#include "readcolumn.h"
#include "readmatrix.hpp"
+//**********************************************************************************************************************
+vector<string> ReadDistCommand::getValidParameters(){
+ try {
+ string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadDistCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ReadDistCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"phylip","column","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadDistCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ReadDistCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadDistCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ReadDistCommand::ReadDistCommand(string option) {
try {
globaldata = GlobalData::getInstance();
it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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 = hasPath(it->second);
+ 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 = hasPath(it->second);
+ 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 = hasPath(it->second);
+ 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; }
}
convert(temp, precision);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
- sim = isTrue(temp);
+ 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));
+ cutoff += (5 / (precision * 10.0));
if (abort == false) {
distFileName = globaldata->inputFileName;
m->mothurOut("For this use the read.dist command should be in the following format: \n");
m->mothurOut("read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) \n");
m->mothurOut("The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. \n");
- m->mothurOut("The sim parameter is used to indicate that your distance file contains similiarity values instead of distance values. The default is false, if sim=true then mothur will convert the similairity values to distances. \n");
+ m->mothurOut("The sim parameter is used to indicate that your distance file contains similarity values instead of distance values. The default is false, if sim=true then mothur will convert the similarity values to distances. \n");
m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
m->mothurOut("The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command.\n");
m->mothurOut("For this use the read.dist command should be in the following format: \n");
time_t start = time(NULL);
size_t numDists = 0;
- vector<string> outputNames;
-
if (format == "matrix") {
ifstream in;
- openInputFile(distFileName, in);
+ m->openInputFile(distFileName, in);
matrix = new FullMatrix(in); //reads the matrix file
in.close();
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 += hasPath(groupfile); }
+ if(outputDir == "") { outputDir += m->hasPath(groupfile); }
- string newGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "editted.groups";
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
outputNames.push_back(newGroupFile);
ofstream outGroups;
- openOutputFile(newGroupFile, outGroups);
+ m->openOutputFile(newGroupFile, outGroups);
for (int i = 0; i < matrix->getNumSeqs(); i++) {
if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }