ValidParameters::ValidParameters() {
try {
- parameters["phylip"] = "phylip";
- parameters["column"] = "column";
- parameters["list"] = "list";
- parameters["rabund"] = "rabund";
- parameters["sabund"] = "sabund";
- parameters["name"] = "name";
- parameters["group"] = "group";
- parameters["order"] = "order";
- parameters["fasta"] = "fasta";
- parameters["tree"] = "tree";
- parameters["fileroot"] = "fileroot";
- parameters["cutoff"] = "cutoff";
- parameters["method"] = "method";
- parameters["format"] = "format";
- parameters["precision"] = "precision";
- parameters["label"] = "label";
- parameters["line"] = "line";
- parameters["iters"] = "iters";
- parameters["jumble"] = "jumble";
- parameters["freq"] = "freq";
- parameters["abund"] = "abund";
- parameters["random"] = "random";
- parameters["groups"] = "groups";
- parameters["calc"] = "calc";
- parameters["sharedrarefaction"] = "sharedrarefaction";
- parameters["sharedsummary"] = "sharedsummary";
- parameters["shared"] = "shared";
- parameters["single"] = "single";
- parameters["rarefaction"] = "rarefaction";
-
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";
if(!valid)
{
cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
+ cout << "The valid paramters for the " << command << " command are: ";
+ for(int i = 0; i < numParams-1; i++)
+ cout << cParams.at(i) << ", ";
+ cout << "and " << cParams.at(numParams-1) << ".\n";
return false;
}
int pVal;
double piSentinel = 3.14159;
vector<string> range = parameterRanges[parameter];
-
- valid = convertTest(value, pVal);
-
- if(!valid)
- return false;
+ vector<string> values;
+ splitAtDash(value, values);
-
- /********************************************************************************************************
- Special Cases
- *********************************************************************************************************/
-
- if(parameter.compare("precision") == 0)
+ for(int i = 0; i < values.size(); i++)
{
- double logNum = log10((double)pVal);
- double diff = (double)((int)logNum - logNum);
- if(diff != 0)
+ value = values.at(i);
+ valid = convertTest(value, pVal);
+
+ if(!valid)
+ return false;
+
+
+
+ /********************************************************************************************************
+ Special Cases
+ *********************************************************************************************************/
+
+ if(parameter.compare("precision") == 0)
{
- cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+ 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";
+ 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
+ {
+ cout << "The range can only be 'between' or 'only' the bounding numbers.\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
- {
- cout << "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
- {
- cout << "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
- {
- cout << "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)
- return true;
- if(a != piSentinel && b == piSentinel)
+ if(range.at(0).compare(">") == 0)
+ d = 0;
+ else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
+ d = 1;
+ else
{
- if(d == 0)
- valid = a0;
- else
- valid = a1;
+ cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
+ return false;
}
- else if(a == piSentinel && b != piSentinel)
+
+ if(range.at(2).compare("<") == 0)
+ 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";
+ return false;
+ }
+
+ bool a0 = pVal > a;
+ bool a1 = pVal >= a;
+ bool b0 = pVal < b;
+ bool b1 = pVal <= b;
+
+ if(c != 1)
{
- if(e == 0)
- valid = b0;
+ 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
- valid = b1;
+ {
+ 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(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);
+ if(a != piSentinel && b == piSentinel)
+ valid = (pVal == a);
+ else if(a == piSentinel && b != piSentinel)
+ valid = (pVal == b);
else
- valid = (a1 && b1);
+ valid = (pVal == a || pVal == b);
}
- }
- else
- {
- if(a == piSentinel && b == piSentinel)
- return true;
- 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)
- return true;
-
- else
- {
- cout << "The '" << parameter << "' parameter needs to be ";
- if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
+
+
+ if(!valid)
{
- if(a != piSentinel)
- {
- cout << ">";
- if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
- }
- if(b == piSentinel)
- cout << ".\n";
- else if(a != piSentinel)
- cout << " and ";
- if(b != piSentinel)
+ cout << "The '" << parameter << "' parameter needs to be ";
+ if(c == 1)
+ cout << "either '" << a << "' or '" << b << "'.\n";
+ else
{
- cout << "<";
- if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
+ if(a != piSentinel)
+ {
+ cout << ">";
+ if(d != 0)
+ cout << "=";
+ cout << " '" << a << "'";
+ }
+ if(b == piSentinel)
+ cout << ".\n";
+ else if(a != piSentinel)
+ cout << " and ";
+ if(b != piSentinel)
+ {
+ cout << "<";
+ if(e != 0)
+ cout << "=";
+ cout << " '" << b << ".\n";
+ }
}
+ return false;
}
- 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";
try {
//{"parameter1","parameter2",...,"last parameter"};
- string readdistArray[] = {"phylip","name","cutoff","precision"};
+ string readdistArray[] = {"phylip","column", "name","cutoff","precision"};
commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
- string readotuArray[] = {"list","order","group","shared", "sabund"};
+ string readotuArray[] = {"list","order","shared", "line", "label","group","shared", "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","single","precision","abund"};
+ string collectsingleArray[] = {"freq","line","label","calc","precision","abund"};
commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
- string collectsharedArray[] = {"jumble","freq","line","label","shared","groups"};
+ string collectsharedArray[] = {"jumble","freq","line","label","calc","groups"};
commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
string getgroupArray[] = {};
string getlineArray[] = {};
commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
- string rarefactionsingleArray[] = {"iters","freq","line","label","rarefaction","abund"};
+ string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
- string rarefactionsharedArray[] = {"iters","jumble","line","label","sharedrarefaction"};
+ string rarefactionsharedArray[] = {"iters","jumble","line","label","calc"};
commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
-
- string summarysingleArray[] = {"line","label","summary","abund"};
+
+ 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","sharedsummary"};
+ string summarysharedArray[] = {"jumble","line","label","calc"};
commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
+ string parsimonyArray[] = {"random","group","iters"};
+ commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
+
+ string unifracWeightedArray[] = {"group","iters"};
+ commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
+
+ string unifracUnweightedArray[] = {"group","iters"};
+ commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
+
+ string heatmapArray[] = {"group","line","label","sorted"};
+ 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 quitArray[] = {};
commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
}
}
-/***********************************************************************/
projects / mothur.git / blobdiff