//**********************************************************************************************************************
//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
-ClusterCommand::ClusterCommand(string option){
+ClusterCommand::ClusterCommand(string option) {
try{
globaldata = GlobalData::getInstance();
+
abort = false;
//allow user to run help
else {
//valid paramters for this command
- string Array[] = {"cutoff","precision","method","showabund","timing"};
+ string Array[] = {"cutoff","precision","method","showabund","timing","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
}
}
+ //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)) {
- mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); mothurOutEndLine();
+ m->mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); m->mothurOutEndLine();
abort = true;
}
if (method == "not found") { method = "furthest"; }
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
- else { mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
showabund = validParameter.validFile(parameters, "showabund", false);
if (showabund == "not found") { showabund = "T"; }
if (abort == false) {
- //get matrix, list and rabund for execute
+
+ //get matrix, list and rabund for execute
if(globaldata->gSparseMatrix != NULL) { matrix = globaldata->gSparseMatrix; }
if(globaldata->gListVector != NULL){
}
//create cluster
- if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix); }
- else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix); }
- else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix); }
+ 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); }
tag = cluster->getTag();
-
- fileroot = getRootName(globaldata->inputFileName);
+
+ if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
+ fileroot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
openOutputFile(fileroot+ tag + ".sabund", sabundFile);
openOutputFile(fileroot+ tag + ".rabund", rabundFile);
openOutputFile(fileroot+ tag + ".list", listFile);
+
+ outputNames.push_back(fileroot+ tag + ".sabund");
+ outputNames.push_back(fileroot+ tag + ".rabund");
+ outputNames.push_back(fileroot+ tag + ".list");
}
}
}
catch(exception& e) {
- errorOut(e, "ClusterCommand", "ClusterCommand");
+ m->errorOut(e, "ClusterCommand", "ClusterCommand");
exit(1);
}
}
void ClusterCommand::help(){
try {
- mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
- mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
- mothurOut("The cluster command should be in the following format: \n");
- mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- mothurOut("The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n");
+ 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, 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) {
- errorOut(e, "ClusterCommand", "help");
+ m->errorOut(e, "ClusterCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
time_t estart = time(NULL);
- int ndist = matrix->getNNodes();
+ //int ndist = matrix->getNNodes();
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
print_start = true;
start = time(NULL);
loops = 0;
+ double saveCutoff = cutoff;
while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
if (print_start && isTrue(timing)) {
- mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/"
+ m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/"
+ toString(roundDist(matrix->getSmallDist(), precision))
+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
cout.flush();
loops++;
- cluster->update();
+ cluster->update(cutoff);
float dist = matrix->getSmallDist();
float rndDist = roundDist(dist, precision);
}
if (print_start && isTrue(timing)) {
- mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
+ m->mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
cout.flush();
print_start = false;
sabundFile.close();
rabundFile.close();
listFile.close();
- if (isTrue(timing)) {
- mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster " + toString(ndist) + " distances"); mothurOutEndLine();
- }
+
+ if (saveCutoff != cutoff) { 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 (isTrue(timing)) {
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
+ //}
+
+
return 0;
}
catch(exception& e) {
- errorOut(e, "ClusterCommand", "execute");
+ m->errorOut(e, "ClusterCommand", "execute");
exit(1);
}
}
void ClusterCommand::printData(string label){
try {
if (isTrue(timing)) {
- mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
- + "\tclusters. Updates: " + toString(loops)); mothurOutEndLine();
+ m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
+ + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
}
print_start = true;
loops = 0;
oldList.print(listFile);
}
catch(exception& e) {
- errorOut(e, "ClusterCommand", "printData");
+ m->errorOut(e, "ClusterCommand", "printData");
exit(1);
}
projects / mothur.git / blobdiff