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/*
* sequenceParser.cpp
* Mothur
*
* Created by westcott on 9/9/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "sequenceparser.h"
/************************************************************/
SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFile, vector<string> groupsSelected) {
try {
m = MothurOut::getInstance();
hasName = true;
//read group file
GroupMap groupMap;
int error = groupMap.readMap(groupFile, groupsSelected); //only store info for groups selected
if (error == 1) { m->setControl_pressed(true); }
//initialize maps
namesOfGroups = groupMap.getNamesOfGroups();
//run splitGroups command to parse files
string inputString = "";
if (groupsSelected.size() != 0) { sort(groupsSelected.begin(), groupsSelected.end()); }
else { groupsSelected = namesOfGroups; }
for (int i = 0; i < groupsSelected.size(); i++) { util.checkGroupName(groupsSelected[i]); }
inputString += "processors=1, groups=" + util.getStringFromVector(groupsSelected, "-"); //split.groups is paraplellized, we don't want the thread spinning up threads.
inputString += ", fasta=" + fastaFile;
inputString += ", name=" + nameFile;
inputString += ", group=" + groupFile;
m->mothurOut("\n/******************************************/\n");
m->mothurOut("Running command: split.groups(" + inputString + ")\n");
Command* splitCommand = new SplitGroupCommand(inputString);
splitCommand->execute();
//type -> files in groups order. fasta -> vector<string>. fastaFileForGroup1 stored in filenames["fasta"][1]
map<string, vector<string> > filenames = splitCommand->getOutputFiles();
delete splitCommand;
m->mothurOut("/******************************************/\n");
vector<string> parsedFastaFiles = filenames["fasta"]; //sorted in groups order
vector<string> parsedNameFiles = filenames["name"]; //sorted in groups order
vector<string> parsedGroupFiles = filenames["group"]; //sorted in groups order
if (parsedNameFiles.size() != groupsSelected.size()) { cout << "should never get here, quitting\n\n"; m->setControl_pressed(true); }
for (int i = 0; i < groupsSelected.size(); i++) {
vector<string> thisSamplesFiles;
thisSamplesFiles.push_back(parsedFastaFiles[i]);
thisSamplesFiles.push_back(parsedNameFiles[i]);
thisSamplesFiles.push_back(parsedGroupFiles[i]);
groupToFiles[groupsSelected[i]] = thisSamplesFiles;
}
//reset current files changed by split.groups
CurrentFile* current; current = CurrentFile::getInstance();
current->setNameFile(nameFile);
current->setFastaFile(fastaFile);
current->setGroupFile(groupFile);
}
catch(exception& e) {
m->errorOut(e, "SequenceParser", "SequenceParser");
exit(1);
}
}
/************************************************************/
//leaves all seqs map blank to be filled when asked for
SequenceParser::SequenceParser(string groupFile, string fastaFile, vector<string> groupsSelected) {
try {
m = MothurOut::getInstance();
hasName = false;
//read group file
GroupMap groupMap;
int error = groupMap.readMap(groupFile, groupsSelected); //only store info for groups selected
if (error == 1) { m->setControl_pressed(true); }
//initialize maps
namesOfGroups = groupMap.getNamesOfGroups();
//run splitGroups command to parse files
string inputString = "";
if (groupsSelected.size() != 0) {
sort(groupsSelected.begin(), groupsSelected.end());
for (int i = 0; i < groupsSelected.size(); i++) { util.checkGroupName(groupsSelected[i]); }
inputString += "groups=" + util.getStringFromVector(groupsSelected, "-");
}else {
groupsSelected = namesOfGroups;
for (int i = 0; i < groupsSelected.size(); i++) { util.checkGroupName(groupsSelected[i]); }
}
inputString += ", fasta=" + fastaFile;
inputString += ", group=" + groupFile;
m->mothurOut("\n/******************************************/\n");
m->mothurOut("Running command: split.groups(" + inputString + ")\n");
Command* splitCommand = new SplitGroupCommand(inputString);
splitCommand->execute();
//type -> files in groups order. fasta -> vector<string>. fastaFileForGroup1 stored in filenames["fasta"][1]
map<string, vector<string> > filenames = splitCommand->getOutputFiles();
delete splitCommand;
m->mothurOut("/******************************************/\n");
vector<string> parsedFastaFiles = filenames["fasta"]; //sorted in groups order
vector<string> parsedGroupFiles = filenames["group"]; //sorted in groups order
if (parsedFastaFiles.size() != groupsSelected.size()) { cout << "should never get here, quitting\n\n"; m->setControl_pressed(true); }
for (int i = 0; i < groupsSelected.size(); i++) {
vector<string> thisSamplesFiles;
thisSamplesFiles.push_back(parsedFastaFiles[i]);
thisSamplesFiles.push_back(parsedGroupFiles[i]);
groupToFiles[groupsSelected[i]] = thisSamplesFiles;
}
//reset current files changed by split.groups
CurrentFile* current; current = CurrentFile::getInstance();
current->setFastaFile(fastaFile);
current->setGroupFile(groupFile);
}
catch(exception& e) {
m->errorOut(e, "SequenceParser", "SequenceParser");
exit(1);
}
}
/************************************************************/
SequenceParser::~SequenceParser(){ }
/************************************************************/
int SequenceParser::getNumGroups(){ return namesOfGroups.size(); }
/************************************************************/
vector<string> SequenceParser::getNamesOfGroups(){ return namesOfGroups; }
/************************************************************/
vector<string> SequenceParser::getFiles(string group){
try {
map<string, vector<string> >::iterator it;
it = groupToFiles.find(group);
if (it != groupToFiles.end()) {
return it->second;
}else {
m->mothurOut("[ERROR]: cannot find files for group " + group + ", quitting.\n"); m->setControl_pressed(true);
}
return nullVector;
}
catch(exception& e) {
m->errorOut(e, "SequenceParser", "getFiles");
exit(1);
}
}
/************************************************************/
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