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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "TaxonNameLoader.h"
#include "types.h"
#include <assert.h>
#include <string.h>
#include <sstream>
#include <iostream>
using namespace std;
void TaxonNameLoader::load(string file){
m_current=0;
m_size=0;
m_stream.open(file.c_str());
if(!m_stream){
cout<<"File "<<file<<" is invalid."<<endl;
m_stream.close();
}
while(!m_stream.eof()){
char line[1024];
line[0]='\0';
m_stream.getline(line,1024);
if(strlen(line)>0){
m_size++;
}
}
m_stream.close();
m_stream.open(file.c_str());
cout<<"File "<<file<<" has "<<m_size<<" entries"<<endl;
}
bool TaxonNameLoader::hasNext(){
return m_current<m_size;
}
void TaxonNameLoader::getNext(TaxonIdentifier*taxon,string*name,string*rank){
char line[1024];
line[0]='\0';
m_stream.getline(line,1024);
string theLine=line;
int firstTab=0;
int secondTab=0;
int tabSymbols=0;
while(firstTab<(int)theLine.length() && tabSymbols!=1){
if(theLine[firstTab]=='\t'){
tabSymbols++;
}
firstTab++;
}
tabSymbols=0;
while(secondTab<(int)theLine.length() && tabSymbols!=2){
if(theLine[secondTab]=='\t'){
tabSymbols++;
}
secondTab++;
}
TaxonIdentifier theTaxon;
string theName;
istringstream virtualStream;
virtualStream.str(theLine);
virtualStream>>theTaxon;
int symbols=secondTab-firstTab-1;
theName=theLine.substr(firstTab,symbols);
(*taxon)=theTaxon;
(*name)=theName;
(*rank)=theLine.substr(secondTab);
m_current++;
if(m_current==m_size){
m_stream.close();
}
}
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