//**********************************************************************************************************************
-LibShuffCommand::LibShuffCommand(){
+LibShuffCommand::LibShuffCommand(string option){
try {
srand( (unsigned)time( NULL ) );
globaldata = GlobalData::getInstance();
- convert(globaldata->getCutOff(), cutOff); //get the cutoff
- convert(globaldata->getIters(), iters); //get the number of iterations
- convert(globaldata->getStep(), step); //get the step size for the discrete command
- matrix = globaldata->gMatrix; //get the distance matrix
- setGroups(); //set the groups to be analyzed
+ abort = false;
+ Groups.clear();
+
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"iters","groups","step","form","cutoff"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //make sure the user has already run the read.dist command
+ if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
+ cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; abort = true;;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter->validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; savegroups = groups; }
+ else {
+ savegroups = groups;
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ string temp;
+ temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
+ convert(temp, iters);
+
+ temp = validParameter->validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
+ convert(temp, cutOff);
+
+ temp = validParameter->validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
+ convert(temp, step);
+
+ userform = validParameter->validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
+
+ delete validParameter;
+
+ if (abort == false) {
+
+ matrix = globaldata->gMatrix; //get the distance matrix
+ setGroups(); //set the groups to be analyzed
- if(globaldata->getForm() == "discrete"){
- form = new DLibshuff(matrix, iters, step, cutOff);
- }
- else{
- form = new SLibshuff(matrix, iters, cutOff);
+ if(userform == "discrete"){
+ form = new DLibshuff(matrix, iters, step, cutOff);
+ }
+ else{
+ form = new SLibshuff(matrix, iters, cutOff);
+ }
+ }
+
}
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
}
+//**********************************************************************************************************************
+
+void LibShuffCommand::help(){
+ try {
+ cout << "The libshuff command can only be executed after a successful read.dist command including a groupfile." << "\n";
+ cout << "The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
+ cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix." << "\n";
+ cout << "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form." << "\n";
+ cout << "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete." << "\n";
+ cout << "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep)." << "\n";
+ cout << "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01." << "\n";
+ cout << "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the LibShuffCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int LibShuffCommand::execute(){
try {
-
+
+ if (abort == true) { return 0; }
+
savedDXYValues = form->evaluateAll();
savedMinValues = form->getSavedMins();
globaldata->Groups.clear();
delete form;
+ //delete globaldata's copy of the gmatrix to free up memory
+ delete globaldata->gMatrix; globaldata->gMatrix = NULL;
+
return 0;
}
catch(exception& e) {
globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
}
} else {
- if (globaldata->getGroups() != "all") {
+ if (savegroups != "all") {
//check that groups are valid
for (int i = 0; i < globaldata->Groups.size(); i++) {
if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
// erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ globaldata->Groups.erase(globaldata->Groups.begin()+i);
}
}
projects / mothur.git / blobdiff