#include "readcolumn.h"
#include "readmatrix.hpp"
+//**********************************************************************************************************************
ReadDistCommand::ReadDistCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- 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", "column", "name", "cutoff", "precision", "group","outputdir","inputdir"};
+ /*//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);
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; }
}
// ...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, "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));
+ cutoff += (5 / (precision * 10.0));
if (abort == false) {
distFileName = globaldata->inputFileName;
}
}
}
-
+*/
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ReadDistCommand::help(){
- try {
- m->mothurOut("The read.dist command parameter options are phylip or column, group, name, cutoff and precision\n");
- m->mothurOut("The read.dist command can be used in two ways. The first is to read a phylip or column and run the cluster command\n");
- 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("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");
- m->mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ReadDistCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-ReadDistCommand::~ReadDistCommand(){
- if (abort == false) {
- if (format != "matrix") {
- delete read;
- delete nameMap;
- }
- }
-}
-
//**********************************************************************************************************************
int ReadDistCommand::execute(){
try {
- if (abort == true) { return 0; }
-
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->mothurOut(getHelpString()); m->mothurOutEndLine();
+/*
time_t start = time(NULL);
size_t numDists = 0;
- vector<string> outputNames;
-cout << format << endl;
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; }
+ 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;
groupMap = new GroupMap(groupfile);
groupMap->readMap();
- if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+ if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
globaldata->gGroupmap = groupMap;
}
}
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); m->mothurOutEndLine();
+ */
return 0;
}
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