//Insere um indice no arquivo de indices
void insertIndexOnFile(indice *index)
{
if(openIndex())
{
//Altera o cabeçalho com o contador da lista
fseek(ind,0,SEEK_SET);
int head=0;
fread(&head,sizeof(int),1,ind);
int cont=head;
cont=cont+1;
fseek(ind,0,SEEK_SET);
fwrite(&cont,sizeof(int),1,ind);
fflush(ind);
//insere o indice
fseek(ind,0,SEEK_END);
fwrite(&index->id_locacao,sizeof(int),1,ind);
fwrite(&index->offset,sizeof(int),1,ind);
}
closeIndex();
}
//Cria lista de indices a partir do arquivo de indices
void getAllIndexesOnFile(indice **lista)
{
if(openIndex())
{
int tam = getIndexCount();
int count=0;
fseek(ind,4,SEEK_SET);
while(count<tam)
{
indice *i=(indice *)malloc(sizeof(indice));
fread(&i->id_locacao,sizeof(int),1,ind);
fread(&i->offset,sizeof(int),1,ind);
i->prox=NULL;
insertIndexOnList(lista,i);
count++;
}
}
closeIndex();
}
//Remove indice do arquivo de indices
void removeIndexFromFile(indice *i,indice **lista)
{
if(openIndex())
{
//zera o contador da lista
fseek(ind,0,SEEK_SET);
int cont=0;
//insere os indices, menos o que foi excluido
fseek(ind,4,SEEK_SET);
while(*lista!=NULL)
{
if((*lista)->id_locacao!=i->id_locacao)
{
fwrite(&(*lista)->id_locacao,sizeof(int),1,ind);
fwrite(&(*lista)->offset,sizeof(int),1,ind);
cont++;
}
*lista = (*lista)->prox;
}
fseek(ind,0,SEEK_SET);
fwrite(&cont,sizeof(int),1,ind);
fflush(ind);
}
closeIndex();
}
void SingleChromosomeBCFIndex::close() {
if (fBcfFile_) {
bgzf_close(fBcfFile_);
fBcfFile_ = NULL;
}
closeIndex();
}
void testExtractFromWildcardQuery( CuTest * tc )
{
Directory * pIndex = setUpIndex();
IndexReader * pReader = IndexReader::open( pIndex );
TermSet termSet;
WildcardQuery * wildcard;
Term * t1;
Query * rewrite;
t1 = _CLNEW Term( _T("data"), _T("aaaa?") );
wildcard = _CLNEW WildcardQuery( t1 );
rewrite = wildcard->rewrite( pReader );
rewrite->extractTerms( &termSet );
_CLLDECDELETE( t1 );
assertEqualsMsg( _T( "wrong number of terms" ), 3, termSet.size() );
for( TermSet::iterator itTerms = termSet.begin(); itTerms != termSet.end(); itTerms++ )
{
Term * pTerm = *itTerms;
if( 0 != _tcscmp( _T( "aaaaa" ), pTerm->text())
&& 0 != _tcscmp( _T( "aaaab" ), pTerm->text())
&& 0 != _tcscmp( _T( "aaaac" ), pTerm->text()))
{
assertTrueMsg( _T( "wrong term" ), false );
}
}
clearTermSet( termSet );
if( rewrite != wildcard )
_CLDELETE( rewrite );
_CLDELETE( wildcard );
t1 = _CLNEW Term( _T("data"), _T("aaa*") );
wildcard = _CLNEW WildcardQuery( t1 );
rewrite = wildcard->rewrite( pReader );
rewrite->extractTerms( &termSet );
_CLLDECDELETE( t1 );
assertEqualsMsg( _T( "wrong number of terms" ), 5, termSet.size() );
for( TermSet::iterator itTerms = termSet.begin(); itTerms != termSet.end(); itTerms++ )
{
Term * pTerm = *itTerms;
assertTrueMsg( _T( "wrong term" ), ( 0 == _tcsncmp( _T( "aaa" ), pTerm->text(), 3 )));
}
clearTermSet( termSet );
if( rewrite != wildcard )
_CLDELETE( rewrite );
_CLDELETE( wildcard );
pReader->close();
_CLDELETE( pReader );
closeIndex( pIndex );
pIndex = NULL;
}
/**
* @brief CommandServer::disconnect Disconnects from all clients
* @return true on success
*/
bool CommandServer::disconnect()
{
Stop();
Join();
auto it = m_connections.begin();
while(it != m_connections.end()) {
closeIndex((it++)->second);
}
m_connections.clear();
return true;
}
//zera o contador de indice
void emptyIndex()
{
if(openIndex())
{
//Coloca o ponteiro no cabeçalho do arquivo
fseek(ind,0,SEEK_SET);
//nula a lista de espaços disponiveis
int nullValue=0;
fwrite(&nullValue,sizeof(int),1,ind);
}
closeIndex();
}
int SingleChromosomeBCFIndex::openIndex() {
closeIndex();
// read everything
size_t fsize = getFileSize(indexFile_.c_str());
REprintf("fsize = %ld\n", (long int)fsize);
data_ = new uint8_t[fsize];
FILE* fp = fopen(indexFile_.c_str(), "rb");
if (fread(data_, sizeof(uint8_t), fsize, fp) != fsize) {
REprintf("Read incomplete index\n");
return -1;
}
// verify file integrity
int64_t* d = (int64_t*) data_;
if (fsize != sizeof(Record) * (2L + d[1])) { // d[0, 1]: number of sample; number of marker
REprintf("Check file integrity!\n");
REprintf("d = %ld %ld fsize = %ld\n", d[0], d[1], (int)fsize);
return -1;
}
return 0;
}
void testExtractFromTermQuery( CuTest * tc )
{
Directory * pIndex = setUpIndex();
IndexReader * pReader = IndexReader::open( pIndex );
TermSet termSet;
Term * t1 = _CLNEW Term( _T("data"), _T("aaaaa") );
Term * t2 = _CLNEW Term( _T("data"), _T("bbbbb") );
Query * q1 = _CLNEW TermQuery( t1 );
Query * q2 = _CLNEW TermQuery( t2 );
Query * rewrite1 = q1->rewrite( pReader );
Query * rewrite2 = q2->rewrite( pReader );
rewrite1->extractTerms( &termSet );
assertEqualsMsg( _T( "wrong number of terms" ), 1, termSet.size() );
assertEqualsMsg( _T( "wrong term" ), 0, t1->compareTo( *(termSet.begin())) );
clearTermSet( termSet );
rewrite2->extractTerms( &termSet );
assertEqualsMsg( _T( "wrong number of terms" ), 1, termSet.size() );
assertEqualsMsg( _T( "wrong term" ), 0, t2->compareTo( *(termSet.begin())) );
clearTermSet( termSet );
_CLLDECDELETE( t1 );
_CLLDECDELETE( t2 );
if( q1 != rewrite1 )
_CLDELETE( rewrite1 );
_CLDELETE( q1 );
if( q2 != rewrite2 )
_CLDELETE( rewrite2 );
_CLDELETE( q2 );
pReader->close();
_CLDELETE( pReader );
closeIndex( pIndex );
pIndex = NULL;
}
void testExtractFromFuzzyQuery( CuTest * tc )
{
Directory * pIndex = setUpIndex();
IndexReader * pReader = IndexReader::open( pIndex );
TermSet termSet;
FuzzyQuery * fuzzy;
Term * t1;
Query * rewrite;
t1 = _CLNEW Term( _T("data"), _T("aaaab") );
fuzzy = _CLNEW FuzzyQuery( t1, 0.7f );
rewrite = fuzzy->rewrite( pReader );
rewrite->extractTerms( &termSet );
_CLLDECDELETE( t1 );
assertEqualsMsg( _T( "wrong number of terms" ), 4, termSet.size() );
for( TermSet::iterator itTerms = termSet.begin(); itTerms != termSet.end(); itTerms++ )
{
Term * pTerm = *itTerms;
if( 0 != _tcscmp( _T( "aaaaa" ), pTerm->text())
&& 0 != _tcscmp( _T( "aaaab" ), pTerm->text())
&& 0 != _tcscmp( _T( "aaabb" ), pTerm->text())
&& 0 != _tcscmp( _T( "aaaac" ), pTerm->text()))
{
assertTrueMsg( _T( "wrong term" ), false );
}
}
clearTermSet( termSet );
if( rewrite != fuzzy )
_CLDELETE( rewrite );
_CLDELETE( fuzzy );
pReader->close();
_CLDELETE( pReader );
closeIndex( pIndex );
pIndex = NULL;
}
void testExtractFromBooleanQuery( CuTest * tc )
{
Directory * pIndex = setUpIndex();
IndexReader * pReader = IndexReader::open( pIndex );
TermSet termSet;
Term * t1 = _CLNEW Term( _T("data"), _T("aaaab") );
Term * t2 = _CLNEW Term( _T("data"), _T("aaabb") );
Term * t3 = _CLNEW Term( _T("data"), _T("aaabb") );
BooleanQuery * bq = _CLNEW BooleanQuery();
bq->add( _CLNEW TermQuery( t1 ), true, BooleanClause::SHOULD );
bq->add( _CLNEW TermQuery( t2 ), true, BooleanClause::SHOULD );
bq->add( _CLNEW TermQuery( t3 ), true, BooleanClause::SHOULD );
Query * rewrite = bq->rewrite( pReader );
rewrite->extractTerms( &termSet );
assertEqualsMsg( _T( "wrong number of terms" ), 2, termSet.size() );
for( TermSet::iterator itTerms = termSet.begin(); itTerms != termSet.end(); itTerms++ )
{
Term * pTerm = *itTerms;
assertTrueMsg( _T( "wrong term" ), ( 0 == t1->compareTo( pTerm ) || 0 == t2->compareTo( pTerm )));
}
clearTermSet( termSet );
_CLLDECDELETE( t1 );
_CLLDECDELETE( t2 );
_CLLDECDELETE( t3 );
if( rewrite != bq )
_CLDELETE( rewrite );
_CLDELETE( bq );
pReader->close();
_CLDELETE( pReader );
closeIndex( pIndex );
pIndex = NULL;
}
