#include "makegroupcommand.h"
#include "sequence.hpp"
+
//**********************************************************************************************************************
-vector<string> MakeGroupCommand::getValidParameters(){
+vector<string> MakeGroupCommand::setParameters(){
try {
- string Array[] = {"fasta", "groups","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ 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, "MakeGroupCommand", "getValidParameters");
+ m->errorOut(e, "MakeGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-MakeGroupCommand::MakeGroupCommand(){
+string MakeGroupCommand::getHelpString(){
try {
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
+ string helpString = "";
+ helpString += "The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n";
+ helpString += "The make.group command parameters are fasta, groups and output. Fasta and group are required.\n";
+ helpString += "The output parameter allows you to specify the name of groupfile created. \n";
+ helpString += "The make.group command should be in the following format: \n";
+ helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
+ helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+ m->errorOut(e, "MakeGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MakeGroupCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","groups"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeGroupCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> MakeGroupCommand::getRequiredFiles(){
+MakeGroupCommand::MakeGroupCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "MakeGroupCommand", "getRequiredFiles");
+ m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
exit(1);
}
}
+
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(string option) {
try {
- 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 {
-
- //valid paramters for this command
- string AlignArray[] = {"fasta","groups","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
//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 = ""; }
-
- filename = outputDir;
fastaFileName = validParameter.validFile(parameters, "fasta", false);
- if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
- else {
+ if (fastaFileName == "not found") { //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else {
m->splitAtDash(fastaFileName, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = m->openInputFile(tryPath, in, "noerror");
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
fastaFileNames[i] = tryPath;
}
}
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ableToOpen = m->openInputFile(tryPath, in, "noerror");
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
fastaFileNames[i] = tryPath;
}
}
//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 = ""; }
+ output = validParameter.validFile(parameters, "output", false);
+ if (output == "not found") { output = ""; }
+ else{ filename = output; }
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
else { m->splitAtDash(groups, groupsNames); }
if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; }
}
-
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-MakeGroupCommand::~MakeGroupCommand(){ }
-
-//**********************************************************************************************************************
-
-void MakeGroupCommand::help(){
- try {
- m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
- m->mothurOut("The make.group command parameters are fasta and groups, both are required.\n");
- m->mothurOut("The make.group command should be in the following format: \n");
- m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups. \n");
- m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "MakeGroupCommand", "help");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
int MakeGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
-
+
filename = outputDir + filename;
ofstream out;
m->mothurOutEndLine();
m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
m->mothurOutEndLine();
-
+
+ //set group file as new current groupfile
+ string current = "";
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
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