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 m = MothurOut::getInstance();
17 initParameterRanges();
20 m->errorOut(e, "ValidParameters", "ValidParameters");
25 /***********************************************************************/
27 ValidParameters::~ValidParameters() {}
29 /***********************************************************************/
30 bool ValidParameters::isValidParameter(string parameter, vector<string> cParams, string value) {
33 //vector<string> cParams = commandParameters[command];
34 int numParams = cParams.size();
35 for(int i = 0; i < numParams; i++) {
36 if(cParams.at(i).compare(parameter) == 0) {
42 m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine();
43 m->mothurOut("The valid parameters are: ");
44 for(int i = 0; i < numParams-1; i++)
45 m->mothurOut(cParams.at(i) + ", ");
46 m->mothurOut("and " + cParams.at(numParams-1) + ".\n");
50 if(parameterRanges.count(parameter) != 1)
54 double piSentinel = 3.14159;
55 vector<string> range = parameterRanges[parameter];
57 vector<string> values;
58 splitAtDash(value, values);
60 for(int i = 0; i < values.size(); i++) {
62 valid = convertTest(value, pVal);
69 /********************************************************************************************************
71 *********************************************************************************************************/
73 if(parameter.compare("precision") == 0) {
74 double logNum = log10((double)pVal);
75 double diff = (double)((int)logNum - logNum);
77 m->mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
82 /************************************************************************************************************/
88 if(range.at(1).compare("NA") == 0)
91 a = atoi(range.at(1).c_str());
93 if(range.at(3).compare("NA") == 0)
96 b = atoi(range.at(3).c_str());
98 if(range.at(4).compare("between") == 0)
100 else if(range.at(4).compare("only") == 0)
103 m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
107 if(range.at(0).compare(">") == 0)
109 else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
112 m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
116 if(range.at(2).compare("<") == 0)
118 else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
121 m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
131 if(a != piSentinel && b == piSentinel) {
137 else if(a == piSentinel && b != piSentinel) {
146 else if(d == 0 && e == 1)
148 else if(d == 1 && e == 0)
155 if(a != piSentinel && b == piSentinel)
157 else if(a == piSentinel && b != piSentinel)
160 valid = (pVal == a || pVal == b);
165 m->mothurOut("The '" + parameter + "' parameter needs to be ");
167 m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
169 if(a != piSentinel) {
173 m->mothurOut(" '" + toString(a) + "'");
176 m->mothurOut( "'.\n");
177 else if(a != piSentinel)
178 m->mothurOut(" and ");
179 if(b != piSentinel) {
183 m->mothurOut(" '" + toString(b) + "'.\n");
191 catch(exception& e) {
192 m->errorOut(e, "ValidParameters", "isValidParameters");
196 /*******************************************************/
198 /******************************************************/
200 string ValidParameters::validFile(map<string, string> container, string parameter, bool isFile) {
204 map<string, string>::iterator it;
206 it = container.find(parameter);
207 if(it != container.end()){ //no parameter given
214 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
215 MPI_Comm_size(MPI_COMM_WORLD, &processors);
220 ableToOpen = openInputFile(it->second, in);
224 for(int i = 1; i < processors; i++) {
225 MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
228 MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
231 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
234 if (ableToOpen == 1) { return "not open"; }
236 }else { return "not found"; }
241 catch(exception& e) {
242 m->errorOut(e, "ValidParameters", "validFile");
247 /***********************************************************************/
249 /***********************************************************************/
250 void ValidParameters::initParameterRanges() {
254 /**************************************************************************************************************
255 {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
256 A number representing the lower bound ("NA" if there is no lower bound),
257 "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
258 A number representing the upper bound ("NA" if there is no lower bound),
259 "between" if between lower and upper bounds or "only" if exactly one of the bounds};
262 # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
263 ***********************************************************************************************************/
265 string precisionArray[] = {">=","10", "<","NA", "between"};
266 parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
268 string itersArray[] = {">=","10", "<","NA", "between"};
269 parameterRanges["iters"] = addParameters(itersArray, rangeSize);
271 string abundArray[] = {">=","5", "<","NA", "between"};
272 parameterRanges["abund"] = addParameters(abundArray, rangeSize);
274 string softArray[] = {">=","0", "<=","100", "between"};
275 parameterRanges["soft"] = addParameters(softArray, rangeSize);
277 string sizeArray[] = {">=","1", "<","NA", "between"};
278 parameterRanges["size"] = addParameters(sizeArray, rangeSize);
280 catch(exception& e) {
281 m->errorOut(e, "ValidParameters", "initParameterRanges");
286 /***********************************************************************/
288 /***********************************************************************/
289 vector<string> ValidParameters::addParameters(string parameters[], int size) {
291 vector<string> pVector (parameters, parameters+size);
294 catch(exception& e) {
295 m->errorOut(e, "ValidParameters", "addParameters");