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 pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
17 CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
18 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
19 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
20 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
21 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
22 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
23 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
24 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
25 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
26 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
27 CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
28 CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
29 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
30 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
31 CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
32 CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
33 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
34 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
35 CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
36 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
37 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
39 vector<string> myArray;
40 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
44 m->errorOut(e, "SetCurrentCommand", "setParameters");
48 //**********************************************************************************************************************
49 string SetCurrentCommand::getHelpString(){
51 string helpString = "";
52 helpString += "The set.current command allows you to set the current files saved by mothur.\n";
53 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";
54 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";
55 helpString += "The set.current command should be in the following format: \n";
56 helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
60 m->errorOut(e, "SetCurrentCommand", "getHelpString");
66 //**********************************************************************************************************************
67 SetCurrentCommand::SetCurrentCommand(){
69 abort = true; calledHelp = true;
73 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
77 //**********************************************************************************************************************
78 SetCurrentCommand::SetCurrentCommand(string option) {
80 abort = false; calledHelp = false;
82 //allow user to run help
83 if(option == "help") { help(); abort = true; calledHelp = true; }
86 //valid paramters for this command
87 vector<string> myArray = setParameters();
89 OptionParser parser(option);
90 map<string,string> parameters = parser.getParameters();
92 ValidParameters validParameter;
93 map<string,string>::iterator it;
94 //check to make sure all parameters are valid for command
95 for (it = parameters.begin(); it != parameters.end(); it++) {
96 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
100 //if the user changes the input directory command factory will send this info to us in the output parameter
101 string inputDir = validParameter.validFile(parameters, "inputdir", false);
102 if (inputDir == "not found"){ inputDir = ""; }
105 it = parameters.find("phylip");
106 //user has given a template file
107 if(it != parameters.end()){
108 path = m->hasPath(it->second);
109 //if the user has not given a path then, add inputdir. else leave path alone.
110 if (path == "") { parameters["phylip"] = inputDir + it->second; }
113 it = parameters.find("column");
114 //user has given a template file
115 if(it != parameters.end()){
116 path = m->hasPath(it->second);
117 //if the user has not given a path then, add inputdir. else leave path alone.
118 if (path == "") { parameters["column"] = inputDir + it->second; }
121 it = parameters.find("fasta");
122 //user has given a template file
123 if(it != parameters.end()){
124 path = m->hasPath(it->second);
125 //if the user has not given a path then, add inputdir. else leave path alone.
126 if (path == "") { parameters["fasta"] = inputDir + it->second; }
129 it = parameters.find("list");
130 //user has given a template file
131 if(it != parameters.end()){
132 path = m->hasPath(it->second);
133 //if the user has not given a path then, add inputdir. else leave path alone.
134 if (path == "") { parameters["list"] = inputDir + it->second; }
137 it = parameters.find("rabund");
138 //user has given a template file
139 if(it != parameters.end()){
140 path = m->hasPath(it->second);
141 //if the user has not given a path then, add inputdir. else leave path alone.
142 if (path == "") { parameters["rabund"] = inputDir + it->second; }
145 it = parameters.find("sabund");
146 //user has given a template file
147 if(it != parameters.end()){
148 path = m->hasPath(it->second);
149 //if the user has not given a path then, add inputdir. else leave path alone.
150 if (path == "") { parameters["sabund"] = inputDir + it->second; }
153 it = parameters.find("name");
154 //user has given a template file
155 if(it != parameters.end()){
156 path = m->hasPath(it->second);
157 //if the user has not given a path then, add inputdir. else leave path alone.
158 if (path == "") { parameters["name"] = inputDir + it->second; }
161 it = parameters.find("group");
162 //user has given a template file
163 if(it != parameters.end()){
164 path = m->hasPath(it->second);
165 //if the user has not given a path then, add inputdir. else leave path alone.
166 if (path == "") { parameters["group"] = inputDir + it->second; }
169 it = parameters.find("design");
170 //user has given a template file
171 if(it != parameters.end()){
172 path = m->hasPath(it->second);
173 //if the user has not given a path then, add inputdir. else leave path alone.
174 if (path == "") { parameters["design"] = inputDir + it->second; }
177 it = parameters.find("order");
178 //user has given a template file
179 if(it != parameters.end()){
180 path = m->hasPath(it->second);
181 //if the user has not given a path then, add inputdir. else leave path alone.
182 if (path == "") { parameters["order"] = inputDir + it->second; }
185 it = parameters.find("tree");
186 //user has given a template file
187 if(it != parameters.end()){
188 path = m->hasPath(it->second);
189 //if the user has not given a path then, add inputdir. else leave path alone.
190 if (path == "") { parameters["tree"] = inputDir + it->second; }
193 it = parameters.find("shared");
194 //user has given a template file
195 if(it != parameters.end()){
196 path = m->hasPath(it->second);
197 //if the user has not given a path then, add inputdir. else leave path alone.
198 if (path == "") { parameters["shared"] = inputDir + it->second; }
201 it = parameters.find("ordergroup");
202 //user has given a template file
203 if(it != parameters.end()){
204 path = m->hasPath(it->second);
205 //if the user has not given a path then, add inputdir. else leave path alone.
206 if (path == "") { parameters["ordergroup"] = inputDir + it->second; }
209 it = parameters.find("relabund");
210 //user has given a template file
211 if(it != parameters.end()){
212 path = m->hasPath(it->second);
213 //if the user has not given a path then, add inputdir. else leave path alone.
214 if (path == "") { parameters["relabund"] = inputDir + it->second; }
217 it = parameters.find("fasta");
218 //user has given a template file
219 if(it != parameters.end()){
220 path = m->hasPath(it->second);
221 //if the user has not given a path then, add inputdir. else leave path alone.
222 if (path == "") { parameters["fasta"] = inputDir + it->second; }
225 it = parameters.find("qfile");
226 //user has given a template file
227 if(it != parameters.end()){
228 path = m->hasPath(it->second);
229 //if the user has not given a path then, add inputdir. else leave path alone.
230 if (path == "") { parameters["qfile"] = inputDir + it->second; }
233 it = parameters.find("sff");
234 //user has given a template file
235 if(it != parameters.end()){
236 path = m->hasPath(it->second);
237 //if the user has not given a path then, add inputdir. else leave path alone.
238 if (path == "") { parameters["sff"] = inputDir + it->second; }
241 it = parameters.find("oligos");
242 //user has given a template file
243 if(it != parameters.end()){
244 path = m->hasPath(it->second);
245 //if the user has not given a path then, add inputdir. else leave path alone.
246 if (path == "") { parameters["oligos"] = inputDir + it->second; }
249 it = parameters.find("accnos");
250 //user has given a template file
251 if(it != parameters.end()){
252 path = m->hasPath(it->second);
253 //if the user has not given a path then, add inputdir. else leave path alone.
254 if (path == "") { parameters["accnos"] = inputDir + it->second; }
257 it = parameters.find("taxonomy");
258 //user has given a template file
259 if(it != parameters.end()){
260 path = m->hasPath(it->second);
261 //if the user has not given a path then, add inputdir. else leave path alone.
262 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
266 //check for parameters
267 phylipfile = validParameter.validFile(parameters, "phylip", true);
268 if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
269 else if (phylipfile == "not found") { phylipfile = ""; }
270 if (phylipfile != "") { m->setPhylipFile(phylipfile); }
272 columnfile = validParameter.validFile(parameters, "column", true);
273 if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
274 else if (columnfile == "not found") { columnfile = ""; }
275 if (columnfile != "") { m->setColumnFile(columnfile); }
277 listfile = validParameter.validFile(parameters, "list", true);
278 if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
279 else if (listfile == "not found") { listfile = ""; }
280 if (listfile != "") { m->setListFile(listfile); }
282 rabundfile = validParameter.validFile(parameters, "rabund", true);
283 if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
284 else if (rabundfile == "not found") { rabundfile = ""; }
285 if (rabundfile != "") { m->setRabundFile(rabundfile); }
287 sabundfile = validParameter.validFile(parameters, "sabund", true);
288 if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
289 else if (sabundfile == "not found") { sabundfile = ""; }
290 if (sabundfile != "") { m->setSabundFile(sabundfile); }
292 namefile = validParameter.validFile(parameters, "name", true);
293 if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
294 else if (namefile == "not found") { namefile = ""; }
295 if (namefile != "") { m->setNameFile(namefile); }
297 groupfile = validParameter.validFile(parameters, "group", true);
298 if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
299 else if (groupfile == "not found") { groupfile = ""; }
300 if (groupfile != "") { m->setGroupFile(groupfile); }
302 designfile = validParameter.validFile(parameters, "design", true);
303 if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
304 else if (designfile == "not found") { designfile = ""; }
305 if (designfile != "") { m->setDesignFile(designfile); }
307 orderfile = validParameter.validFile(parameters, "order", true);
308 if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
309 else if (orderfile == "not found") { orderfile = ""; }
310 if (orderfile != "") { m->setOrderFile(orderfile); }
312 treefile = validParameter.validFile(parameters, "tree", true);
313 if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
314 else if (treefile == "not found") { treefile = ""; }
315 if (treefile != "") { m->setTreeFile(treefile); }
317 sharedfile = validParameter.validFile(parameters, "shared", true);
318 if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
319 else if (sharedfile == "not found") { sharedfile = ""; }
320 if (sharedfile != "") { m->setSharedFile(sharedfile); }
322 ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
323 if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
324 else if (ordergroupfile == "not found") { ordergroupfile = ""; }
325 if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
327 relabundfile = validParameter.validFile(parameters, "relabund", true);
328 if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
329 else if (relabundfile == "not found") { relabundfile = ""; }
330 if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
332 fastafile = validParameter.validFile(parameters, "fasta", true);
333 if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
334 else if (fastafile == "not found") { fastafile = ""; }
335 if (fastafile != "") { m->setFastaFile(fastafile); }
337 qualfile = validParameter.validFile(parameters, "qfile", true);
338 if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
339 else if (qualfile == "not found") { qualfile = ""; }
340 if (qualfile != "") { m->setQualFile(qualfile); }
342 sfffile = validParameter.validFile(parameters, "sff", true);
343 if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
344 else if (sfffile == "not found") { sfffile = ""; }
345 if (sfffile != "") { m->setSFFFile(sfffile); }
347 oligosfile = validParameter.validFile(parameters, "oligos", true);
348 if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
349 else if (oligosfile == "not found") { oligosfile = ""; }
350 if (oligosfile != "") { m->setOligosFile(oligosfile); }
352 accnosfile = validParameter.validFile(parameters, "accnos", true);
353 if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
354 else if (accnosfile == "not found") { accnosfile = ""; }
355 if (accnosfile != "") { m->setAccnosFile(accnosfile); }
357 taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
358 if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
359 else if (taxonomyfile == "not found") { taxonomyfile = ""; }
360 if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
362 clearTypes = validParameter.validFile(parameters, "clear", false);
363 if (clearTypes == "not found") { clearTypes = ""; }
364 else { m->splitAtDash(clearTypes, types); }
368 catch(exception& e) {
369 m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
373 //**********************************************************************************************************************
375 int SetCurrentCommand::execute(){
378 if (abort == true) { if (calledHelp) { return 0; } return 2; }
380 //user wants to clear a type
381 if (types.size() != 0) {
382 for (int i = 0; i < types.size(); i++) {
384 if (m->control_pressed) { break; }
386 //look for file types
387 if (types[i] == "fasta") {
389 }else if (types[i] == "qfile") {
391 }else if (types[i] == "phylip") {
392 m->setPhylipFile("");
393 }else if (types[i] == "column") {
394 m->setColumnFile("");
395 }else if (types[i] == "list") {
397 }else if (types[i] == "rabund") {
398 m->setRabundFile("");
399 }else if (types[i] == "sabund") {
400 m->setSabundFile("");
401 }else if (types[i] == "name") {
403 }else if (types[i] == "group") {
405 }else if (types[i] == "order") {
407 }else if (types[i] == "ordergroup") {
408 m->setOrderGroupFile("");
409 }else if (types[i] == "tree") {
411 }else if (types[i] == "shared") {
412 m->setSharedFile("");
413 }else if (types[i] == "relabund") {
414 m->setRelAbundFile("");
415 }else if (types[i] == "design") {
416 m->setDesignFile("");
417 }else if (types[i] == "sff") {
419 }else if (types[i] == "oligos") {
420 m->setOligosFile("");
421 }else if (types[i] == "accnos") {
422 m->setAccnosFile("");
423 }else if (types[i] == "taxonomy") {
424 m->setTaxonomyFile("");
425 }else if (types[i] == "all") {
426 m->clearCurrentFiles();
428 m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
433 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
434 m->printCurrentFiles();
439 catch(exception& e) {
440 m->errorOut(e, "SetCurrentCommand", "execute");
445 //**********************************************************************************************************************