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 parameters["phylip"] = "phylip";
17 parameters["column"] = "column";
18 parameters["list"] = "list";
19 parameters["rabund"] = "rabund";
20 parameters["sabund"] = "sabund";
21 parameters["name"] = "name";
22 parameters["group"] = "group";
23 parameters["order"] = "order";
24 parameters["fasta"] = "fasta";
25 parameters["tree"] = "tree";
26 parameters["fileroot"] = "fileroot";
27 parameters["cutoff"] = "cutoff";
28 parameters["method"] = "method";
29 parameters["format"] = "format";
30 parameters["precision"] = "precision";
31 parameters["label"] = "label";
32 parameters["line"] = "line";
33 parameters["iters"] = "iters";
34 parameters["jumble"] = "jumble";
35 parameters["freq"] = "freq";
36 parameters["abund"] = "abund";
37 parameters["random"] = "random";
38 parameters["groups"] = "groups";
39 parameters["calc"] = "calc";
40 parameters["sharedrarefaction"] = "sharedrarefaction";
41 parameters["sharedsummary"] = "sharedsummary";
42 parameters["shared"] = "shared";
43 parameters["single"] = "single";
44 parameters["rarefaction"] = "rarefaction";
46 initCommandParameters();
47 initParameterRanges();
50 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
54 cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
59 /***********************************************************************/
61 ValidParameters::~ValidParameters() {}
64 /***********************************************************************/
65 bool ValidParameters::isValidParameter(string parameter, string command, string value) {
68 vector<string> cParams = commandParameters[command];
69 int numParams = cParams.size();
70 for(int i = 0; i < numParams; i++)
72 if(cParams.at(i).compare(parameter) == 0)
80 cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
84 if(parameterRanges.count(parameter) != 1)
88 double piSentinel = 3.14159;
89 vector<string> range = parameterRanges[parameter];
91 valid = convertTest(value, pVal);
98 /********************************************************************************************************
100 *********************************************************************************************************/
102 if(parameter.compare("precision") == 0)
104 double logNum = log10((double)pVal);
105 double diff = (double)((int)logNum - logNum);
108 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
113 /************************************************************************************************************/
119 if(range.at(1).compare("NA") == 0)
122 a = atoi(range.at(1).c_str());
124 if(range.at(3).compare("NA") == 0)
127 b = atoi(range.at(3).c_str());
129 if(range.at(4).compare("between") == 0)
131 else if(range.at(4).compare("only") == 0)
135 cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
139 if(range.at(0).compare(">") == 0)
141 else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
145 cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
149 if(range.at(2).compare("<") == 0)
151 else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
155 cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
166 if(a == piSentinel && b == piSentinel)
168 if(a != piSentinel && b == piSentinel)
175 else if(a == piSentinel && b != piSentinel)
186 else if(d == 0 && e == 1)
188 else if(d == 1 && e == 0)
196 if(a == piSentinel && b == piSentinel)
198 if(a != piSentinel && b == piSentinel)
200 else if(a == piSentinel && b != piSentinel)
203 valid = (pVal == a || pVal == b);
211 cout << "The '" << parameter << "' parameter needs to be ";
213 cout << "either '" << a << "' or '" << b << "'.\n";
221 cout << " '" << a << "'";
225 else if(a != piSentinel)
232 cout << " '" << b << ".\n";
238 catch(exception& e) {
239 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
243 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
248 /***********************************************************************/
250 /***********************************************************************/
251 void ValidParameters::initCommandParameters() {
253 //{"parameter1","parameter2",...,"last parameter"};
255 string readdistArray[] = {"phylip","name","cutoff","precision"};
256 commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
258 string readotuArray[] = {"list","order","group","shared", "sabund"};
259 commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
261 string clusterArray[] = {"cutoff","precision","method"};
262 commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
264 string deconvoluteArray[] = {"fasta"};
265 commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
267 string collectsingleArray[] = {"freq","line","label","single","precision","abund"};
268 commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
270 string collectsharedArray[] = {"jumble","freq","line","label","shared","groups"};
271 commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
273 string getgroupArray[] = {};
274 commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
276 string getlabelArray[] = {};
277 commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
279 string getlineArray[] = {};
280 commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
282 string rarefactionsingleArray[] = {"iters","freq","line","label","rarefaction","abund"};
283 commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
285 string rarefactionsharedArray[] = {"iters","jumble","line","label","sharedrarefaction"};
286 commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
288 string summarysingleArray[] = {"line","label","summary","abund"};
289 commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
291 string summarysharedArray[] = {"jumble","line","label","sharedsummary"};
292 commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
294 string quitArray[] = {};
295 commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
298 catch(exception& e) {
299 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
303 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
308 /***********************************************************************/
310 /***********************************************************************/
311 void ValidParameters::initParameterRanges() {
315 /**************************************************************************************************************
316 {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
317 A number representing the lower bound ("NA" if there is no lower bound),
318 "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
319 A number representing the upper bound ("NA" if there is no lower bound),
320 "between" if between lower and upper bounds or "only" if exactly one of the bounds};
323 # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
324 ***********************************************************************************************************/
326 string precisionArray[] = {">=","10", "<","NA", "between"};
327 parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
329 string itersArray[] = {">=","10", "<","NA", "between"};
330 parameterRanges["iters"] = addParameters(itersArray, rangeSize);
332 string jumbleArray[] = {">","0", "<","1", "only"};
333 parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
335 string freqArray[] = {">","1", "<","NA", "between"};
336 parameterRanges["freq"] = addParameters(freqArray, rangeSize);
338 string lineArray[] = {">=","1", "<","NA", "between"};
339 parameterRanges["line"] = addParameters(lineArray, rangeSize);
341 string abundArray[] = {">=","5", "<","NA", "between"};
342 parameterRanges["abund"] = addParameters(abundArray, rangeSize);
344 catch(exception& e) {
345 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
349 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
354 /***********************************************************************/
356 /***********************************************************************/
357 vector<string> ValidParameters::addParameters(string parameters[], int size) {
359 vector<string> pVector (parameters, parameters+size);
362 catch(exception& e) {
363 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
367 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
372 /***********************************************************************/