//**********************************************************************************************************************
//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
-HClusterCommand::HClusterCommand(string option){
+HClusterCommand::HClusterCommand(string option) {
try{
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing"};
+ string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
abort = true;
}
globaldata->newRead();
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ //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 = ""; }
+
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a hcluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
+ if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; 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) {
-
- fileroot = getRootName(distfile);
+
+ if (outputDir == "") { outputDir += hasPath(distfile); }
+ fileroot = outputDir + getRootName(getSimpleName(distfile));
if (method == "furthest") { tag = "fn"; }
else if (method == "nearest") { tag = "nn"; }
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, "HClusterCommand", "HClusterCommand");
+ m->errorOut(e, "HClusterCommand", "HClusterCommand");
exit(1);
}
}
void HClusterCommand::help(){
try {
- mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
- mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
- mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
- mothurOut("The hcluster command should be in the following format: \n");
- mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- mothurOut("The acceptable hcluster methods are furthest and nearest, but we hope to add average in the future.\n\n");
+ m->mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
+ m->mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
+ m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
+ m->mothurOut("The hcluster command should be in the following format: \n");
+ m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+ m->mothurOut("The acceptable hcluster methods are furthest and nearest, but we hope to add average in the future.\n\n");
}
catch(exception& e) {
- errorOut(e, "HClusterCommand", "help");
+ m->errorOut(e, "HClusterCommand", "help");
exit(1);
}
}
list = new ListVector(globaldata->nameMap->getListVector());
}
- mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); m->mothurOutEndLine();
estart = time(NULL);
//list vector made by read contains all sequence names
if(list != NULL){
rabund = new RAbundVector(list->getRAbundVector());
}else{
- mothurOut("Error: no list vector!"); mothurOutEndLine(); return 0;
+ m->mothurOut("Error: no list vector!"); m->mothurOutEndLine(); return 0;
}
float previousDist = 0.00000;
rabundFile.close();
listFile.close();
delete cluster;
-
- mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); 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();
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- errorOut(e, "HClusterCommand", "execute");
+ m->errorOut(e, "HClusterCommand", "execute");
exit(1);
}
}
void HClusterCommand::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, "HClusterCommand", "printData");
+ m->errorOut(e, "HClusterCommand", "printData");
exit(1);
}
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