ValidParameters::~ValidParameters() {}
-
/***********************************************************************/
bool ValidParameters::isValidParameter(string parameter, string command, 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)
- {
+ for(int i = 0; i < numParams; i++) {
+ if(cParams.at(i).compare(parameter) == 0) {
valid = true;
i = numParams;
}
}
- if(!valid)
- {
+ 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++)
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)
- {
+ 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;
}
c = 0;
else if(range.at(4).compare("only") == 0)
c = 1;
- else
- {
+ else {
cout << "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
- {
+ else {
cout << "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
- {
+ else {
cout << "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)
- {
+ if(!valid) {
cout << "The '" << parameter << "' parameter needs to be ";
if(c == 1)
cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSentinel)
- {
+ else {
+ if(a != piSentinel) {
cout << ">";
if(d != 0)
cout << "=";
cout << " '" << a << "'";
}
if(b == piSentinel)
- cout << ".\n";
+ cout << "'.\n";
else if(a != piSentinel)
cout << " and ";
- if(b != piSentinel)
- {
+ if(b != piSentinel) {
cout << "<";
if(e != 0)
cout << "=";
- cout << " '" << b << ".\n";
+ cout << " '" << b << "'.\n";
}
}
return false;
try {
//{"parameter1","parameter2",...,"last parameter"};
- string readdistArray[] = {"phylip","column", "name","cutoff","precision"};
+ 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","shared", "sabund", "rabund"};
+ string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
string readtreeArray[] = {"tree","group"};
string deconvoluteArray[] = {"fasta"};
commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
- string collectsingleArray[] = {"freq","line","label","calc","precision","abund"};
+ string collectsingleArray[] = {"freq","line","label","calc","abund","size"};
commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
- string collectsharedArray[] = {"jumble","freq","line","label","calc","groups"};
+ string collectsharedArray[] = {"freq","line","label","calc","groups"};
commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
string getgroupArray[] = {};
string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
- string rarefactionsharedArray[] = {"iters","jumble","line","label","calc"};
+ 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"};
+ string summarysingleArray[] = {"line","label","calc","abund","size"};
commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
- string summarysharedArray[] = {"jumble","line","label","calc"};
+ string summarysharedArray[] = {"line","label","calc","groups"};
commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
- string parsimonyArray[] = {"random","group","iters"};
+ string parsimonyArray[] = {"random","groups","iters"};
commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
- string unifracWeightedArray[] = {"group","iters"};
+ string unifracWeightedArray[] = {"groups","iters"};
commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
- string unifracUnweightedArray[] = {"group","iters"};
+ string unifracUnweightedArray[] = {"groups","iters"};
commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
- string heatmapArray[] = {"group","line","label","sorted"};
+ string heatmapArray[] = {"groups","line","label","sorted","scale"};
commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+
+ string filterseqsArray[] = {"fasta","phylip","clustal","nexus", "trump", "soft", "filter"};
+ commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
- string vennArray[] = {"groups","line","label"};
+ string vennArray[] = {"groups","line","label","calc"};
commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
+ string binseqsArray[] = {"fasta","line","label","name", "group"};
+ commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
+
+ string distsharedArray[] = {"line","label","calc","groups"};
+ commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
+
+ string getOTURepArray[] = {"fasta","list","line","label","name", "group"};
+ 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 bootstrapArray[] = {"line","label","calc","groups","iters"};
+ commandParameters["bootstrap.shared"] = addParameters(bootstrapArray, sizeof(bootstrapArray)/sizeof(string));
+
+ string concensusArray[] = {};
+ commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
+
+ string distanceArray[] = {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
+ commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+
+ string AlignArray[] = {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+ commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
+
string quitArray[] = {};
commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
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"};
- parameterRanges["line"] = addParameters(lineArray, rangeSize);
+ //string lineArray[] = {">=","1", "<","NA", "between"};
+ //parameterRanges["line"] = addParameters(lineArray, 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) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
}
-
projects / mothur.git / blobdiff