ValidParameters::ValidParameters() {
try {
- initCommandParameters();
initParameterRanges();
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ValidParameters", "ValidParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************************/
ValidParameters::~ValidParameters() {}
/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter, string command, string value) {
+bool ValidParameters::isValidParameter(string parameter, vector<string> cParams, string value) {
try {
bool valid = false;
- vector<string> cParams = commandParameters[command];
+ //vector<string> cParams = commandParameters[command];
int numParams = cParams.size();
- for(int i = 0; i < numParams; i++)
- {
- if(cParams.at(i).compare(parameter) == 0)
- {
+ for(int i = 0; i < numParams; i++) {
+ if(cParams.at(i).compare(parameter) == 0) {
valid = true;
i = numParams;
}
}
- if(!valid)
- {
- cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
- cout << "The valid paramters for the " << command << " command are: ";
+ if(!valid) {
+ mothurOut(parameter + " is not a valid parameter."); mothurOutEndLine();
+ mothurOut("The valid parameters are: ");
for(int i = 0; i < numParams-1; i++)
- cout << cParams.at(i) << ", ";
- cout << "and " << cParams.at(numParams-1) << ".\n";
+ mothurOut(cParams.at(i) + ", ");
+ mothurOut("and " + cParams.at(numParams-1) + ".\n");
return false;
}
vector<string> values;
splitAtDash(value, values);
- for(int i = 0; i < values.size(); i++)
- {
+ for(int i = 0; i < values.size(); i++) {
value = values.at(i);
valid = convertTest(value, pVal);
Special Cases
*********************************************************************************************************/
- if(parameter.compare("precision") == 0)
- {
+ if(parameter.compare("precision") == 0) {
double logNum = log10((double)pVal);
double diff = (double)((int)logNum - logNum);
- if(diff != 0)
- {
- cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+ if(diff != 0) {
+ mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
return false;
}
}
c = 0;
else if(range.at(4).compare("only") == 0)
c = 1;
- else
- {
- cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
+ else {
+ mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
return false;
}
d = 0;
else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
d = 1;
- else
- {
- cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
+ else {
+ mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
return false;
}
e = 0;
else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
e = 1;
- else
- {
- cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
+ else {
+ mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
return false;
}
bool b0 = pVal < b;
bool b1 = pVal <= b;
- if(c != 1)
- {
- if(a != piSentinel && b == piSentinel)
- {
+ if(c != 1) {
+ if(a != piSentinel && b == piSentinel) {
if(d == 0)
valid = a0;
else
valid = a1;
}
- else if(a == piSentinel && b != piSentinel)
- {
+ else if(a == piSentinel && b != piSentinel) {
if(e == 0)
valid = b0;
else
valid = b1;
}
- else
- {
+ else {
if(d == 0 && e == 0)
valid = (a0 && b0);
else if(d == 0 && e == 1)
valid = (a1 && b1);
}
}
- else
- {
+ else {
if(a != piSentinel && b == piSentinel)
valid = (pVal == a);
else if(a == piSentinel && b != piSentinel)
}
- if(!valid)
- {
- cout << "The '" << parameter << "' parameter needs to be ";
+ if(!valid) {
+ mothurOut("The '" + parameter + "' parameter needs to be ");
if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSentinel)
- {
- cout << ">";
+ mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
+ else {
+ if(a != piSentinel) {
+ mothurOut(">");
if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
+ mothurOut("=");
+ mothurOut(" '" + toString(a) + "'");
}
if(b == piSentinel)
- cout << ".\n";
+ mothurOut( "'.\n");
else if(a != piSentinel)
- cout << " and ";
- if(b != piSentinel)
- {
- cout << "<";
+ mothurOut(" and ");
+ if(b != piSentinel) {
+ mothurOut("<");
if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
+ mothurOut("=");
+ mothurOut(" '" + toString(b) + "'.\n");
}
}
return false;
return true;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ValidParameters", "isValidParameters");
exit(1);
}
}
+/*******************************************************/
-/***********************************************************************/
-
-/***********************************************************************/
-void ValidParameters::initCommandParameters() {
- try {
- //{"parameter1","parameter2",...,"last parameter"};
-
- string readdistArray[] = {"phylip","column", "name","cutoff","precision", "group"};
-
- commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
-
- string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
- commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
-
- string readtreeArray[] = {"tree","group"};
- commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
-
- string clusterArray[] = {"cutoff","precision","method"};
- commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
-
- string deconvoluteArray[] = {"fasta"};
- commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
-
- string collectsingleArray[] = {"freq","line","label","calc","abund"};
- commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
-
- string collectsharedArray[] = {"jumble","freq","line","label","calc","groups"};
- commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
-
- string getgroupArray[] = {};
- commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
-
- string getlabelArray[] = {};
- commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
+/******************************************************/
- string getlineArray[] = {};
- commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
-
- string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
- commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
-
- string rarefactionsharedArray[] = {"iters","jumble","line","label","calc","groups"};
- commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
-
- string libshuffArray[] = {"iters","groups","step","form","cutoff"};
- commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
-
- string summarysingleArray[] = {"line","label","calc","abund"};
- commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
-
- string summarysharedArray[] = {"jumble","line","label","calc","groups"};
- commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
-
- string parsimonyArray[] = {"random","groups","iters"};
- commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
-
- string unifracWeightedArray[] = {"groups","iters"};
- commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
-
- string unifracUnweightedArray[] = {"groups","iters"};
- commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
-
- string heatmapArray[] = {"groups","line","label","sorted","scale"};
- commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
-
- string vennArray[] = {"groups","line","label","calc"};
- commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
-
- string binseqsArray[] = {"fasta","line","label","name"};
- commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
-
- string getOTURepArray[] = {"fasta","list","line","label","name"};
- commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
-
- string treeGroupsArray[] = {"line","label","calc","groups"};
- commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
+string ValidParameters::validFile(map<string, string> container, string parameter, bool isFile) {
+ try {
+ int ableToOpen;
+ ifstream in;
+ map<string, string>::iterator it;
- string bootstrapArray[] = {"line","label","calc","groups","iters"};
- commandParameters["bootstrap.shared"] = addParameters(bootstrapArray, sizeof(bootstrapArray)/sizeof(string));
+ it = container.find(parameter);
+ if(it != container.end()){ //no parameter given
+ if(isFile == true) {
+ ableToOpen = openInputFile(it->second, in);
+ if (ableToOpen == 1) { return "not open"; }
+ in.close();
+ }
+ }else { return "not found"; }
- string quitArray[] = {};
- commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
-
+ return it->second;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ValidParameters", "validFile");
exit(1);
}
}
string itersArray[] = {">=","10", "<","NA", "between"};
parameterRanges["iters"] = addParameters(itersArray, rangeSize);
- string jumbleArray[] = {">","0", "<","1", "only"};
- parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
-
- string freqArray[] = {">","1", "<","NA", "between"};
+ string freqArray[] = {">=","1", "<","NA", "between"};
parameterRanges["freq"] = addParameters(freqArray, rangeSize);
//string lineArray[] = {">=","1", "<","NA", "between"};
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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ValidParameters", "initParameterRanges");
exit(1);
}
}
return pVector;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ValidParameters", "addParameters");
exit(1);
}
}