#include "clusterclassic.h"
//**********************************************************************************************************************
-vector<string> ClusterDoturCommand::getValidParameters(){
+vector<string> ClusterDoturCommand::setParameters(){
try {
- string AlignArray[] = {"phylip","name","hard","cutoff","precision","method","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "getValidParameters");
+ m->errorOut(e, "ClusterDoturCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ClusterDoturCommand::ClusterDoturCommand(){
+string ClusterDoturCommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
+ string helpString = "";
+ helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
+ helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
+ helpString += "The cluster.classic command should be in the following format: \n";
+ helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
+ helpString += "The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then average is assumed.\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
+ m->errorOut(e, "ClusterDoturCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ClusterDoturCommand::getRequiredParameters(){
+string ClusterDoturCommand::getOutputFileNameTag(string type, string inputName=""){
try {
- string Array[] = {"phylip"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "list") { outputFileName = "list"; }
+ else if (type == "rabund") { outputFileName = "rabund"; }
+ else if (type == "sabund") { outputFileName = "sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
}
catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "getRequiredParameters");
+ m->errorOut(e, "ClusterDoturCommand", "getOutputFileNameTag");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ClusterDoturCommand::getRequiredFiles(){
+ClusterDoturCommand::ClusterDoturCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "getRequiredFiles");
+ m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
exit(1);
}
}
ClusterDoturCommand::ClusterDoturCommand(string option) {
try{
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"phylip","name","cutoff","hard","precision","method","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("When executing the cluster.dotur command you must enter a phylip file."); m->mothurOutEndLine(); abort = true; }
+ else if (phylipfile == "not found") {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setPhylipFile(phylipfile); }
//check for optional parameter and set defaults
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
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);
+ m->mothurConvert(temp, precision);
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; }
+ temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
hard = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
+ sim = m->isTrue(temp);
+
method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "furthest"; }
+ if (method == "not found") { method = "average"; }
if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) {
if (method == "furthest") { tag = "fn"; }
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void ClusterDoturCommand::help(){
- try {
- m->mothurOut("The cluster.classic command clusters using the algorithm from dotur. \n");
- m->mothurOut("The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, precision. Phylip is required.\n");
- m->mothurOut("The cluster.classic command should be in the following format: \n");
- m->mothurOut("cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- m->mothurOut("The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then furthest is assumed.\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-ClusterDoturCommand::~ClusterDoturCommand(){}
-
//**********************************************************************************************************************
int ClusterDoturCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if(namefile != ""){
nameMap = new NameAssignment(namefile);
}
//reads phylip file storing data in 2D vector, also fills list and rabund
- ClusterClassic* cluster = new ClusterClassic(cutoff, method);
+ ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
cluster->readPhylipFile(phylipfile, nameMap);
if (m->control_pressed) { delete cluster; delete list; delete rabund; return 0; }
if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
- 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");
+ string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+ string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+ string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+
+ m->openOutputFile(sabundFileName, sabundFile);
+ m->openOutputFile(rabundFileName, rabundFile);
+ m->openOutputFile(listFileName, listFile);
+
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
int estart = time(NULL);
- while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 0)){
- if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
+ if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
cluster->update(cutoff);
// m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
//}
+ //set list file as new current listfile
+ string current = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ //set rabund file as new current rabundfile
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ //set sabund file as new current sabundfile
+ itTypes = outputTypes.find("sabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
projects / mothur.git / blobdiff