globaldata = GlobalData::getInstance();
validCommand = new ValidCommands();
validParameter = new ValidParameters();
- validCalculator = new ValidCalculators();
+}
+/*******************************************************/
+
+/******************************************************/
+
+void ErrorCheck::refresh() {
columnfile = globaldata->getColumnFile();
phylipfile = globaldata->getPhylipFile();
listfile = globaldata->getListFile();
cutoff = globaldata->getCutOff();
format = globaldata->getFormat();
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; */
+
}
+
/*******************************************************/
/******************************************************/
bool ErrorCheck::checkInput(string input) {
errorFree = true;
clear();
-
+
+ //refresh variable
+ refresh();
+
//get command name and parameters
int openParen = input.find_first_of('(');
int closeParen = input.find_last_of(')');
if (validCommand->isValidCommand(commandName) != true) { return false; }
string parameter, value;
+
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
- globaldata->splitAtComma(value, optionText);
- globaldata->splitAtEquals(parameter, value);
+ splitAtComma(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 (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
if (parameter == "name" ) { namefile = value; }
if (parameter == "order" ) { orderfile = value; }
if (parameter == "fasta" ) { fastafile = value; }
- if (parameter == "treefile" ) { treefile = value; }
+ if (parameter == "tree" ) { treefile = value; }
if (parameter == "group" ) { groupfile = value; }
+ if (parameter == "shared" ) { sharedfile = value; }
if (parameter == "cutoff" ) { cutoff = value; }
if (parameter == "precision" ) { precision = value; }
if (parameter == "iters" ) { iters = value; }
if (parameter == "fileroot" ) { fileroot = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
-
- if (parameter == "single") {//stores estimators in a vector
- singleEsimators.clear(); //clears out old values
- globaldata->splitAtDash(value, singleEsimators);
- for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
- }
- }
- if (parameter == "rarefaction") {//stores estimators in a vector
- rareEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, rareEstimators);
- for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
- }
- }
- if (parameter == "shared") {//stores estimators in a vector
- sharedEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, sharedEstimators);
- for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
- }
- }
- if (parameter == "summary") { //stores summaries to be used in a vector
- summaryEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, summaryEstimators);
- for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
- }
- }
- if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
- sharedRareEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, sharedRareEstimators);
- for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
- }
- }
+ if (parameter == "abund" ) { abund = value; }
+ if (parameter == "random" ) { randomtree = value; }
}
//gets the last parameter and value
if (errorFree) { //gets the last parameter and value
value = optionText;
- globaldata->splitAtEquals(parameter, value);
+ 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 (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
if (parameter == "name" ) { namefile = value; }
if (parameter == "order" ) { orderfile = value; }
if (parameter == "group" ) { groupfile = value; }
+ if (parameter == "shared" ) { sharedfile = value; }
if (parameter == "fasta" ) { fastafile = value; }
- if (parameter == "treefile" ) { treefile = value; }
+ if (parameter == "tree" ) { treefile = value; }
if (parameter == "cutoff" ) { cutoff = value; }
if (parameter == "precision" ) { precision = value; }
if (parameter == "iters" ) { iters = value; }
if (parameter == "fileroot" ) { fileroot = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
-
- if (parameter == "single") {//stores estimators in a vector
- singleEsimators.clear(); //clears out old values
- globaldata->splitAtDash(value, singleEsimators);
- for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
- }
- }
- if (parameter == "rarefaction") {//stores estimators in a vector
- rareEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, rareEstimators);
- for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
- }
- }
- if (parameter == "shared") {//stores estimators in a vector
- sharedEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, sharedEstimators);
- for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
- }
- }
- if (parameter == "summary") { //stores summaries to be used in a vector
- summaryEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, summaryEstimators);
- for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
- }
- }
- if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
- sharedRareEstimators.clear(); //clears out old values
- globaldata->splitAtDash(value, sharedRareEstimators);
- for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
- //is it a valid calculator
- if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
- }
- }
-
+ if (parameter == "random" ) { randomtree = value; }
+ if (parameter == "abund" ) { abund = value; }
}
}
//make sure the user does not use both the line and label parameters
if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
-
if (commandName == "read.dist") {
validateReadFiles();
validateReadFiles();
validateReadPhil();
}
+ }else if (commandName == "read.shared") {
+ //you want to do shared commands with just the shared file
+ validateReadFiles();
}else if (commandName == "read.tree") {
validateTreeFiles(); //checks the treefile and groupfile parameters
}else if (commandName == "deconvolute") {
}
//are you trying to cluster before you have read something
- if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
- (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+ if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
+ ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
errorFree = false;
}
+ if (commandName == "parsimony") {
+ //are you trying to use parsimony without reading a tree or saying you want random distribution
+ if (randomtree == "") {
+ if (globaldata->gTree.size() == 0) {
+ cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false; }
+ }
+ }
+
+ if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
+ if (globaldata->gTree.size() == 0) {//no trees were read
+ cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; }
+ }
+
//check for valid method
+ if(commandName == "get.group") {
+ if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
+ }
+ if (commandName == "get.label" || commandName == "get.line") {
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; }
+ }
if (commandName == "cluster") {
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
}
if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
- if (globaldata->getListFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
- else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+ if (globaldata->getSharedFile() == "") {
+ if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+ else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+ }
}
-
-
+
return errorFree;
}
//unable to open
if (ableToOpen == 1) { errorFree = false; }
else { globaldata->inputFileName = fastafile; }
+ }else if (sharedfile != "") {
+ ableToOpen = openInputFile(sharedfile, filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { errorFree = false; }
+ else { globaldata->inputFileName = sharedfile; }
}else{ //no file given
errorFree = false;
}
}
/*******************************************************/
+/******************************************************
+//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
namefile = "";
groupfile = "";
orderfile = "";
+ sharedfile = "";
line = "";
label = "";
method = "furthest";
projects / mothur.git / blobdiff