#include "clustercommand.h"
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClusterCommand::ClusterCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "ClusterCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"phylip","column","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
//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->getSparseMatrix() != NULL) { matrix = new SparseMatrix(*globaldata->getSparseMatrix()); }
- // 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->getListVector() != NULL){
- list = new ListVector(*globaldata->getListVector());
- 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);
- }
- //saves precision legnth for formatting below
- length = globaldata->getPrecision().length();
+ abort = false;
- if(globaldata->getCutOff() != ""){
- convert(globaldata->getCutOff(), cutoff);
- cutoff += (5 / (precision * 10.0));
- }
-
- fileroot = getRootName(globaldata->getFileRoot());
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
+ abort = true;
+ }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //error checking to make sure they read a distance file
+ if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
+ m->mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); m->mothurOutEndLine();
+ abort = true;
+ }
- openOutputFile(fileroot+ tag + ".sabund", sabundFile);
- openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- openOutputFile(fileroot+ tag + ".list", listFile);
+ //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, "hard", false); if (temp == "not found") { temp = "F"; }
+ hard = m->isTrue(temp);
+
+ 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"; }
+
+ if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
+ else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }
+
+ showabund = validParameter.validFile(parameters, "showabund", false);
+ if (showabund == "not found") { showabund = "T"; }
+
+ timing = validParameter.validFile(parameters, "timing", false);
+ if (timing == "not found") { timing = "F"; }
+
+ if (abort == false) {
+
+
+ //get matrix, list and rabund for execute
+ if(globaldata->gSparseMatrix != NULL) { matrix = globaldata->gSparseMatrix; }
+
+ if(globaldata->gListVector != NULL){
+ list = globaldata->gListVector;
+ rabund = new RAbundVector(list->getRAbundVector());
+ }
+
+ //create cluster
+ if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
+ else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
+ else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method); }
+ else if(method == "weighted"){ cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method); }
+ tag = cluster->getTag();
+
+ if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); }
+ fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
+
+ m->openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+ m->openOutputFile(fileroot+ tag + ".rabund", rabundFile);
+ m->openOutputFile(fileroot+ tag + ".list", listFile);
+
+ outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+ outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
+ outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+ }
+ }
}
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";
+ m->errorOut(e, "ClusterCommand", "ClusterCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ClusterCommand class function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void ClusterCommand::help(){
+ try {
+ m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
+ m->mothurOut("The cluster command parameter options are method, cuttoff, hard, precision, showabund and timing. No parameters are required.\n");
+ m->mothurOut("The cluster command should be in the following format: \n");
+ m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+ m->mothurOut("The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "help");
exit(1);
}
}
+
//**********************************************************************************************************************
ClusterCommand::~ClusterCommand(){
- delete cluster;
- delete matrix;
- delete list;
- delete rabund;
+ if (abort == false) {
+ delete cluster;
+ delete rabund;
+ }
}
//**********************************************************************************************************************
int ClusterCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
+ time_t estart = time(NULL);
+ //int ndist = matrix->getNNodes();
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
oldList = *list;
+
+ print_start = true;
+ start = time(NULL);
+ loops = 0;
+ double saveCutoff = cutoff;
+
+ while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
+
+ if (m->control_pressed) { //clean up
+ delete globaldata->gSparseMatrix; globaldata->gSparseMatrix = NULL;
+ delete globaldata->gListVector; globaldata->gListVector = NULL;
+ if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
+ else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
+ sabundFile.close();rabundFile.close();listFile.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ return 0;
+ }
- float x;
- x=0.1;
- toString(x, 2);
+ if (print_start && m->isTrue(timing)) {
+ m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/"
+ + toString(m->roundDist(matrix->getSmallDist(), precision))
+ + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
+ cout.flush();
+ print_start = false;
+ }
+
+ loops++;
+
+ cluster->update(cutoff);
- while(matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
- cluster->update();
float dist = matrix->getSmallDist();
- float rndDist = roundDist(dist, precision);
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(dist, precision);
+ }else{
+ rndDist = m->roundDist(dist, precision);
+ }
if(previousDist <= 0.0000 && dist != previousDist){
printData("unique");
oldRAbund = *rabund;
oldList = *list;
}
+
+ if (print_start && m->isTrue(timing)) {
+ m->mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
+ + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
+ cout.flush();
+ print_start = false;
+ }
if(previousDist <= 0.0000){
printData("unique");
}
//delete globaldata's copy of the sparsematrix and listvector to free up memory
- SparseMatrix* clearM = NULL;
- globaldata->setSparseMatrix(clearM);
- ListVector* clearL = NULL;
- globaldata->setListVector(clearL);
-
-
+ delete globaldata->gSparseMatrix; globaldata->gSparseMatrix = NULL;
+ delete globaldata->gListVector; globaldata->gListVector = NULL;
+
//saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
globaldata->setNameFile("");
globaldata->setFormat("list");
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+
+ if (saveCutoff != cutoff) {
+ if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
+ else { saveCutoff = m->roundDist(saveCutoff, precision); }
+
+ m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+
+ //if (m->isTrue(timing)) {
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
+ //}
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ClusterCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ClusterCommand", "execute");
exit(1);
}
-
}
//**********************************************************************************************************************
void ClusterCommand::printData(string label){
try {
+ if (m->isTrue(timing)) {
+ m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
+ + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
+ }
+ print_start = true;
+ loops = 0;
+ start = time(NULL);
+
oldRAbund.setLabel(label);
- oldRAbund.getSAbundVector().print(cout);
+ if (m->isTrue(showabund)) {
+ oldRAbund.getSAbundVector().print(cout);
+ }
oldRAbund.print(rabundFile);
oldRAbund.getSAbundVector().print(sabundFile);
oldList.print(listFile);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ClusterCommand class function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ClusterCommand", "printData");
exit(1);
}
+
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff