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; }
88 //valid paramters for this command
89 vector<string> myArray = setParameters();
91 OptionParser parser(option);
92 map<string,string> parameters = parser.getParameters();
94 ValidParameters validParameter;
95 map<string,string>::iterator it;
96 //check to make sure all parameters are valid for command
97 for (it = parameters.begin(); it != parameters.end(); it++) {
98 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
102 //if the user changes the input directory command factory will send this info to us in the output parameter
103 string inputDir = validParameter.validFile(parameters, "inputdir", false);
104 if (inputDir == "not found"){ inputDir = ""; }
107 it = parameters.find("phylip");
108 //user has given a template file
109 if(it != parameters.end()){
110 path = m->hasPath(it->second);
111 //if the user has not given a path then, add inputdir. else leave path alone.
112 if (path == "") { parameters["phylip"] = inputDir + it->second; }
115 it = parameters.find("column");
116 //user has given a template file
117 if(it != parameters.end()){
118 path = m->hasPath(it->second);
119 //if the user has not given a path then, add inputdir. else leave path alone.
120 if (path == "") { parameters["column"] = inputDir + it->second; }
123 it = parameters.find("fasta");
124 //user has given a template file
125 if(it != parameters.end()){
126 path = m->hasPath(it->second);
127 //if the user has not given a path then, add inputdir. else leave path alone.
128 if (path == "") { parameters["fasta"] = inputDir + it->second; }
131 it = parameters.find("list");
132 //user has given a template file
133 if(it != parameters.end()){
134 path = m->hasPath(it->second);
135 //if the user has not given a path then, add inputdir. else leave path alone.
136 if (path == "") { parameters["list"] = inputDir + it->second; }
139 it = parameters.find("rabund");
140 //user has given a template file
141 if(it != parameters.end()){
142 path = m->hasPath(it->second);
143 //if the user has not given a path then, add inputdir. else leave path alone.
144 if (path == "") { parameters["rabund"] = inputDir + it->second; }
147 it = parameters.find("sabund");
148 //user has given a template file
149 if(it != parameters.end()){
150 path = m->hasPath(it->second);
151 //if the user has not given a path then, add inputdir. else leave path alone.
152 if (path == "") { parameters["sabund"] = inputDir + it->second; }
155 it = parameters.find("name");
156 //user has given a template file
157 if(it != parameters.end()){
158 path = m->hasPath(it->second);
159 //if the user has not given a path then, add inputdir. else leave path alone.
160 if (path == "") { parameters["name"] = inputDir + it->second; }
163 it = parameters.find("group");
164 //user has given a template file
165 if(it != parameters.end()){
166 path = m->hasPath(it->second);
167 //if the user has not given a path then, add inputdir. else leave path alone.
168 if (path == "") { parameters["group"] = inputDir + it->second; }
171 it = parameters.find("design");
172 //user has given a template file
173 if(it != parameters.end()){
174 path = m->hasPath(it->second);
175 //if the user has not given a path then, add inputdir. else leave path alone.
176 if (path == "") { parameters["design"] = inputDir + it->second; }
179 it = parameters.find("order");
180 //user has given a template file
181 if(it != parameters.end()){
182 path = m->hasPath(it->second);
183 //if the user has not given a path then, add inputdir. else leave path alone.
184 if (path == "") { parameters["order"] = inputDir + it->second; }
187 it = parameters.find("tree");
188 //user has given a template file
189 if(it != parameters.end()){
190 path = m->hasPath(it->second);
191 //if the user has not given a path then, add inputdir. else leave path alone.
192 if (path == "") { parameters["tree"] = inputDir + it->second; }
195 it = parameters.find("shared");
196 //user has given a template file
197 if(it != parameters.end()){
198 path = m->hasPath(it->second);
199 //if the user has not given a path then, add inputdir. else leave path alone.
200 if (path == "") { parameters["shared"] = inputDir + it->second; }
203 it = parameters.find("ordergroup");
204 //user has given a template file
205 if(it != parameters.end()){
206 path = m->hasPath(it->second);
207 //if the user has not given a path then, add inputdir. else leave path alone.
208 if (path == "") { parameters["ordergroup"] = inputDir + it->second; }
211 it = parameters.find("relabund");
212 //user has given a template file
213 if(it != parameters.end()){
214 path = m->hasPath(it->second);
215 //if the user has not given a path then, add inputdir. else leave path alone.
216 if (path == "") { parameters["relabund"] = inputDir + it->second; }
219 it = parameters.find("fasta");
220 //user has given a template file
221 if(it != parameters.end()){
222 path = m->hasPath(it->second);
223 //if the user has not given a path then, add inputdir. else leave path alone.
224 if (path == "") { parameters["fasta"] = inputDir + it->second; }
227 it = parameters.find("qfile");
228 //user has given a template file
229 if(it != parameters.end()){
230 path = m->hasPath(it->second);
231 //if the user has not given a path then, add inputdir. else leave path alone.
232 if (path == "") { parameters["qfile"] = inputDir + it->second; }
235 it = parameters.find("sff");
236 //user has given a template file
237 if(it != parameters.end()){
238 path = m->hasPath(it->second);
239 //if the user has not given a path then, add inputdir. else leave path alone.
240 if (path == "") { parameters["sff"] = inputDir + it->second; }
243 it = parameters.find("oligos");
244 //user has given a template file
245 if(it != parameters.end()){
246 path = m->hasPath(it->second);
247 //if the user has not given a path then, add inputdir. else leave path alone.
248 if (path == "") { parameters["oligos"] = inputDir + it->second; }
251 it = parameters.find("accnos");
252 //user has given a template file
253 if(it != parameters.end()){
254 path = m->hasPath(it->second);
255 //if the user has not given a path then, add inputdir. else leave path alone.
256 if (path == "") { parameters["accnos"] = inputDir + it->second; }
259 it = parameters.find("taxonomy");
260 //user has given a template file
261 if(it != parameters.end()){
262 path = m->hasPath(it->second);
263 //if the user has not given a path then, add inputdir. else leave path alone.
264 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
267 it = parameters.find("flow");
268 //user has given a template file
269 if(it != parameters.end()){
270 path = m->hasPath(it->second);
271 //if the user has not given a path then, add inputdir. else leave path alone.
272 if (path == "") { parameters["flow"] = inputDir + it->second; }
276 //check for parameters
277 phylipfile = validParameter.validFile(parameters, "phylip", true);
278 if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
279 else if (phylipfile == "not found") { phylipfile = ""; }
280 if (phylipfile != "") { m->setPhylipFile(phylipfile); }
282 columnfile = validParameter.validFile(parameters, "column", true);
283 if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
284 else if (columnfile == "not found") { columnfile = ""; }
285 if (columnfile != "") { m->setColumnFile(columnfile); }
287 listfile = validParameter.validFile(parameters, "list", true);
288 if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
289 else if (listfile == "not found") { listfile = ""; }
290 if (listfile != "") { m->setListFile(listfile); }
292 rabundfile = validParameter.validFile(parameters, "rabund", true);
293 if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
294 else if (rabundfile == "not found") { rabundfile = ""; }
295 if (rabundfile != "") { m->setRabundFile(rabundfile); }
297 sabundfile = validParameter.validFile(parameters, "sabund", true);
298 if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
299 else if (sabundfile == "not found") { sabundfile = ""; }
300 if (sabundfile != "") { m->setSabundFile(sabundfile); }
302 namefile = validParameter.validFile(parameters, "name", true);
303 if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
304 else if (namefile == "not found") { namefile = ""; }
305 if (namefile != "") { m->setNameFile(namefile); }
307 groupfile = validParameter.validFile(parameters, "group", true);
308 if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
309 else if (groupfile == "not found") { groupfile = ""; }
310 if (groupfile != "") { m->setGroupFile(groupfile); }
312 designfile = validParameter.validFile(parameters, "design", true);
313 if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
314 else if (designfile == "not found") { designfile = ""; }
315 if (designfile != "") { m->setDesignFile(designfile); }
317 orderfile = validParameter.validFile(parameters, "order", true);
318 if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
319 else if (orderfile == "not found") { orderfile = ""; }
320 if (orderfile != "") { m->setOrderFile(orderfile); }
322 treefile = validParameter.validFile(parameters, "tree", true);
323 if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
324 else if (treefile == "not found") { treefile = ""; }
325 if (treefile != "") { m->setTreeFile(treefile); }
327 sharedfile = validParameter.validFile(parameters, "shared", true);
328 if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
329 else if (sharedfile == "not found") { sharedfile = ""; }
330 if (sharedfile != "") { m->setSharedFile(sharedfile); }
332 ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
333 if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
334 else if (ordergroupfile == "not found") { ordergroupfile = ""; }
335 if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
337 relabundfile = validParameter.validFile(parameters, "relabund", true);
338 if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
339 else if (relabundfile == "not found") { relabundfile = ""; }
340 if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
342 fastafile = validParameter.validFile(parameters, "fasta", true);
343 if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
344 else if (fastafile == "not found") { fastafile = ""; }
345 if (fastafile != "") { m->setFastaFile(fastafile); }
347 qualfile = validParameter.validFile(parameters, "qfile", true);
348 if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
349 else if (qualfile == "not found") { qualfile = ""; }
350 if (qualfile != "") { m->setQualFile(qualfile); }
352 sfffile = validParameter.validFile(parameters, "sff", true);
353 if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
354 else if (sfffile == "not found") { sfffile = ""; }
355 if (sfffile != "") { m->setSFFFile(sfffile); }
357 oligosfile = validParameter.validFile(parameters, "oligos", true);
358 if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
359 else if (oligosfile == "not found") { oligosfile = ""; }
360 if (oligosfile != "") { m->setOligosFile(oligosfile); }
362 accnosfile = validParameter.validFile(parameters, "accnos", true);
363 if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
364 else if (accnosfile == "not found") { accnosfile = ""; }
365 if (accnosfile != "") { m->setAccnosFile(accnosfile); }
367 taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
368 if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
369 else if (taxonomyfile == "not found") { taxonomyfile = ""; }
370 if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
372 flowfile = validParameter.validFile(parameters, "flow", true);
373 if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
374 else if (flowfile == "not found") { flowfile = ""; }
375 if (flowfile != "") { m->setFlowFile(flowfile); }
377 processors = validParameter.validFile(parameters, "processors", false);
378 if (processors == "not found") { processors = "1"; }
379 if (processors != "") { m->setProcessors(processors); }
381 clearTypes = validParameter.validFile(parameters, "clear", false);
382 if (clearTypes == "not found") { clearTypes = ""; }
383 else { m->splitAtDash(clearTypes, types); }
387 catch(exception& e) {
388 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
392 //**********************************************************************************************************************
394 int SetCurrentCommand::execute(){
397 if (abort == true) { if (calledHelp) { return 0; } return 2; }
399 //user wants to clear a type
400 if (types.size() != 0) {
401 for (int i = 0; i < types.size(); i++) {
403 if (m->control_pressed) { break; }
405 //look for file types
406 if (types[i] == "fasta") {
408 }else if (types[i] == "qfile") {
410 }else if (types[i] == "phylip") {
411 m->setPhylipFile("");
412 }else if (types[i] == "column") {
413 m->setColumnFile("");
414 }else if (types[i] == "list") {
416 }else if (types[i] == "rabund") {
417 m->setRabundFile("");
418 }else if (types[i] == "sabund") {
419 m->setSabundFile("");
420 }else if (types[i] == "name") {
422 }else if (types[i] == "group") {
424 }else if (types[i] == "order") {
426 }else if (types[i] == "ordergroup") {
427 m->setOrderGroupFile("");
428 }else if (types[i] == "tree") {
430 }else if (types[i] == "shared") {
431 m->setSharedFile("");
432 }else if (types[i] == "relabund") {
433 m->setRelAbundFile("");
434 }else if (types[i] == "design") {
435 m->setDesignFile("");
436 }else if (types[i] == "sff") {
438 }else if (types[i] == "oligos") {
439 m->setOligosFile("");
440 }else if (types[i] == "accnos") {
441 m->setAccnosFile("");
442 }else if (types[i] == "taxonomy") {
443 m->setTaxonomyFile("");
444 }else if (types[i] == "flow") {
446 }else if (types[i] == "processors") {
447 m->setProcessors("1");
448 }else if (types[i] == "all") {
449 m->clearCurrentFiles();
451 m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
456 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
457 m->printCurrentFiles();
462 catch(exception& e) {
463 m->errorOut(e, "SetCurrentCommand", "execute");
468 //**********************************************************************************************************************