+++ /dev/null
-/*
- * readdistcommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 1/20/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "readdistcommand.h"
-#include "readphylip.h"
-#include "readcolumn.h"
-#include "readmatrix.hpp"
-
-//**********************************************************************************************************************
-ReadDistCommand::ReadDistCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- 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", "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;
-
- //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 (columnfile != "") {
- if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; 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
- string temp;
- temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
- m->mothurConvert(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(namefile != ""){
- nameMap = new NameAssignment(namefile);
- nameMap->readMap();
- }else{
- nameMap = NULL;
- }
- }
- }
-*/
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "ReadDistCommand", "ReadDistCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-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;
- 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
- 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) {
- m->errorOut(e, "ReadDistCommand", "execute");
- exit(1);
- }
-}
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