5 * Created by Sarah Westcott on 1/5/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "validparameter.h"
12 /***********************************************************************/
14 ValidParameters::ValidParameters() {
16 initCommandParameters();
17 initParameterRanges();
21 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
25 cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
30 /***********************************************************************/
32 ValidParameters::~ValidParameters() {}
34 /***********************************************************************/
35 bool ValidParameters::isValidParameter(string parameter, string command, string value) {
38 vector<string> cParams = commandParameters[command];
39 int numParams = cParams.size();
40 for(int i = 0; i < numParams; i++) {
41 if(cParams.at(i).compare(parameter) == 0) {
47 cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
48 cout << "The valid paramters for the " << command << " command are: ";
49 for(int i = 0; i < numParams-1; i++)
50 cout << cParams.at(i) << ", ";
51 cout << "and " << cParams.at(numParams-1) << ".\n";
55 if(parameterRanges.count(parameter) != 1)
59 double piSentinel = 3.14159;
60 vector<string> range = parameterRanges[parameter];
62 vector<string> values;
63 splitAtDash(value, values);
65 for(int i = 0; i < values.size(); i++) {
67 valid = convertTest(value, pVal);
74 /********************************************************************************************************
76 *********************************************************************************************************/
78 if(parameter.compare("precision") == 0) {
79 double logNum = log10((double)pVal);
80 double diff = (double)((int)logNum - logNum);
82 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
87 /************************************************************************************************************/
93 if(range.at(1).compare("NA") == 0)
96 a = atoi(range.at(1).c_str());
98 if(range.at(3).compare("NA") == 0)
101 b = atoi(range.at(3).c_str());
103 if(range.at(4).compare("between") == 0)
105 else if(range.at(4).compare("only") == 0)
108 cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
112 if(range.at(0).compare(">") == 0)
114 else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
117 cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
121 if(range.at(2).compare("<") == 0)
123 else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
126 cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
136 if(a != piSentinel && b == piSentinel) {
142 else if(a == piSentinel && b != piSentinel) {
151 else if(d == 0 && e == 1)
153 else if(d == 1 && e == 0)
160 if(a != piSentinel && b == piSentinel)
162 else if(a == piSentinel && b != piSentinel)
165 valid = (pVal == a || pVal == b);
170 cout << "The '" << parameter << "' parameter needs to be ";
172 cout << "either '" << a << "' or '" << b << "'.\n";
174 if(a != piSentinel) {
178 cout << " '" << a << "'";
182 else if(a != piSentinel)
184 if(b != piSentinel) {
188 cout << " '" << b << "'.\n";
196 catch(exception& e) {
197 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
201 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
206 /***********************************************************************/
208 /***********************************************************************/
209 void ValidParameters::initCommandParameters() {
211 //{"parameter1","parameter2",...,"last parameter"};
213 string readdistArray[] = {"phylip","column", "name","cutoff","precision", "group"};
214 commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
216 string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
217 commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
219 string readtreeArray[] = {"tree","group"};
220 commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
222 string clusterArray[] = {"cutoff","precision","method"};
223 commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
225 string deconvoluteArray[] = {"fasta"};
226 commandParameters["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
228 string collectsingleArray[] = {"freq","line","label","calc","abund","size"};
229 commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
231 string collectsharedArray[] = {"freq","line","label","calc","groups"};
232 commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
234 string getgroupArray[] = {};
235 commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
237 string getlabelArray[] = {};
238 commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
240 string getlineArray[] = {};
241 commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
243 string getsabundArray[] = {"line", "label"};
244 commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string));
246 string getrabundArray[] = {"line", "label"};
247 commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/sizeof(string));
249 string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
250 commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
252 string rarefactionsharedArray[] = {"iters","jumble","line","label","calc","groups"};
253 commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
255 string libshuffArray[] = {"iters","groups","step","form","cutoff"};
256 commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
258 string summarysingleArray[] = {"line","label","calc","abund","size"};
259 commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
261 string summarysharedArray[] = {"line","label","calc","groups"};
262 commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
264 string parsimonyArray[] = {"random","groups","iters"};
265 commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
267 string unifracWeightedArray[] = {"groups","iters"};
268 commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
270 string unifracUnweightedArray[] = {"groups","iters"};
271 commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
273 string heatmapArray[] = {"groups","line","label","sorted","scale"};
274 commandParameters["heatmap.bin"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
276 string heatmapSimArray[] = {"groups","line","label"};
277 commandParameters["heatmap.sim"] = addParameters(heatmapSimArray, sizeof(heatmapSimArray)/sizeof(string));
279 string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
280 commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
282 string summaryseqsArray[] = {"fasta"};
283 commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
285 string screenseqsArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
286 commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string));
288 string reverseseqsArray[] = {"fasta"};
289 commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
291 string trimseqsArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
292 commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
294 string vennArray[] = {"groups","line","label","calc"};
295 commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
297 string binseqsArray[] = {"fasta","line","label","name", "group"};
298 commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
300 string distsharedArray[] = {"line","label","calc","groups"};
301 commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
303 string getOTURepArray[] = {"fasta","list","line","label","name", "group"};
304 commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
306 string treeGroupsArray[] = {"line","label","calc","groups", "phylip", "column", "name"};
307 commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
309 string bootstrapArray[] = {"line","label","calc","groups","iters"};
310 commandParameters["bootstrap.shared"] = addParameters(bootstrapArray, sizeof(bootstrapArray)/sizeof(string));
312 string concensusArray[] = {};
313 commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
315 string distanceArray[] = {"fasta", "phylip", "calc", "countends", "cutoff", "processors"};
316 commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
318 string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
319 commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
321 string quitArray[] = {};
322 commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
325 catch(exception& e) {
326 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
330 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
335 /***********************************************************************/
337 /***********************************************************************/
338 void ValidParameters::initParameterRanges() {
342 /**************************************************************************************************************
343 {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
344 A number representing the lower bound ("NA" if there is no lower bound),
345 "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
346 A number representing the upper bound ("NA" if there is no lower bound),
347 "between" if between lower and upper bounds or "only" if exactly one of the bounds};
350 # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
351 ***********************************************************************************************************/
353 string precisionArray[] = {">=","10", "<","NA", "between"};
354 parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
356 string itersArray[] = {">=","10", "<","NA", "between"};
357 parameterRanges["iters"] = addParameters(itersArray, rangeSize);
359 string jumbleArray[] = {">","0", "<","1", "only"};
360 parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
362 string freqArray[] = {">=","1", "<","NA", "between"};
363 parameterRanges["freq"] = addParameters(freqArray, rangeSize);
365 //string lineArray[] = {">=","1", "<","NA", "between"};
366 //parameterRanges["line"] = addParameters(lineArray, rangeSize);
368 string abundArray[] = {">=","5", "<","NA", "between"};
369 parameterRanges["abund"] = addParameters(abundArray, rangeSize);
371 string softArray[] = {">=","0", "<=","100", "between"};
372 parameterRanges["soft"] = addParameters(softArray, rangeSize);
374 string sizeArray[] = {">=","1", "<","NA", "between"};
375 parameterRanges["size"] = addParameters(sizeArray, rangeSize);
377 catch(exception& e) {
378 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
382 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
387 /***********************************************************************/
389 /***********************************************************************/
390 vector<string> ValidParameters::addParameters(string parameters[], int size) {
392 vector<string> pVector (parameters, parameters+size);
395 catch(exception& e) {
396 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
400 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";