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() {}
35 /***********************************************************************/
36 bool ValidParameters::isValidParameter(string parameter, string command, string value) {
39 vector<string> cParams = commandParameters[command];
40 int numParams = cParams.size();
41 for(int i = 0; i < numParams; i++)
43 if(cParams.at(i).compare(parameter) == 0)
51 cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
52 cout << "The valid paramters for the " << command << " command are: ";
53 for(int i = 0; i < numParams-1; i++)
54 cout << cParams.at(i) << ", ";
55 cout << "and " << cParams.at(numParams-1) << ".\n";
59 if(parameterRanges.count(parameter) != 1)
63 double piSentinel = 3.14159;
64 vector<string> range = parameterRanges[parameter];
66 vector<string> values;
67 splitAtDash(value, values);
69 for(int i = 0; i < values.size(); i++)
72 valid = convertTest(value, pVal);
79 /********************************************************************************************************
81 *********************************************************************************************************/
83 if(parameter.compare("precision") == 0)
85 double logNum = log10((double)pVal);
86 double diff = (double)((int)logNum - logNum);
89 cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
94 /************************************************************************************************************/
100 if(range.at(1).compare("NA") == 0)
103 a = atoi(range.at(1).c_str());
105 if(range.at(3).compare("NA") == 0)
108 b = atoi(range.at(3).c_str());
110 if(range.at(4).compare("between") == 0)
112 else if(range.at(4).compare("only") == 0)
116 cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
120 if(range.at(0).compare(">") == 0)
122 else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
126 cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
130 if(range.at(2).compare("<") == 0)
132 else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
136 cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
147 if(a != piSentinel && b == piSentinel)
154 else if(a == piSentinel && b != piSentinel)
165 else if(d == 0 && e == 1)
167 else if(d == 1 && e == 0)
175 if(a != piSentinel && b == piSentinel)
177 else if(a == piSentinel && b != piSentinel)
180 valid = (pVal == a || pVal == b);
186 cout << "The '" << parameter << "' parameter needs to be ";
188 cout << "either '" << a << "' or '" << b << "'.\n";
196 cout << " '" << a << "'";
200 else if(a != piSentinel)
207 cout << " '" << b << ".\n";
215 catch(exception& e) {
216 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
220 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
225 /***********************************************************************/
227 /***********************************************************************/
228 void ValidParameters::initCommandParameters() {
230 //{"parameter1","parameter2",...,"last parameter"};
232 string readdistArray[] = {"phylip","column","name","cutoff","precision","group"};
233 commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
235 string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
236 commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
238 string readtreeArray[] = {"tree","group"};
239 commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
241 string clusterArray[] = {"cutoff","precision","method"};
242 commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
244 string deconvoluteArray[] = {"fasta"};
245 commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
247 string collectsingleArray[] = {"freq","line","label","calc","abund"};
248 commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
250 string collectsharedArray[] = {"jumble","freq","line","label","calc","groups"};
251 commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
253 string getgroupArray[] = {};
254 commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
256 string getlabelArray[] = {};
257 commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
259 string getlineArray[] = {};
260 commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
262 string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
263 commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
265 string rarefactionsharedArray[] = {"iters","jumble","line","label","calc","groups"};
266 commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
268 string libshuffArray[] = {"iters","groups","step","form","cutoff"};
269 commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
271 string summarysingleArray[] = {"line","label","calc","abund"};
272 commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
274 string summarysharedArray[] = {"jumble","line","label","calc","groups"};
275 commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
277 string parsimonyArray[] = {"random","groups","iters"};
278 commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
280 string unifracWeightedArray[] = {"groups","iters"};
281 commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
283 string unifracUnweightedArray[] = {"groups","iters"};
284 commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
286 string heatmapArray[] = {"groups","line","label","sorted"};
287 commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
289 string vennArray[] = {"groups","line","label","calc"};
290 commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
292 string binseqsArray[] = {"fasta","line","label","name"};
293 commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
295 string getOTURepArray[] = {"fasta","list","line","label","name"};
296 commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
298 string quitArray[] = {};
299 commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
302 catch(exception& e) {
303 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
307 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
312 /***********************************************************************/
314 /***********************************************************************/
315 void ValidParameters::initParameterRanges() {
319 /**************************************************************************************************************
320 {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
321 A number representing the lower bound ("NA" if there is no lower bound),
322 "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
323 A number representing the upper bound ("NA" if there is no lower bound),
324 "between" if between lower and upper bounds or "only" if exactly one of the bounds};
327 # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
328 ***********************************************************************************************************/
330 string precisionArray[] = {">=","10", "<","NA", "between"};
331 parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
333 string itersArray[] = {">=","10", "<","NA", "between"};
334 parameterRanges["iters"] = addParameters(itersArray, rangeSize);
336 string jumbleArray[] = {">","0", "<","1", "only"};
337 parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
339 string freqArray[] = {">","1", "<","NA", "between"};
340 parameterRanges["freq"] = addParameters(freqArray, rangeSize);
342 //string lineArray[] = {">=","1", "<","NA", "between"};
343 //parameterRanges["line"] = addParameters(lineArray, rangeSize);
345 string abundArray[] = {">=","5", "<","NA", "between"};
346 parameterRanges["abund"] = addParameters(abundArray, rangeSize);
348 catch(exception& e) {
349 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
353 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
358 /***********************************************************************/
360 /***********************************************************************/
361 vector<string> ValidParameters::addParameters(string parameters[], int size) {
363 vector<string> pVector (parameters, parameters+size);
366 catch(exception& e) {
367 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
371 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";