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";
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) {
}
}
if(!valid) {
- cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
- cout << "The valid paramters for the " << command << " command are: ";
+ cout << "'" << parameter << "' is not a valid parameter." << endl;
+ cout << "The valid parameters are: ";
for(int i = 0; i < numParams-1; i++)
cout << cParams.at(i) << ", ";
cout << "and " << cParams.at(numParams-1) << ".\n";
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["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
-
- string collectsingleArray[] = {"freq","line","label","calc","abund","size"};
- commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
-
- string collectsharedArray[] = {"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 getsabundArray[] = {"line", "label"};
- commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string));
-
- string getrabundArray[] = {"line", "label"};
- commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/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","size"};
- commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
-
- string summarysharedArray[] = {"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.bin"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
-
- string heatmapSimArray[] = {"groups","line","label"};
- commandParameters["heatmap.sim"] = addParameters(heatmapSimArray, sizeof(heatmapSimArray)/sizeof(string));
-
- string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
- commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
-
- string summaryseqsArray[] = {"fasta"};
- commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
-
- string screenseqsArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
- commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string));
-
- string reverseseqsArray[] = {"fasta"};
- commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
-
- string trimseqsArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
- commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
-
- 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", "phylip", "column", "name"};
- 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", "calc", "countends", "cutoff", "processors"};
- commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+string ValidParameters::validFile(map<string, string> container, string parameter, bool isFile) {
+ try {
+ int ableToOpen;
+ ifstream in;
+ map<string, string>::iterator it;
- string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
- commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/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";
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function validFile. 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";
+ cout << "An unknown error has occurred in the ValidParameters class function validFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
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"};
parameterRanges["freq"] = addParameters(freqArray, rangeSize);
projects / mothur.git / blobdiff