2 * setcurrentcommand.cpp
5 * Created by westcott on 3/16/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "setcurrentcommand.h"
12 //**********************************************************************************************************************
13 vector<string> SetCurrentCommand::setParameters(){
16 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
17 CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
18 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
19 CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
20 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
21 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
22 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
23 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
24 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
25 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
26 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
27 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
28 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
29 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
30 CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
31 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
32 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
33 CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
34 CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
35 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
36 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
37 CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
38 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
39 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
41 vector<string> myArray;
42 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
46 m->errorOut(e, "SetCurrentCommand", "setParameters");
50 //**********************************************************************************************************************
51 string SetCurrentCommand::getHelpString(){
53 string helpString = "";
54 helpString += "The set.current command allows you to set the current files saved by mothur.\n";
55 helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n";
56 helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
57 helpString += "The set.current command should be in the following format: \n";
58 helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
62 m->errorOut(e, "SetCurrentCommand", "getHelpString");
68 //**********************************************************************************************************************
69 SetCurrentCommand::SetCurrentCommand(){
71 abort = true; calledHelp = true;
75 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
79 //**********************************************************************************************************************
80 SetCurrentCommand::SetCurrentCommand(string option) {
82 abort = false; calledHelp = false;
84 //allow user to run help
85 if(option == "help") { help(); abort = true; calledHelp = true; }
86 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
89 //valid paramters for this command
90 vector<string> myArray = setParameters();
92 OptionParser parser(option);
93 map<string,string> parameters = parser.getParameters();
95 ValidParameters validParameter;
96 map<string,string>::iterator it;
97 //check to make sure all parameters are valid for command
98 for (it = parameters.begin(); it != parameters.end(); it++) {
99 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
103 //if the user changes the input directory command factory will send this info to us in the output parameter
104 string inputDir = validParameter.validFile(parameters, "inputdir", false);
105 if (inputDir == "not found"){ inputDir = ""; }
108 it = parameters.find("phylip");
109 //user has given a template file
110 if(it != parameters.end()){
111 path = m->hasPath(it->second);
112 //if the user has not given a path then, add inputdir. else leave path alone.
113 if (path == "") { parameters["phylip"] = inputDir + it->second; }
116 it = parameters.find("column");
117 //user has given a template file
118 if(it != parameters.end()){
119 path = m->hasPath(it->second);
120 //if the user has not given a path then, add inputdir. else leave path alone.
121 if (path == "") { parameters["column"] = inputDir + it->second; }
124 it = parameters.find("fasta");
125 //user has given a template file
126 if(it != parameters.end()){
127 path = m->hasPath(it->second);
128 //if the user has not given a path then, add inputdir. else leave path alone.
129 if (path == "") { parameters["fasta"] = inputDir + it->second; }
132 it = parameters.find("list");
133 //user has given a template file
134 if(it != parameters.end()){
135 path = m->hasPath(it->second);
136 //if the user has not given a path then, add inputdir. else leave path alone.
137 if (path == "") { parameters["list"] = inputDir + it->second; }
140 it = parameters.find("rabund");
141 //user has given a template file
142 if(it != parameters.end()){
143 path = m->hasPath(it->second);
144 //if the user has not given a path then, add inputdir. else leave path alone.
145 if (path == "") { parameters["rabund"] = inputDir + it->second; }
148 it = parameters.find("sabund");
149 //user has given a template file
150 if(it != parameters.end()){
151 path = m->hasPath(it->second);
152 //if the user has not given a path then, add inputdir. else leave path alone.
153 if (path == "") { parameters["sabund"] = inputDir + it->second; }
156 it = parameters.find("name");
157 //user has given a template file
158 if(it != parameters.end()){
159 path = m->hasPath(it->second);
160 //if the user has not given a path then, add inputdir. else leave path alone.
161 if (path == "") { parameters["name"] = inputDir + it->second; }
164 it = parameters.find("group");
165 //user has given a template file
166 if(it != parameters.end()){
167 path = m->hasPath(it->second);
168 //if the user has not given a path then, add inputdir. else leave path alone.
169 if (path == "") { parameters["group"] = inputDir + it->second; }
172 it = parameters.find("design");
173 //user has given a template file
174 if(it != parameters.end()){
175 path = m->hasPath(it->second);
176 //if the user has not given a path then, add inputdir. else leave path alone.
177 if (path == "") { parameters["design"] = inputDir + it->second; }
180 it = parameters.find("order");
181 //user has given a template file
182 if(it != parameters.end()){
183 path = m->hasPath(it->second);
184 //if the user has not given a path then, add inputdir. else leave path alone.
185 if (path == "") { parameters["order"] = inputDir + it->second; }
188 it = parameters.find("tree");
189 //user has given a template file
190 if(it != parameters.end()){
191 path = m->hasPath(it->second);
192 //if the user has not given a path then, add inputdir. else leave path alone.
193 if (path == "") { parameters["tree"] = inputDir + it->second; }
196 it = parameters.find("shared");
197 //user has given a template file
198 if(it != parameters.end()){
199 path = m->hasPath(it->second);
200 //if the user has not given a path then, add inputdir. else leave path alone.
201 if (path == "") { parameters["shared"] = inputDir + it->second; }
204 it = parameters.find("ordergroup");
205 //user has given a template file
206 if(it != parameters.end()){
207 path = m->hasPath(it->second);
208 //if the user has not given a path then, add inputdir. else leave path alone.
209 if (path == "") { parameters["ordergroup"] = inputDir + it->second; }
212 it = parameters.find("relabund");
213 //user has given a template file
214 if(it != parameters.end()){
215 path = m->hasPath(it->second);
216 //if the user has not given a path then, add inputdir. else leave path alone.
217 if (path == "") { parameters["relabund"] = inputDir + it->second; }
220 it = parameters.find("fasta");
221 //user has given a template file
222 if(it != parameters.end()){
223 path = m->hasPath(it->second);
224 //if the user has not given a path then, add inputdir. else leave path alone.
225 if (path == "") { parameters["fasta"] = inputDir + it->second; }
228 it = parameters.find("qfile");
229 //user has given a template file
230 if(it != parameters.end()){
231 path = m->hasPath(it->second);
232 //if the user has not given a path then, add inputdir. else leave path alone.
233 if (path == "") { parameters["qfile"] = inputDir + it->second; }
236 it = parameters.find("sff");
237 //user has given a template file
238 if(it != parameters.end()){
239 path = m->hasPath(it->second);
240 //if the user has not given a path then, add inputdir. else leave path alone.
241 if (path == "") { parameters["sff"] = inputDir + it->second; }
244 it = parameters.find("oligos");
245 //user has given a template file
246 if(it != parameters.end()){
247 path = m->hasPath(it->second);
248 //if the user has not given a path then, add inputdir. else leave path alone.
249 if (path == "") { parameters["oligos"] = inputDir + it->second; }
252 it = parameters.find("accnos");
253 //user has given a template file
254 if(it != parameters.end()){
255 path = m->hasPath(it->second);
256 //if the user has not given a path then, add inputdir. else leave path alone.
257 if (path == "") { parameters["accnos"] = inputDir + it->second; }
260 it = parameters.find("taxonomy");
261 //user has given a template file
262 if(it != parameters.end()){
263 path = m->hasPath(it->second);
264 //if the user has not given a path then, add inputdir. else leave path alone.
265 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
268 it = parameters.find("flow");
269 //user has given a template file
270 if(it != parameters.end()){
271 path = m->hasPath(it->second);
272 //if the user has not given a path then, add inputdir. else leave path alone.
273 if (path == "") { parameters["flow"] = inputDir + it->second; }
277 //check for parameters
278 phylipfile = validParameter.validFile(parameters, "phylip", true);
279 if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
280 else if (phylipfile == "not found") { phylipfile = ""; }
281 if (phylipfile != "") { m->setPhylipFile(phylipfile); }
283 columnfile = validParameter.validFile(parameters, "column", true);
284 if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
285 else if (columnfile == "not found") { columnfile = ""; }
286 if (columnfile != "") { m->setColumnFile(columnfile); }
288 listfile = validParameter.validFile(parameters, "list", true);
289 if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
290 else if (listfile == "not found") { listfile = ""; }
291 if (listfile != "") { m->setListFile(listfile); }
293 rabundfile = validParameter.validFile(parameters, "rabund", true);
294 if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
295 else if (rabundfile == "not found") { rabundfile = ""; }
296 if (rabundfile != "") { m->setRabundFile(rabundfile); }
298 sabundfile = validParameter.validFile(parameters, "sabund", true);
299 if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
300 else if (sabundfile == "not found") { sabundfile = ""; }
301 if (sabundfile != "") { m->setSabundFile(sabundfile); }
303 namefile = validParameter.validFile(parameters, "name", true);
304 if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
305 else if (namefile == "not found") { namefile = ""; }
306 if (namefile != "") { m->setNameFile(namefile); }
308 groupfile = validParameter.validFile(parameters, "group", true);
309 if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
310 else if (groupfile == "not found") { groupfile = ""; }
311 if (groupfile != "") { m->setGroupFile(groupfile); }
313 designfile = validParameter.validFile(parameters, "design", true);
314 if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
315 else if (designfile == "not found") { designfile = ""; }
316 if (designfile != "") { m->setDesignFile(designfile); }
318 orderfile = validParameter.validFile(parameters, "order", true);
319 if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
320 else if (orderfile == "not found") { orderfile = ""; }
321 if (orderfile != "") { m->setOrderFile(orderfile); }
323 treefile = validParameter.validFile(parameters, "tree", true);
324 if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
325 else if (treefile == "not found") { treefile = ""; }
326 if (treefile != "") { m->setTreeFile(treefile); }
328 sharedfile = validParameter.validFile(parameters, "shared", true);
329 if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
330 else if (sharedfile == "not found") { sharedfile = ""; }
331 if (sharedfile != "") { m->setSharedFile(sharedfile); }
333 ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
334 if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
335 else if (ordergroupfile == "not found") { ordergroupfile = ""; }
336 if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
338 relabundfile = validParameter.validFile(parameters, "relabund", true);
339 if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
340 else if (relabundfile == "not found") { relabundfile = ""; }
341 if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
343 fastafile = validParameter.validFile(parameters, "fasta", true);
344 if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
345 else if (fastafile == "not found") { fastafile = ""; }
346 if (fastafile != "") { m->setFastaFile(fastafile); }
348 qualfile = validParameter.validFile(parameters, "qfile", true);
349 if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
350 else if (qualfile == "not found") { qualfile = ""; }
351 if (qualfile != "") { m->setQualFile(qualfile); }
353 sfffile = validParameter.validFile(parameters, "sff", true);
354 if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
355 else if (sfffile == "not found") { sfffile = ""; }
356 if (sfffile != "") { m->setSFFFile(sfffile); }
358 oligosfile = validParameter.validFile(parameters, "oligos", true);
359 if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
360 else if (oligosfile == "not found") { oligosfile = ""; }
361 if (oligosfile != "") { m->setOligosFile(oligosfile); }
363 accnosfile = validParameter.validFile(parameters, "accnos", true);
364 if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
365 else if (accnosfile == "not found") { accnosfile = ""; }
366 if (accnosfile != "") { m->setAccnosFile(accnosfile); }
368 taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
369 if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
370 else if (taxonomyfile == "not found") { taxonomyfile = ""; }
371 if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
373 flowfile = validParameter.validFile(parameters, "flow", true);
374 if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
375 else if (flowfile == "not found") { flowfile = ""; }
376 if (flowfile != "") { m->setFlowFile(flowfile); }
378 processors = validParameter.validFile(parameters, "processors", false);
379 if (processors == "not found") { processors = "1"; }
380 if (processors != "") { m->setProcessors(processors); }
382 clearTypes = validParameter.validFile(parameters, "clear", false);
383 if (clearTypes == "not found") { clearTypes = ""; }
384 else { m->splitAtDash(clearTypes, types); }
388 catch(exception& e) {
389 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
393 //**********************************************************************************************************************
395 int SetCurrentCommand::execute(){
398 if (abort == true) { if (calledHelp) { return 0; } return 2; }
400 //user wants to clear a type
401 if (types.size() != 0) {
402 for (int i = 0; i < types.size(); i++) {
404 if (m->control_pressed) { break; }
406 //look for file types
407 if (types[i] == "fasta") {
409 }else if (types[i] == "qfile") {
411 }else if (types[i] == "phylip") {
412 m->setPhylipFile("");
413 }else if (types[i] == "column") {
414 m->setColumnFile("");
415 }else if (types[i] == "list") {
417 }else if (types[i] == "rabund") {
418 m->setRabundFile("");
419 }else if (types[i] == "sabund") {
420 m->setSabundFile("");
421 }else if (types[i] == "name") {
423 }else if (types[i] == "group") {
425 }else if (types[i] == "order") {
427 }else if (types[i] == "ordergroup") {
428 m->setOrderGroupFile("");
429 }else if (types[i] == "tree") {
431 }else if (types[i] == "shared") {
432 m->setSharedFile("");
433 }else if (types[i] == "relabund") {
434 m->setRelAbundFile("");
435 }else if (types[i] == "design") {
436 m->setDesignFile("");
437 }else if (types[i] == "sff") {
439 }else if (types[i] == "oligos") {
440 m->setOligosFile("");
441 }else if (types[i] == "accnos") {
442 m->setAccnosFile("");
443 }else if (types[i] == "taxonomy") {
444 m->setTaxonomyFile("");
445 }else if (types[i] == "flow") {
447 }else if (types[i] == "processors") {
448 m->setProcessors("1");
449 }else if (types[i] == "all") {
450 m->clearCurrentFiles();
452 m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
457 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
458 m->printCurrentFiles();
463 catch(exception& e) {
464 m->errorOut(e, "SetCurrentCommand", "execute");
469 //**********************************************************************************************************************