtreecommand.h"
13 #include "readotucommand.h"
14 #include "clustercommand.h"
15 #include "collectcommand.h"
16 #include "collectsharedcommand.h"
17 #include "getgroupcommand.h"
18 #include "getlabelcommand.h"
19 #include "rarefactcommand.h"
20 #include "summarycommand.h"
21 #include "summarysharedcommand.h"
22 #include "rarefactsharedcommand.h"
23 #include "quitcommand.h"
24 #include "helpcommand.h"
25 #include "commandfactory.hpp"
26 #include "deconvolutecommand.h"
27 #include "parsimonycommand.h"
28 #include "unifracunweightedcommand.h"
29 #include "unifracweightedcommand.h"
30 #include "libshuffcommand.h"
31 #include "heatmapcommand.h"
32 #include "heatmapsimcommand.h"
33 #include "filterseqscommand.h"
34 #include "venncommand.h"
35 #include "nocommands.h"
36 #include "binsequencecommand.h"
37 #include "getoturepcommand.h"
38 #include "treegroupscommand.h"
39 #include "bootstrapsharedcommand.h"
40 //#include "consensuscommand.h"
41 #include "distancecommand.h"
42 #include "aligncommand.h"
43 #include "matrixoutputcommand.h"
44 #include "getsabundcommand.h"
45 #include "getrabundcommand.h"
46 #include "seqsummarycommand.h"
47 #include "screenseqscommand.h"
48 #include "reversecommand.h"
49 #include "trimseqscommand.h"
50 #include "mergefilecommand.h"
51 #include "chimeraseqscommand.h"
52 #include "listseqscommand.h"
53 #include "getseqscommand.h"
54 #include "removeseqscommand.h"
55 #include "systemcommand.h"
56 #include "secondarystructurecommand.h"
57 #include "getsharedotucommand.h"
58 #include "getlistcountcommand.h"
59 #include "hclustercommand.h"
60 #include "classifyseqscommand.h"
61 #include "phylotypecommand.h"
62 #include "mgclustercommand.h"
63 #include "preclustercommand.h"
64 #include "pcacommand.h"
65 #include "otuhierarchycommand.h"
66 #include "setdircommand.h"
67 #include "parselistscommand.h"
68 #include "parsesffcommand.h"
69 #include "chimeraccodecommand.h"
70 #include "chimeracheckcommand.h"
71 #include "chimeraslayercommand.h"
72 #include "chimerapintailcommand.h"
73 #include "chimerabellerophoncommand.h"
74 #include "setlogfilecommand.h"
75 #include "phylodiversitycommand.h"
76 #include "makegroupcommand.h"
77 #include "chopseqscommand.h"
78 #include "clearcutcommand.h"
79 #include "catchallcommand.h"
80 #include "splitabundcommand.h"
81 #include "clustersplitcommand.h"
82 #include "classifyotucommand.h"
83 #include "degapseqscommand.h"
84 #include "getrelabundcommand.h"
85 #include "sensspeccommand.h"
86 #include "sffinfocommand.h"
87 #include "seqerrorcommand.h"
88 #include "normalizesharedcommand.h"
90 /*******************************************************/
92 /******************************************************/
93 CommandFactory* CommandFactory::getInstance() {
94 if( _uniqueInstance == 0) {
95 _uniqueInstance = new CommandFactory();
97 return _uniqueInstance;
99 /***********************************************************/
101 /***********************************************************/
102 //note: This class is resposible for knowing which commands are mpiEnabled,
103 //If a command is not enabled only process 0 will execute the command.
104 //This avoids redundant outputs on pieces of code we have not paralellized.
105 //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.
106 //example: commands["dist.seqs"] = "MPIEnabled";
108 CommandFactory::CommandFactory(){
110 m = MothurOut::getInstance();
112 command = new NoCommand(s);
114 outputDir = ""; inputDir = "";
118 //initialize list of valid commands
119 commands["read.dist"] = "read.dist";
120 commands["read.otu"] = "read.otu";
121 commands["read.tree"] = "read.tree";
122 commands["bin.seqs"] = "bin.seqs";
123 commands["get.oturep"] = "get.oturep";
124 commands["cluster"] = "cluster";
125 commands["unique.seqs"] = "unique.seqs";
126 commands["dist.shared"] = "dist.shared";
127 commands["collect.single"] = "collect.single";
128 commands["collect.shared"] = "collect.shared";
129 commands["rarefaction.single"] = "rarefaction.single";
130 commands["rarefaction.shared"] = "rarefaction.shared";
131 commands["summary.single"] = "summary.single";
132 commands["summary.shared"] = "summary.shared";
133 commands["parsimony"] = "parsimony";
134 commands["unifrac.weighted"] = "unifrac.weighted";
135 commands["unifrac.unweighted"] = "unifrac.unweighted";
136 commands["libshuff"] = "libshuff";
137 commands["tree.shared"] = "tree.shared";
138 commands["heatmap.bin"] = "heatmap.bin";
139 commands["heatmap.sim"] = "heatmap.sim";
140 commands["venn"] = "venn";
141 commands["get.group"] = "get.group";
142 commands["get.label"] = "get.label";
143 commands["get.sabund"] = "get.sabund";
144 commands["get.rabund"] = "get.rabund";
145 commands["bootstrap.shared"] = "bootstrap.shared";
146 //commands["consensus"] = "consensus";
147 commands["help"] = "help";
148 commands["reverse.seqs"] = "reverse.seqs";
149 commands["trim.seqs"] = "trim.seqs";
150 commands["list.seqs"] = "list.seqs";
151 commands["get.seqs"] = "get.seqs";
152 commands["remove.seqs"] = "get.seqs";
153 commands["system"] = "system";
154 commands["align.check"] = "align.check";
155 commands["get.sharedseqs"] = "get.sharedseqs";
156 commands["get.otulist"] = "get.otulist";
157 commands["hcluster"] = "hcluster";
158 commands["phylotype"] = "phylotype";
159 commands["mgcluster"] = "mgcluster";
160 commands["pre.cluster"] = "pre.cluster";
161 commands["pcoa"] = "pcoa";
162 commands["otu.hierarchy"] = "otu.hierarchy";
163 commands["set.dir"] = "set.dir";
164 commands["merge.files"] = "merge.files";
165 commands["parse.list"] = "parse.list";
166 commands["parse.sff"] = "parse.sff";
167 commands["set.logfile"] = "set.logfile";
168 commands["phylo.diversity"] = "phylo.diversity";
169 commands["make.group"] = "make.group";
170 commands["chop.seqs"] = "chop.seqs";
171 commands["clearcut"] = "clearcut";
172 commands["catchall"] = "catchall";
173 commands["split.abund"] = "split.abund";
174 commands["classify.otu"] = "classify.otu";
175 commands["degap.seqs"] = "degap.seqs";
176 commands["get.relabund"] = "get.relabund";
177 commands["sffinfo"] = "sffinfo";
178 commands["normalize.shared"] = "normalize.shared";
179 commands["classify.seqs"] = "MPIEnabled";
180 commands["dist.seqs"] = "MPIEnabled";
181 commands["filter.seqs"] = "MPIEnabled";
182 commands["align.seqs"] = "MPIEnabled";
183 commands["chimera.seqs"] = "chimera.seqs";
184 commands["chimera.ccode"] = "MPIEnabled";
185 commands["chimera.check"] = "MPIEnabled";
186 commands["chimera.slayer"] = "MPIEnabled";
187 commands["chimera.pintail"] = "MPIEnabled";
188 commands["chimera.bellerophon"] = "MPIEnabled";
189 commands["screen.seqs"] = "MPIEnabled";
190 commands["summary.seqs"] = "MPIEnabled";
191 commands["cluster.split"] = "MPIEnabled";
192 commands["sens.spec"] = "sens.spec";
193 commands["seq.error"] = "seq.error";
194 commands["quit"] = "MPIEnabled";
197 /***********************************************************/
199 /***********************************************************/
200 bool CommandFactory::MPIEnabled(string commandName) {
202 it = commands.find(commandName);
203 if (it != commands.end()) {
204 if (it->second == "MPIEnabled") { return true; }
208 /***********************************************************/
210 /***********************************************************/
211 CommandFactory::~CommandFactory(){
216 /***********************************************************/
218 /***********************************************************/
219 //This function calls the appropriate command fucntions based on user input.
220 Command* CommandFactory::getCommand(string commandName, string optionString){
222 delete command; //delete the old command
224 //user has opted to redirect output from dir where input files are located to some other place
225 if (outputDir != "") {
226 if (optionString != "") { optionString += ", outputdir=" + outputDir; }
227 else { optionString += "outputdir=" + outputDir; }
230 //user has opted to redirect input from dir where mothur.exe is located to some other place
231 if (inputDir != "") {
232 if (optionString != "") { optionString += ", inputdir=" + inputDir; }
233 else { optionString += "inputdir=" + inputDir; }
236 if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
237 else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
238 else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
239 else if(commandName == "cluster") { command = new ClusterCommand(optionString); }
240 else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
241 else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
242 else if(commandName == "help") { command = new HelpCommand(optionString); }
243 else if(commandName == "quit") { command = new QuitCommand(optionString); }
244 else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
245 else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
246 else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
247 else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
248 else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
249 else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
250 else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
251 else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
252 else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
253 else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
254 else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
255 else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
256 else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
257 else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
258 else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
259 else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
260 else if(commandName == "venn") { command = new VennCommand(optionString); }
261 else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
262 else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
263 else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
264 else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
265 else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
266 else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
267 else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
268 else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
269 else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
270 else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
271 else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
272 else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
273 else if(commandName == "chimera.seqs") { command = new ChimeraSeqsCommand(optionString); }
274 else if(commandName == "list.seqs") { command = new ListSeqsCommand(optionString); }
275 else if(commandName == "get.seqs") { command = new GetSeqsCommand(optionString); }
276 else if(commandName == "remove.seqs") { command = new RemoveSeqsCommand(optionString); }
277 else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
278 else if(commandName == "system") { command = new SystemCommand(optionString); }
279 else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
280 else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
281 else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
282 else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
283 else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(optionString); }
284 else if(commandName == "chimera.ccode") { command = new ChimeraCcodeCommand(optionString); }
285 else if(commandName == "chimera.check") { command = new ChimeraCheckCommand(optionString); }
286 else if(commandName == "chimera.slayer") { command = new ChimeraSlayerCommand(optionString); }
287 else if(commandName == "chimera.pintail") { command = new ChimeraPintailCommand(optionString); }
288 else if(commandName == "chimera.bellerophon") { command = new ChimeraBellerophonCommand(optionString); }
289 else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
290 else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
291 else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
292 else if(commandName == "pcoa") { command = new PCACommand(optionString); }
293 else if(commandName == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
294 else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
295 else if(commandName == "set.logfile") { command = new SetLogFileCommand(optionString); }
296 else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
297 else if(commandName == "parse.sff") { command = new ParseSFFCommand(optionString); }
298 else if(commandName == "phylo.diversity") { command = new PhyloDiversityCommand(optionString); }
299 else if(commandName == "make.group") { command = new MakeGroupCommand(optionString); }
300 else if(commandName == "chop.seqs") { command = new ChopSeqsCommand(optionString); }
301 else if(commandName == "clearcut") { command = new ClearcutCommand(optionString); }
302 else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
303 else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
304 else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
305 else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(optionString); }
306 else if(commandName == "degap.seqs") { command = new DegapSeqsCommand(optionString); }
307 else if(commandName == "get.relabund") { command = new GetRelAbundCommand(optionString); }
308 else if(commandName == "sens.spec") { command = new SensSpecCommand(optionString); }
309 else if(commandName == "seq.error") { command = new SeqErrorCommand(optionString); }
310 else if(commandName == "sffinfo") { command = new SffInfoCommand(optionString); }
311 else if(commandName == "normalize.shared") { command = new NormalizeSharedCommand(optionString); }
312 else { command = new NoCommand(optionString); }
316 catch(exception& e) {
317 m->errorOut(e, "CommandFactory", "getCommand");
321 /***********************************************************/
322 //This function is used to interrupt a command
323 Command* CommandFactory::getCommand(){
325 delete command; //delete the old command
328 command = new NoCommand(s);
332 catch(exception& e) {
333 m->errorOut(e, "CommandFactory", "getCommand");
337 /***********************************************************************/
338 bool CommandFactory::isValidCommand(string command) {
341 //is the command in the map
342 if ((commands.find(command)) != (commands.end())) {
345 m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
346 for (it = commands.begin(); it != commands.end(); it++) {
347 m->mothurOut(it->first + ", ");
349 m->mothurOutEndLine();
354 catch(exception& e) {
355 m->errorOut(e, "CommandFactory", "isValidCommand");
360 /***********************************************************************/
361 void CommandFactory::printCommands(ostream& out) {
363 out << "Valid commands are: ";
364 for (it = commands.begin(); it != commands.end(); it++) {
365 out << it->first << ",";
369 catch(exception& e) {
370 m->errorOut(e, "CommandFactory", "printCommands");
374 /***********************************************************************/