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"
83 /*******************************************************/
85 /******************************************************/
86 CommandFactory* CommandFactory::getInstance() {
87 if( _uniqueInstance == 0) {
88 _uniqueInstance = new CommandFactory();
90 return _uniqueInstance;
92 /***********************************************************/
94 /***********************************************************/
95 //note: This class is resposible for knowing which commands are mpiEnabled,
96 //If a command is not enabled only process 0 will execute the command.
97 //This avoids redundant outputs on pieces of code we have not paralellized.
98 //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.
99 //example: commands["dist.seqs"] = "MPIEnabled";
101 CommandFactory::CommandFactory(){
103 m = MothurOut::getInstance();
105 command = new NoCommand(s);
107 outputDir = ""; inputDir = "";
111 //initialize list of valid commands
112 commands["read.dist"] = "read.dist";
113 commands["read.otu"] = "read.otu";
114 commands["read.tree"] = "read.tree";
115 commands["bin.seqs"] = "bin.seqs";
116 commands["get.oturep"] = "get.oturep";
117 commands["cluster"] = "cluster";
118 commands["unique.seqs"] = "unique.seqs";
119 commands["dist.shared"] = "dist.shared";
120 commands["collect.single"] = "collect.single";
121 commands["collect.shared"] = "collect.shared";
122 commands["rarefaction.single"] = "rarefaction.single";
123 commands["rarefaction.shared"] = "rarefaction.shared";
124 commands["summary.single"] = "summary.single";
125 commands["summary.shared"] = "summary.shared";
126 commands["parsimony"] = "parsimony";
127 commands["unifrac.weighted"] = "unifrac.weighted";
128 commands["unifrac.unweighted"] = "unifrac.unweighted";
129 commands["libshuff"] = "libshuff";
130 commands["tree.shared"] = "tree.shared";
131 commands["heatmap.bin"] = "heatmap.bin";
132 commands["heatmap.sim"] = "heatmap.sim";
133 commands["venn"] = "venn";
134 commands["get.group"] = "get.group";
135 commands["get.label"] = "get.label";
136 commands["get.sabund"] = "get.sabund";
137 commands["get.rabund"] = "get.rabund";
138 commands["bootstrap.shared"] = "bootstrap.shared";
139 //commands["consensus"] = "consensus";
140 commands["help"] = "help";
141 commands["reverse.seqs"] = "reverse.seqs";
142 commands["trim.seqs"] = "trim.seqs";
143 commands["list.seqs"] = "list.seqs";
144 commands["get.seqs"] = "get.seqs";
145 commands["remove.seqs"] = "get.seqs";
146 commands["system"] = "system";
147 commands["align.check"] = "align.check";
148 commands["get.sharedseqs"] = "get.sharedseqs";
149 commands["get.otulist"] = "get.otulist";
150 commands["hcluster"] = "hcluster";
151 commands["phylotype"] = "phylotype";
152 commands["mgcluster"] = "mgcluster";
153 commands["pre.cluster"] = "pre.cluster";
154 commands["pcoa"] = "pcoa";
155 commands["otu.hierarchy"] = "otu.hierarchy";
156 commands["set.dir"] = "set.dir";
157 commands["merge.files"] = "merge.files";
158 commands["parse.list"] = "parse.list";
159 commands["parse.sff"] = "parse.sff";
160 commands["set.logfile"] = "set.logfile";
161 commands["phylo.diversity"] = "phylo.diversity";
162 commands["make.group"] = "make.group";
163 commands["chop.seqs"] = "chop.seqs";
164 commands["clearcut"] = "clearcut";
165 commands["catchall"] = "catchall";
166 commands["split.abund"] = "split.abund";
167 commands["cluster.split"] = "cluster.split";
168 commands["classify.seqs"] = "MPIEnabled";
169 commands["dist.seqs"] = "MPIEnabled";
170 commands["filter.seqs"] = "MPIEnabled";
171 commands["align.seqs"] = "MPIEnabled";
172 commands["chimera.seqs"] = "chimera.seqs";
173 commands["chimera.ccode"] = "MPIEnabled";
174 commands["chimera.check"] = "MPIEnabled";
175 commands["chimera.slayer"] = "MPIEnabled";
176 commands["chimera.pintail"] = "MPIEnabled";
177 commands["chimera.bellerophon"] = "MPIEnabled";
178 commands["screen.seqs"] = "MPIEnabled";
179 commands["summary.seqs"] = "MPIEnabled";
180 commands["quit"] = "MPIEnabled";
183 /***********************************************************/
185 /***********************************************************/
186 bool CommandFactory::MPIEnabled(string commandName) {
188 it = commands.find(commandName);
189 if (it != commands.end()) {
190 if (it->second == "MPIEnabled") { return true; }
194 /***********************************************************/
196 /***********************************************************/
197 CommandFactory::~CommandFactory(){
202 /***********************************************************/
204 /***********************************************************/
205 //This function calls the appropriate command fucntions based on user input.
206 Command* CommandFactory::getCommand(string commandName, string optionString){
208 delete command; //delete the old command
210 //user has opted to redirect output from dir where input files are located to some other place
211 if (outputDir != "") {
212 if (optionString != "") { optionString += ", outputdir=" + outputDir; }
213 else { optionString += "outputdir=" + outputDir; }
216 //user has opted to redirect input from dir where mothur.exe is located to some other place
217 if (inputDir != "") {
218 if (optionString != "") { optionString += ", inputdir=" + inputDir; }
219 else { optionString += "inputdir=" + inputDir; }
222 if(commandName == "read.dist") { command = new ReadDistCommand(optionString); }
223 else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); }
224 else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); }
225 else if(commandName == "cluster") { command = new ClusterCommand(optionString); }
226 else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
227 else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
228 else if(commandName == "help") { command = new HelpCommand(optionString); }
229 else if(commandName == "quit") { command = new QuitCommand(optionString); }
230 else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
231 else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
232 else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
233 else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
234 else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
235 else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
236 else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
237 else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
238 else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
239 else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
240 else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
241 else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
242 else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
243 else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
244 else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
245 else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
246 else if(commandName == "venn") { command = new VennCommand(optionString); }
247 else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
248 else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
249 else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
250 else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
251 else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
252 //else if(commandName == "consensus") { command = new ConcensusCommand(optionString); }
253 else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
254 else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
255 else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
256 else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
257 else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
258 else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
259 else if(commandName == "chimera.seqs") { command = new ChimeraSeqsCommand(optionString); }
260 else if(commandName == "list.seqs") { command = new ListSeqsCommand(optionString); }
261 else if(commandName == "get.seqs") { command = new GetSeqsCommand(optionString); }
262 else if(commandName == "remove.seqs") { command = new RemoveSeqsCommand(optionString); }
263 else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
264 else if(commandName == "system") { command = new SystemCommand(optionString); }
265 else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
266 else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
267 else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
268 else if(commandName == "hcluster") { command = new HClusterCommand(optionString); }
269 else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(optionString); }
270 else if(commandName == "chimera.ccode") { command = new ChimeraCcodeCommand(optionString); }
271 else if(commandName == "chimera.check") { command = new ChimeraCheckCommand(optionString); }
272 else if(commandName == "chimera.slayer") { command = new ChimeraSlayerCommand(optionString); }
273 else if(commandName == "chimera.pintail") { command = new ChimeraPintailCommand(optionString); }
274 else if(commandName == "chimera.bellerophon") { command = new ChimeraBellerophonCommand(optionString); }
275 else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
276 else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
277 else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
278 else if(commandName == "pcoa") { command = new PCACommand(optionString); }
279 else if(commandName == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
280 else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
281 else if(commandName == "set.logfile") { command = new SetLogFileCommand(optionString); }
282 else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
283 else if(commandName == "parse.sff") { command = new ParseSFFCommand(optionString); }
284 else if(commandName == "phylo.diversity") { command = new PhyloDiversityCommand(optionString); }
285 else if(commandName == "make.group") { command = new MakeGroupCommand(optionString); }
286 else if(commandName == "chop.seqs") { command = new ChopSeqsCommand(optionString); }
287 else if(commandName == "clearcut") { command = new ClearcutCommand(optionString); }
288 else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
289 else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
290 else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
291 else { command = new NoCommand(optionString); }
295 catch(exception& e) {
296 m->errorOut(e, "CommandFactory", "getCommand");
300 /***********************************************************/
301 //This function is used to interrupt a command
302 Command* CommandFactory::getCommand(){
304 delete command; //delete the old command
307 command = new NoCommand(s);
311 catch(exception& e) {
312 m->errorOut(e, "CommandFactory", "getCommand");
316 /***********************************************************************/
317 bool CommandFactory::isValidCommand(string command) {
320 //is the command in the map
321 if ((commands.find(command)) != (commands.end())) {
324 m->mothurOut(command + " is not a valid command in Mothur. Valid commands are ");
325 for (it = commands.begin(); it != commands.end(); it++) {
326 m->mothurOut(it->first + ", ");
328 m->mothurOutEndLine();
333 catch(exception& e) {
334 m->errorOut(e, "CommandFactory", "isValidCommand");
339 /***********************************************************************/
340 void CommandFactory::printCommands(ostream& out) {
342 out << "Valid commands are ";
343 for (it = commands.begin(); it != commands.end(); it++) {
344 out << it->first << ", ";
348 catch(exception& e) {
349 m->errorOut(e, "CommandFactory", "printCommands");
353 /***********************************************************************/