method = globaldata->getMethod();
randomtree = globaldata->getRandomTree();
sharedfile = globaldata->getSharedFile();
-
-
-
-/* string p[] = {
- "phylip", //0
- "column", //1
- "list", //2
- "rabund", //3
- "sabund", //4
- "name", //5
- "order", //6
- "group", //7
- "fasta", //8
- "treefile", //9
- "cutoff", //10
- "precision", //11
- "iters", //12
- "jumble", //13
- "freq", //14
- "method", //15
- "fileroot", //16
- "line", //17
- "label", //18
- "single", //19
- "rarefaction", //20
- "shared", //21
- "summary", //22
- "sharedrarefaction", //23
- "sharedsummary", //24
- "groups", //25
- "abund", //26
- };
-
- string c0[] = {p[0],p[5],p[10],p[11]};
- string c1[] = {p[2],p[6],p[7]};
- string c2[] = {p[10],p[11],p[15]};
- string c3[] = {p[8]};
- string c4[] = {p[14],p[17],p[18],p[19],p[26]};
- string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
- string c6[] = {""};
- string c7[] = {""};
- string c8[] = {""};
- string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
- string c10[] = {p[12],p[13],p[17],p[18],p[23]};
- string c11[] = {p[17],p[18],p[22],p[26]};
- string c12[] = {p[13],p[17],p[18],p[24]};
- string c13[] = {""};
-
- vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string));
- vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
- vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
- vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
- vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
- vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
- vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
- vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
- vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
- vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
- vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
- vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
- vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
- vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
-
- vector<vector<string> > allCommands;
- allCommands.push_back(v0);
- allCommands.push_back(v1);
- allCommands.push_back(v2);
- allCommands.push_back(v3);
- allCommands.push_back(v4);
- allCommands.push_back(v5);
- allCommands.push_back(v6);
- allCommands.push_back(v7);
- allCommands.push_back(v8);
- allCommands.push_back(v9);
- allCommands.push_back(v10);
- allCommands.push_back(v11);
- allCommands.push_back(v12);
- allCommands.push_back(v13);
-
- string commands[] = {
- "read.dist", //0
- "read.otu", //1
- "cluster", //2
- "deconvolute", //3
- "collect.single", //4
- "collect.shared", //5
- "get.group", //6
- "get.label", //7
- "get.line", //8
- "rarefaction.single", //9
- "rarefaction.shared", //10
- "summary.single", //11
- "summary.shared", //12
- "quit" //13
- };
-
- for(int i = 0; i < allCommands.size(); i++)
- commandParameters[commands[i]] = allCommands.at(i);
-
- //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than};
- piSent = 3.14159;
- double ip0[] = {10, piSent, 0, 1, 0};
- double ip1[] = {10, piSent, 0, 1, 0};
- double ip2[] = {0, 1, 1, 0, 0};
- double ip3[] = {1, piSent, 0, 0, 0};
- double ip4[] = {1, piSent, 0, 1, 0};
- double ip5[] = {5, piSent, 0, 1, 0};
-
- vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double));
- vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double));
- vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double));
- vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double));
- vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double));
- vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
-
- intParams[p[11]] = ipv0;
- intParams[p[12]] = ipv1;
- intParams[p[13]] = ipv2;
- intParams[p[14]] = ipv3;
- intParams[p[17]] = ipv4;
- intParams[p[26]] = ipv5; */
-
}
/*******************************************************/
splitAtEquals(parameter, value);
//is it a valid parameter
- if (validParameter->isValidParameter(parameter) != true) { return false; }
- //if(!validCommandParameter(parameter,commandName)) {
- // cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
- // return false;
- //}
- //if(!validParameterValue(value, parameter)) {
- // 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";
- // else {
- /* vector<double> bounds = intParams[parameter];
- double a = bounds.at(0);
- double b = bounds.at(1);
- double c = bounds.at(2);
- double d = bounds.at(3);
- double e = bounds.at(4);
- cout << "The '" << parameter << "' parameter needs to be ";
- if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSent)
- {
- cout << ">";
- if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
- }
- if(b == piSent)
- cout << ".\n";
- else if(a != piSent)
- cout << " and ";
- if(b != piSent)
- {
- cout << "<";
- if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
- }
- }
- }
- return false;
- } */
-
+ if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
value = optionText;
splitAtEquals(parameter, value);
//is it a valid parameter
- if (validParameter->isValidParameter(parameter) != true) { return false; }
- // if(!validCommandParameter(parameter,commandName)) {
- // cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
- // return false;
- // }
- /* if(!validParameterValue(value, parameter)) {
- 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";
- else {
- vector<double> bounds = intParams[parameter];
- double a = bounds.at(0);
- double b = bounds.at(1);
- double c = bounds.at(2);
- double d = bounds.at(3);
- double e = bounds.at(4);
- cout << "The '" << parameter << "' parameter needs to be ";
- if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSent)
- {
- cout << ">";
- if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
- }
- if(b == piSent)
- cout << ".\n";
- else if(a != piSent)
- cout << " and ";
- if(b != piSent)
- {
- cout << "<";
- if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
- }
- }
- }
- return false;
- }*/
+ if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
}
/*******************************************************/
-/******************************************************
-//This function checks to see if the given paramter
-//is a valid paramter for the given command.
-bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
- try {
- for(int i = 0; i < commandParameters[commandName].size(); i++)
- if(parameter.compare(commandParameters[commandName][i]) == 0)
- return true;
- return false;
- }
-
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-
-/******************************************************
-//This function checks to see if the given paramter value
-//is convertable into an int if that parameter requires it.
-bool ErrorCheck::validParameterValue(string value, string parameter) {
- try {
- int pVal;
- if(intParams.count(parameter) == 1)
- {
- vector<double> bounds = intParams[parameter];
- bool valid = convertTest(value, pVal);
- if(!valid)
- return false;
- if(parameter.compare("precision") == 0)
- {
- double logNum = log10((double)pVal);
- double diff = (double)((int)logNum - logNum);
- if(diff != 0)
- return false;
- }
- double a = bounds.at(0);
- double b = bounds.at(1);
- double c = bounds.at(2);
- double d = bounds.at(3);
- double e = bounds.at(4);
- bool a0 = pVal > a;
- bool a1 = pVal >= a;
- bool b0 = pVal < b;
- bool b1 = pVal <= b;
-
- if(c != 1)
- {
- if(a == piSent && b == piSent)
- return true;
- if(a != piSent && b == piSent)
- {
- if(d == 0)
- return a0;
- else
- return a1;
- }
- else if(a == piSent && b != piSent)
- {
- if(e == 0)
- return b0;
- else
- return b1;
- }
- else
- {
- if(d == 0 && e == 0)
- return (a0 && b0);
- else if(d == 0 && e == 1)
- return (a0 && b1);
- else if(d == 1 && e == 0)
- return (a1 && b0);
- else
- return (a1 && b1);
- }
- }
- else
- {
- if(a == piSent && b == piSent)
- return true;
- if(a != piSent && b == piSent)
- return (pVal == a);
- else if(a == piSent && b != piSent)
- return (pVal == b);
- else
- return (pVal == a || pVal == b);
- }
- }
- return true;
- }
-
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-
/******************************************************/
//This function checks to make sure the user entered appropriate
// format parameters on a distfile read
ValidCommands* validCommand;
ValidParameters* validParameter;
void validateReadFiles();
- // bool validCommandParameter(string, string);
- // bool validParameterValue(string, string);
void validateReadDist();
void validateReadPhil();
void validateParseFiles();
bool errorFree;
vector<string> sharedGroups;
- // map <string, vector<string> > commandParameters;
- /// map <string, vector<double> > intParams;
- // double piSent;
-
};
#endif
}else if (globaldata->helpRequest == "read.otu") {
cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n";
cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n";
- cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, group, order, line and label." << "\n";
+ cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n";
cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n";
cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n";
cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n";
cout << "The get.line command should be in the following format: " << "\n";
cout << "get.line()" << "\n";
cout << "Example get.line()." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
}else if (globaldata->helpRequest == "rarefaction.single") {
cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
cout << "The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
commands["read.tree"] = "read.tree";
commands["cluster"] = "cluster";
commands["deconvolute"] = "deconvolute";
- commands["parsimony"] = "parsimony";
- commands["help"] = "help";
- commands["quit"] = "quit";
commands["collect.single"] = "collect.single";
commands["collect.shared"] = "collect.shared";
- commands["get.group"] = "get.group";
- commands["get.label"] = "get.label";
- commands["get.line"] = "get.line";
commands["rarefaction.single"] = "rarefaction.single";
commands["rarefaction.shared"] = "rarefaction.shared";
commands["summary.single"] = "summary.single";
commands["summary.shared"] = "summary.shared";
+ commands["parsimony"] = "parsimony";
commands["unifrac.weighted"] = "unifrac.weighted";
commands["unifrac.unweighted"] = "unifrac.unweighted";
commands["libshuff"] = "libshuff";
+ commands["get.group"] = "get.group";
+ commands["get.label"] = "get.label";
+ commands["get.line"] = "get.line";
+ commands["help"] = "help";
+ commands["quit"] = "quit";
}
ValidParameters::ValidParameters() {
try {
-
- parameters["phylip"] = "phylip";
- parameters["column"] = "column";
- parameters["list"] = "list";
- parameters["rabund"] = "rabund";
- parameters["sabund"] = "sabund";
- parameters["shared"] = "shared";
- 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["step"] = "step";
- parameters["form"] = "form";
-
+ initialReaddist();
+ initialReadotu();
+ initialReadtree();
+ initialCluster();
+ initialDeconvolute();
+ initialParsimony();
+ initialCollectsingle();
+ initialCollectshared();
+ initialRarefactsingle();
+ initialRarefactshared();
+ initialSummarysingle();
+ initialSummaryshared();
+ initialUnifracweighted();
+ initialUnifracunweighted();
+ initialLibshuff();
}
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) {
+bool ValidParameters::isValidParameter(string parameter, string command) {
try {
- //is the parameter in the map
- if ((parameters.find(parameter)) != (parameters.end())) {
- return true;
- }else{
- cout << parameter << " is not a valid parameter in Mothur. Valid parameters are " << endl;
- for (it = parameters.begin(); it != parameters.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
-
- return false;
- }
+ if (command == "read.dist") {
+ //is it valid
+ if ((readdist.find(parameter)) != (readdist.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the read.dist command. Valid parameters are ";
+ for (it = readdist.begin(); it != readdist.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "read.otu") {
+ //is it valid
+ if ((readotu.find(parameter)) != (readotu.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the read.otu command. Valid parameters are ";
+ for (it = readotu.begin(); it != readotu.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ //are you looking for a calculator for a rarefaction parameter
+ }else if (command == "read.tree") {
+ //is it valid
+ if ((readtree.find(parameter)) != (readtree.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the read.tree command. Valid parameters are ";
+ for (it = readtree.begin(); it != readtree.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ //are you looking for a calculator for a summary parameter
+ }else if (command == "cluster") {
+ //is it valid
+ if ((cluster.find(parameter)) != (cluster.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the cluster command. Valid parameters are ";
+ for (it = cluster.begin(); it != cluster.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; } //are you looking for a calculator for a sharedsummary parameter
+ }else if (command == "deconvolute") {
+ //is it valid
+ if ((deconvolute.find(parameter)) != (deconvolute.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the deconvolute command. Valid parameter is ";
+ for (it = deconvolute.begin(); it != deconvolute.end(); it++) {
+ cout << it->first;
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "parsimony") {
+ //is it valid
+ if ((parsimony.find(parameter)) != (parsimony.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the parsimony command. Valid parameters are ";
+ for (it = parsimony.begin(); it != parsimony.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "collect.single") {
+ //is it valid
+ if ((collectsingle.find(parameter)) != (collectsingle.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the collect.single command. Valid parameters are ";
+ for (it = collectsingle.begin(); it != collectsingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "collect.shared") {
+ //is it valid
+ if ((collectshared.find(parameter)) != (collectshared.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the collect.shared command. Valid parameters are ";
+ for (it = collectshared.begin(); it != collectshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "rarefaction.single") {
+ //is it valid
+ if ((rarefactsingle.find(parameter)) != (rarefactsingle.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the rarefaction.single command. Valid parameters are ";
+ for (it = rarefactsingle.begin(); it != rarefactsingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "rarefaction.shared") {
+ //is it valid
+ if ((rarefactshared.find(parameter)) != (rarefactshared.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the rarefaction.shared command. Valid parameters are ";
+ for (it = rarefactshared.begin(); it != rarefactshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "summary.single") {
+ //is it valid
+ if ((summarysingle.find(parameter)) != (summarysingle.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the summary.single command. Valid parameters are ";
+ for (it = summarysingle.begin(); it != summarysingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "summary.shared") {
+ //is it valid
+ if ((summaryshared.find(parameter)) != (summaryshared.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the summary.shared command. Valid parameters are ";
+ for (it = summaryshared.begin(); it != summaryshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "unifrac.weighted") {
+ //is it valid
+ if ((unifracweighted.find(parameter)) != (unifracweighted.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the unifrac.weighted command. Valid parameters are ";
+ for (it = unifracweighted.begin(); it != unifracweighted.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "unifrac.unweighted") {
+ //is it valid
+ if ((unifracunweighted.find(parameter)) != (unifracunweighted.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the unifrac.unweighted command. Valid parameters are ";
+ for (it = unifracunweighted.begin(); it != unifracunweighted.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "libshuff") {
+ //is it valid
+ if ((libshuff.find(parameter)) != (libshuff.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the libshuff command. Valid parameters are ";
+ for (it = libshuff.begin(); it != libshuff.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ //not a valid paramter
+ }else if (command == "help") { cout << parameter << " is not a valid parameter for the help command. There are no vaild parameters.";
+ }else if (command == "quit") { cout << parameter << " is not a valid parameter for the quit command. There are no vaild parameters.";
+ }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the get.group command. There are no vaild parameters.";
+ }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the get.label command. There are no vaild parameters.";
+ }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the get.line command. There are no vaild parameters."; }
+
+ return false;
}
catch(exception& e) {
}
/***********************************************************************/
+void ValidParameters::initialReaddist() {
+ readdist["phylip"] = "phylip";
+ readdist["column"] = "column";
+ readdist["name"] = "name";
+ readdist["group"] = "group";
+ readdist["cutoff"] = "cutoff";
+ readdist["precision"] = "precision";
+}
+/***********************************************************************/
+void ValidParameters::initialReadotu() {
+ readotu["list"] = "list";
+ readotu["rabund"] = "rabund";
+ readotu["sabund"] = "sabund";
+ readotu["shared"] = "shared";
+ readotu["group"] = "group";
+ readotu["order"] = "order";
+ readotu["label"] = "label";
+ readotu["line"] = "line";
+}
+/***********************************************************************/
+void ValidParameters::initialReadtree() {
+ readtree["group"] = "group";
+ readtree["tree"] = "tree";
+}
+/***********************************************************************/
+void ValidParameters::initialCluster() {
+ cluster["cutoff"] = "cutoff";
+ cluster["method"] = "method";
+ cluster["precision"] = "precision";
+}
+/***********************************************************************/
+void ValidParameters::initialDeconvolute() {
+ deconvolute["fasta"] = "fasta";
+}
+/***********************************************************************/
+void ValidParameters::initialParsimony() {
+ parsimony["iters"] = "iters";
+ parsimony["random"] = "random";
+ parsimony["groups"] = "groups";
+}
+/***********************************************************************/
+void ValidParameters::initialCollectsingle() {
+ collectsingle["label"] = "label";
+ collectsingle["line"] = "line";
+ collectsingle["freq"] = "freq";
+ collectsingle["calc"] = "calc";
+}
+/***********************************************************************/
+void ValidParameters::initialCollectshared() {
+ collectshared["label"] = "label";
+ collectshared["line"] = "line";
+ collectshared["freq"] = "freq";
+ collectshared["calc"] = "calc";
+ collectshared["jumble"] = "jumble";
+}
+/***********************************************************************/
+void ValidParameters::initialRarefactsingle() {
+ rarefactsingle["label"] = "label";
+ rarefactsingle["line"] = "line";
+ rarefactsingle["freq"] = "freq";
+ rarefactsingle["calc"] = "calc";
+ rarefactsingle["iters"] = "iters";
+}
+/***********************************************************************/
+void ValidParameters::initialRarefactshared() {
+ rarefactshared["label"] = "label";
+ rarefactshared["line"] = "line";
+ rarefactshared["jumble"] = "jumble";
+ rarefactshared["calc"] = "calc";
+ rarefactshared["iters"] = "iters";
+}
+/***********************************************************************/
+void ValidParameters::initialSummarysingle() {
+ summarysingle["label"] = "label";
+ summarysingle["line"] = "line";
+ summarysingle["calc"] = "calc";
+}
+/***********************************************************************/
+void ValidParameters::initialSummaryshared() {
+ summaryshared["label"] = "label";
+ summaryshared["line"] = "line";
+ summaryshared["calc"] = "calc";
+ summaryshared["jumble"] = "jumble";
+
+}
+/***********************************************************************/
+void ValidParameters::initialUnifracweighted() {
+ unifracweighted["iters"] = "iters";
+ unifracweighted["groups"] = "groups";
+}
+/***********************************************************************/
+void ValidParameters::initialUnifracunweighted() {
+ unifracunweighted["iters"] = "iters";
+ unifracunweighted["groups"] = "groups";
+}
+/***********************************************************************/
+void ValidParameters::initialLibshuff() {
+ libshuff["cutoff"] = "cutoff";
+ libshuff["iters"] = "iters";
+ libshuff["groups"] = "groups";
+ libshuff["step"] = "step";
+ libshuff["form"] = "form";
+}
+/***********************************************************************/
public:
ValidParameters();
~ValidParameters();
- bool isValidParameter(string);
+ bool isValidParameter(string, string);
+
private:
- map<string, string> parameters;
+ map<string, string> readdist;
+ map<string, string> readotu;
+ map<string, string> readtree;
+ map<string, string> cluster;
+ map<string, string> deconvolute;
+ map<string, string> parsimony;
+ map<string, string> collectsingle;
+ map<string, string> collectshared;
+ map<string, string> rarefactsingle;
+ map<string, string> rarefactshared;
+ map<string, string> summarysingle;
+ map<string, string> summaryshared;
+ map<string, string> unifracweighted;
+ map<string, string> unifracunweighted;
+ map<string, string> libshuff;
+
map<string, string>::iterator it;
+
+ void initialReaddist();
+ void initialReadotu();
+ void initialReadtree();
+ void initialCluster();
+ void initialDeconvolute();
+ void initialParsimony();
+ void initialCollectsingle();
+ void initialCollectshared();
+ void initialRarefactsingle();
+ void initialRarefactshared();
+ void initialSummarysingle();
+ void initialSummaryshared();
+ void initialUnifracweighted();
+ void initialUnifracunweighted();
+ void initialLibshuff();
};
projects / mothur.git / commitdiff