//**********************************************************************************************************************
//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
-ClusterCommand::ClusterCommand(){
+ClusterCommand::ClusterCommand(string option){
try{
globaldata = GlobalData::getInstance();
-
- if(globaldata->gSparseMatrix != NULL) { matrix = new SparseMatrix(*globaldata->gSparseMatrix); }
- // Not sure if we want the address or an entire new memory allocation. Might be nice to have new memory so data
- // doesn't need to be re-read, but then again, it could suck up a ton of memory. Dunno.
- // if(globaldata->getSparseMatrix() != NULL) { matrix = globaldata->getSparseMatrix(); }
-
- if(globaldata->gListVector != NULL){
- list = new ListVector(*globaldata->gListVector);
- rabund = new RAbundVector(list->getRAbundVector());
- //rabund->print(cout);
- }
-
- if(globaldata->getMethod() != "") { method = globaldata->getMethod(); }
- //if no method given use furthest, initialized in globaldata
- if(method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix); tag = "fn"; }
- else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix); tag = "nn"; }
- else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix); tag = "an"; }
- else { cout << "error - not recognized method" << endl; }
-
- if(globaldata->getPrecision() != ""){
- convert(globaldata->getPrecision(), precision);
- }
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- //saves precision legnth for formatting below
- length = globaldata->getPrecision().length();
+ else {
+ //valid paramters for this command
+ string Array[] = {"cutoff","precision","method"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
- if(globaldata->getCutOff() != ""){
- convert(globaldata->getCutOff(), cutoff);
+ //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; }
+ }
+
+ //error checking to make sure they read a distance file
+ if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
+ cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; abort = true;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ //get user cutoff and precision or use defaults
+ string temp;
+ temp = validParameter->validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ //saves precision legnth for formatting below
+ length = temp.length();
+ convert(temp, precision);
+
+ temp = validParameter->validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
+
+ method = validParameter->validFile(parameters, "method", false); if (method == "not found") { method = "furthest"; }
+
+ delete validParameter;
+
+ if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
+ else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; abort = true; }
+
+
+ if (abort == false) {
+
+ //get matrix, list and rabund for execute
+ if(globaldata->gSparseMatrix != NULL) { matrix = new SparseMatrix(*globaldata->gSparseMatrix); }
+
+ if(globaldata->gListVector != NULL){
+ list = new ListVector(*globaldata->gListVector);
+ rabund = new RAbundVector(list->getRAbundVector());
+ }
+
+ //create cluster
+ if(method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix); tag = "fn"; }
+ else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix); tag = "nn"; }
+ else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix); tag = "an"; }
+ else { cout << "error - not recognized method" << endl; abort = true; }
+
+ fileroot = getRootName(globaldata->inputFileName);
+
+ openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+ openOutputFile(fileroot+ tag + ".rabund", rabundFile);
+ openOutputFile(fileroot+ tag + ".list", listFile);
+
+
+ }
+
}
-
- fileroot = getRootName(globaldata->getFileRoot());
- openOutputFile(fileroot+ tag + ".sabund", sabundFile);
- openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- openOutputFile(fileroot+ tag + ".list", listFile);
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void ClusterCommand::help(){
+ try {
+ cout << "The cluster command can only be executed after a successful read.dist command." << "\n";
+ cout << "The cluster command parameter options are method, cuttoff and precision. No parameters are required." << "\n";
+ cout << "The cluster command should be in the following format: " << "\n";
+ cout << "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
+ cout << "The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ClusterCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
ClusterCommand::~ClusterCommand(){
int ClusterCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
projects / mothur.git / blobdiff