*/
#include "readdistcommand.h"
+#include "readphylip.h"
+#include "readcolumn.h"
+#include "readmatrix.hpp"
-ReadDistCommand::ReadDistCommand(){
+//**********************************************************************************************************************
+ReadDistCommand::ReadDistCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
+ abort = false; calledHelp = false;
- filename = globaldata->inputFileName;
- format = globaldata->getFormat();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
- if (format == "column") { read = new ReadColumnMatrix(filename); }
- else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
- else if (format == "matrix") {
- groupMap = new GroupMap(globaldata->getGroupFile());
- groupMap->readMap();
- if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
- globaldata->gGroupmap = groupMap;
- }
+ else {
+ /*//valid paramters for this command
+ string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
+ 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;
- if (format != "matrix" ) {
- if(globaldata->getPrecision() != ""){
- convert(globaldata->getPrecision(), precision);
+ //check to make sure all parameters are valid for command
+ 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 = 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; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = 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; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { globaldata->setPhylipFile(phylipfile); globaldata->setFormat("phylip"); }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else {
+ globaldata->setGroupFile(groupfile);
+ //groupMap = new GroupMap(groupfile);
+ //groupMap->readMap();
}
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { globaldata->setNameFile(namefile); }
+
+ //you are doing a list and group shared
+ if ((phylipfile != "") && (groupfile != "")) {
+ globaldata->setFormat("matrix"); }
+
+ if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a read.dist command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a read.dist command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
- if(globaldata->getCutOff() != ""){
- convert(globaldata->getCutOff(), cutoff);
- cutoff += (5 / (precision * 10.0));
+ if (columnfile != "") {
+ if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
}
- read->setCutoff(cutoff);
+
+ //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"; }
+ convert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
+ sim = m->isTrue(temp);
+ globaldata->sim = sim;
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, cutoff);
+ cutoff += (5 / (precision * 10.0));
+
+ if (abort == false) {
+ distFileName = globaldata->inputFileName;
+ format = globaldata->getFormat();
+
+ if (format == "column") { read = new ReadColumnMatrix(distFileName); }
+ else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
+ else if (format == "matrix") {
+ groupMap = new GroupMap(groupfile);
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; abort = true; }
+ else {
+ if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
+ globaldata->gGroupmap = groupMap;
+ }
+ }
+
+ if (format != "matrix" ) {
+ read->setCutoff(cutoff);
- if(globaldata->getNameFile() != ""){
- nameMap = new NameAssignment(globaldata->getNameFile());
- nameMap->readMap(1,2);
- }
- else{
- nameMap = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }else{
+ nameMap = NULL;
+ }
+ }
}
+*/
}
-
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadDistCommand", "ReadDistCommand");
exit(1);
}
}
-
-//**********************************************************************************************************************
-ReadDistCommand::~ReadDistCommand(){
- delete read;
- delete nameMap;
-}
-
//**********************************************************************************************************************
int ReadDistCommand::execute(){
try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->mothurOut(getHelpString()); m->mothurOutEndLine();
+/*
+ time_t start = time(NULL);
+ size_t numDists = 0;
+
if (format == "matrix") {
ifstream in;
- openInputFile(filename, in);
+ m->openInputFile(distFileName, in);
matrix = new FullMatrix(in); //reads the matrix file
+ in.close();
+
+ if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+
+ //if files don't match...
+ if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {
+ m->mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences."); m->mothurOutEndLine();
+ //create new group file
+ if(outputDir == "") { outputDir += m->hasPath(groupfile); }
+
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
+ outputNames.push_back(newGroupFile);
+ ofstream outGroups;
+ m->openOutputFile(newGroupFile, outGroups);
+
+ for (int i = 0; i < matrix->getNumSeqs(); i++) {
+ if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
+
+ Names temp = matrix->getRowInfo(i);
+ outGroups << temp.seqName << '\t' << temp.groupName << endl;
+ }
+ outGroups.close();
+
+ m->mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); m->mothurOutEndLine();
+
+ //read new groupfile
+ delete groupMap; groupMap = NULL;
+ groupfile = newGroupFile;
+ globaldata->setGroupFile(groupfile);
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
+
+ globaldata->gGroupmap = groupMap;
+ }
+
//memory leak prevention
if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix; }
globaldata->gMatrix = matrix; //save matrix for coverage commands
- }else {
+ numDists = matrix->getSizes()[1];
+ } else {
read->read(nameMap);
+ //to prevent memory leak
+
+ if (m->control_pressed) { return 0; }
+
+ if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
globaldata->gListVector = read->getListVector();
+
+ if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; }
globaldata->gSparseMatrix = read->getMatrix();
+ numDists = globaldata->gSparseMatrix->getNNodes();
}
+
+ if (m->control_pressed) { return 0; }
+
+ if (outputNames.size() != 0) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); 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) - start) + " secs to read "); m->mothurOutEndLine();
+ */
return 0;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadDistCommand", "execute");
exit(1);
}
}
projects / mothur.git / blobdiff