*/
#include "clustercommand.h"
+#include "readphylip.h"
+#include "readcolumn.h"
+#include "readmatrix.hpp"
//**********************************************************************************************************************
-vector<string> ClusterCommand::getValidParameters(){
+vector<string> ClusterCommand::setParameters(){
try {
- string AlignArray[] = {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
+ 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", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
+ CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
+ CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
+ CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+ 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, "ClusterCommand", "getValidParameters");
+ m->errorOut(e, "ClusterCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ClusterCommand::ClusterCommand(){
+string ClusterCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["rabund"] = tempOutNames;
- outputTypes["sabund"] = tempOutNames;
+ string helpString = "";
+ helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
+ helpString += "The cluster command should be in the following format: \n";
+ helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
+ helpString += "The acceptable cluster methods are furthest, nearest, average and weighted. If no method is provided then furthest is assumed.\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ClusterCommand", "ClusterCommand");
+ m->errorOut(e, "ClusterCommand", "getHelpString");
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(){
+ClusterCommand::ClusterCommand(){
try {
- string Array[] = {"phylip","column","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- 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, "ClusterCommand", "getRequiredFiles");
+ m->errorOut(e, "ClusterCommand", "ClusterCommand");
exit(1);
}
}
//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
ClusterCommand::ClusterCommand(string option) {
try{
- globaldata = GlobalData::getInstance();
-
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = 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)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//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;
}
//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;
- }
-
+ 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 = m->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 = m->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 = m->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; }
+ }
+ }
+
+ //check for required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { distfile = phylipfile; format = "phylip"; }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { columnfile = ""; abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { distfile = columnfile; format = "column"; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ if ((phylipfile == "") && (columnfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to column, then phylip
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the cluster command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
+
+ if (columnfile != "") {
+ if (namefile == "") {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
+ 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
temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; }
hard = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
+ sim = m->isTrue(temp);
+
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
convert(temp, cutoff);
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) {
m->errorOut(e, "ClusterCommand", "ClusterCommand");
exit(1);
}
}
-
//**********************************************************************************************************************
-
-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(){
- if (abort == false) {
- delete cluster;
- delete rabund;
- }
-}
-
+ClusterCommand::~ClusterCommand(){}
//**********************************************************************************************************************
int ClusterCommand::execute(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ ReadMatrix* read;
+ if (format == "column") { read = new ReadColumnMatrix(columnfile, sim); } //sim indicates whether its a similarity matrix
+ else if (format == "phylip") { read = new ReadPhylipMatrix(phylipfile, sim); }
+
+ read->setCutoff(cutoff);
+
+ NameAssignment* nameMap = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }
+
+ read->read(nameMap);
+ list = read->getListVector();
+ matrix = read->getMatrix();
+ rabund = new RAbundVector(list->getRAbundVector());
+ delete read;
+
+ if (m->control_pressed) { //clean up
+ delete list; delete matrix; 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;
+ }
+
+ //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(distfile); }
+ fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
+
+ 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");
+
+
time_t estart = time(NULL);
- //int ndist = matrix->getNNodes();
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
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(""); }
+ delete list; delete matrix; delete rabund; delete cluster;
sabundFile.close();rabundFile.close();listFile.close();
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
return 0;
printData(toString(rndPreviousDist, length-1));
}
- //delete globaldata's copy of the sparsematrix and listvector to free up memory
- 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->setListFile(fileroot+ tag + ".list");
- globaldata->setNameFile("");
- globaldata->setFormat("list");
+ delete matrix;
+ delete list;
+ delete rabund;
+ delete cluster;
sabundFile.close();
rabundFile.close();
projects / mothur.git / blobdiff