+++ /dev/null
-/*
- * validparameter.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 1/5/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "validparameter.h"
-
-/***********************************************************************/
-
-ValidParameters::ValidParameters() {
- try {
- m = MothurOut::getInstance();
- initParameterRanges();
- commandName = "";
- }
- catch(exception& e) {
- m->errorOut(e, "ValidParameters", "ValidParameters");
- exit(1);
- }
-}
-/***********************************************************************/
-
-ValidParameters::ValidParameters(string c) {
- try {
- m = MothurOut::getInstance();
- initParameterRanges();
- commandName = c;
- }
- catch(exception& e) {
- m->errorOut(e, "ValidParameters", "ValidParameters");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-ValidParameters::~ValidParameters() {}
-
-/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter, vector<string> cParams, string value) {
- try {
- bool valid = false;
- //vector<string> cParams = commandParameters[command];
- int numParams = cParams.size();
- for(int i = 0; i < numParams; i++) {
- if(cParams.at(i).compare(parameter) == 0) {
- valid = true;
- i = numParams;
- }
- }
- if(!valid) {
- m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine();
- m->mothurOut("The valid parameters are: ");
- for(int i = 0; i < numParams-1; i++)
- m->mothurOut(cParams.at(i) + ", ");
- m->mothurOut("and " + cParams.at(numParams-1) + ".\n");
- return false;
- }
-
- if(parameterRanges.count(parameter) != 1)
- return true;
-
- int pVal;
- double piSentinel = 3.14159;
- vector<string> range = parameterRanges[parameter];
-
- vector<string> values;
- m->splitAtDash(value, values);
-
- for(int i = 0; i < values.size(); i++) {
- value = values.at(i);
- valid = convertTest(value, pVal);
-
- if(!valid)
- return false;
-
-
-
- /********************************************************************************************************
- Special Cases
- *********************************************************************************************************/
-
- if(parameter.compare("precision") == 0) {
- double logNum = log10((double)pVal);
- double diff = (double)((int)logNum - logNum);
- if(diff != 0) {
- m->mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
- return false;
- }
- }
-
- /************************************************************************************************************/
-
-
-
- double a,b,c,d,e;
-
- if(range.at(1).compare("NA") == 0)
- a = piSentinel;
- else
- a = atoi(range.at(1).c_str());
-
- if(range.at(3).compare("NA") == 0)
- b = piSentinel;
- else
- b = atoi(range.at(3).c_str());
-
- if(range.at(4).compare("between") == 0)
- c = 0;
- else if(range.at(4).compare("only") == 0)
- c = 1;
- else {
- m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
- return false;
- }
-
- if(range.at(0).compare(">") == 0)
- d = 0;
- else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
- d = 1;
- else {
- m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
- return false;
- }
-
- if(range.at(2).compare("<") == 0)
- e = 0;
- else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
- e = 1;
- else {
- m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
- return false;
- }
-
- bool a0 = pVal > a;
- bool a1 = pVal >= a;
- bool b0 = pVal < b;
- bool b1 = pVal <= b;
-
- if(c != 1) {
- if(a != piSentinel && b == piSentinel) {
- if(d == 0)
- valid = a0;
- else
- valid = a1;
- }
- else if(a == piSentinel && b != piSentinel) {
- if(e == 0)
- valid = b0;
- else
- valid = b1;
- }
- else {
- if(d == 0 && e == 0)
- valid = (a0 && b0);
- else if(d == 0 && e == 1)
- valid = (a0 && b1);
- else if(d == 1 && e == 0)
- valid = (a1 && b0);
- else
- valid = (a1 && b1);
- }
- }
- else {
- if(a != piSentinel && b == piSentinel)
- valid = (pVal == a);
- else if(a == piSentinel && b != piSentinel)
- valid = (pVal == b);
- else
- valid = (pVal == a || pVal == b);
- }
-
-
- if(!valid) {
- m->mothurOut("The '" + parameter + "' parameter needs to be ");
- if(c == 1)
- m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
- else {
- if(a != piSentinel) {
- m->mothurOut(">");
- if(d != 0)
- m->mothurOut("=");
- m->mothurOut(" '" + toString(a) + "'");
- }
- if(b == piSentinel)
- m->mothurOut( "'.\n");
- else if(a != piSentinel)
- m->mothurOut(" and ");
- if(b != piSentinel) {
- m->mothurOut("<");
- if(e != 0)
- m->mothurOut("=");
- m->mothurOut(" '" + toString(b) + "'.\n");
- }
- }
- return false;
- }
- }
- return true;
- }
- catch(exception& e) {
- m->errorOut(e, "ValidParameters", "isValidParameters");
- exit(1);
- }
-}
-/*******************************************************/
-
-/******************************************************/
-
-string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
- try {
- int ableToOpen;
-
- map<string, string>::iterator it;
-
- it = container.find(parameter);
- if(it != container.end()){ //no parameter given
-
- if(isFile == true) {
-
- int pos = (it->second).find(".tx.");
- if (pos != string::npos) { m->sharedHeaderMode = "tax"; }
- else { m->sharedHeaderMode = "otu"; }
-
- #ifdef USE_MPI
- int pid, processors;
- MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- if (commandName == "") { processors = 1; }
-
- if (pid == 0) {
- #endif
- ifstream in;
- ableToOpen = m->openInputFile(it->second, in, "noerror");
- in.close();
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(it->second);
- m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- container[parameter] = tryPath;
- }
- }
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(it->second);
- m->mothurOut("Unable to open " + it->second + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- container[parameter] = tryPath;
- in2.close();
- }
- }
-
-
-
- #ifdef USE_MPI
- for(int i = 1; i < processors; i++) {
- MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
-
- int length = container[parameter].length();
- MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
- MPI_Send(&(container[parameter][0]), length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
-
- }
- }else {
- MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
-
- int length;
- MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
- //recieve container
- char* tempBuf = new char[length];
- MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
-
- container[parameter] = tempBuf;
- if (container[parameter].length() > length) { container[parameter] = container[parameter].substr(0, length); }
- delete tempBuf;
- }
-
- #endif
-
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
- return "not open";
- }
-
- //check phylip file to make sure its really phylip and not column
- if ((it->first == "phylip") && (ableToOpen != 1)) {
- ifstream inPhylip;
- m->openInputFile(it->second, inPhylip);
-
- string numTest, name;
- inPhylip >> numTest >> name;
- inPhylip.close();
-
- if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, aborting."); m->mothurOutEndLine(); return "not found"; }
- }
- }
- }else { return "not found"; }
-
- return it->second;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ValidParameters", "validFile");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-/***********************************************************************/
-void ValidParameters::initParameterRanges() {
- try {
- int rangeSize = 5;
-
- /**************************************************************************************************************
- {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
- A number representing the lower bound ("NA" if there is no lower bound),
- "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
- A number representing the upper bound ("NA" if there is no lower bound),
- "between" if between lower and upper bounds or "only" if exactly one of the bounds};
-
- # = parameter
- # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
- ***********************************************************************************************************/
-
- string precisionArray[] = {">=","10", "<","NA", "between"};
- parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
-
- string itersArray[] = {">=","1", "<","NA", "between"};
- parameterRanges["iters"] = addParameters(itersArray, rangeSize);
-
- string abundArray[] = {">=","5", "<","NA", "between"};
- parameterRanges["abund"] = addParameters(abundArray, rangeSize);
-
- string softArray[] = {">=","0", "<=","100", "between"};
- parameterRanges["soft"] = addParameters(softArray, rangeSize);
-
- string sizeArray[] = {">=","1", "<","NA", "between"};
- parameterRanges["size"] = addParameters(sizeArray, rangeSize);
- }
- catch(exception& e) {
- m->errorOut(e, "ValidParameters", "initParameterRanges");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-/***********************************************************************/
-vector<string> ValidParameters::addParameters(string parameters[], int size) {
- try {
- vector<string> pVector (parameters, parameters+size);
- return pVector;
- }
- catch(exception& e) {
- m->errorOut(e, "ValidParameters", "addParameters");
- exit(1);
- }
-}
-
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