static
rc_t ConfigRepoSet(DLList* repos, KConfig * kfg, const char* kfgPath, const char *dflt, uint8_t type)
{
const KConfigNode *node;
rc_t rc = KConfigOpenNodeRead ( kfg, & node, kfgPath );
if ( rc == 0 )
{
KNamelist* children;
rc = KConfigNodeListChild ( node, &children );
if ( rc == 0 )
{
uint32_t count;
rc = KNamelistCount ( children, &count );
if ( rc == 0 )
{
uint32_t i;
for (i = 0; i < count; ++i)
{
const char* name;
rc = KNamelistGet ( children, i, &name );
if ( rc == 0 )
{
#define BufSize 4096
char buf[ BufSize ];
size_t bSize = string_size(kfgPath);
string_copy(buf, BufSize, kfgPath, bSize);
if (bSize + string_size(name) < sizeof(buf))
{
NCBIRepository* repo;
string_copy(buf + bSize, sizeof(buf) - bSize, name, string_size(name) + 1);
rc = ConfigRepo( kfg, dflt, buf, buf, type, &repo );
DLListPushTail( repos, (DLNode*) repo );
}
#undef BufSize
}
else
{
rc = RC ( rcSRA, rcMgr, rcConstructing, rcString, rcExcessive );
}
if ( rc != 0 )
{
break;
}
}
}
KNamelistRelease ( children );
}
KConfigNodeRelease ( node );
}
if (GetRCState(rc) == rcNotFound)
{
return 0;
}
return rc;
}
/* Make
*/
static
rc_t SRAPathStringMake ( DLList *list, const char *path, size_t sz, uint8_t alg )
{
SRAPathString *s = (SRAPathString*) malloc ( sizeof * s + sz );
if ( s == NULL )
return RC ( rcSRA, rcMgr, rcUpdating, rcMemory, rcExhausted );
s -> alg = alg;
string_copy ( s -> path, sz + 1, path, sz );
DLListPushTail ( list, & s -> n );
return 0;
}
static rc_t make_pi_ref( pi_ref ** pr, DLList * list, const char * name )
{
rc_t rc = 0;
*pr = calloc( 1, sizeof ** pr );
if ( *pr == NULL )
rc = RC( rcAlign, rcIterator, rcConstructing, rcMemory, rcExhausted );
else
{
(*pr)->name = string_dup_measure ( name, NULL );
DLListInit( &( (*pr)->pi_windows ) );
DLListPushTail ( list, ( DLNode * )(*pr) );
}
return rc;
}
static rc_t add_to_spot_groups( DLList * list, const PlacementRecord *rec )
{
rc_t rc = 0;
spot_group * sg = find_spot_group( list, rec->spot_group, rec->spot_group_len );
if ( sg == NULL )
{
rc = make_spot_group( &sg, list, rec->spot_group, rec->spot_group_len );
}
if ( rc == 0 )
{
DLListPushTail ( &sg->records, ( DLNode * )(rec) );
}
return rc;
}
static rc_t make_pi_window( pi_window ** pw, DLList * list, window * w )
{
rc_t rc = 0;
*pw = calloc( 1, sizeof ** pw );
if ( *pw == NULL )
rc = RC( rcAlign, rcIterator, rcConstructing, rcMemory, rcExhausted );
else
{
(*pw)->w.first = w->first;
(*pw)->w.len = w->len;
DLListInit( &( (*pw)->pi_entries ) );
DLListPushTail ( list, ( DLNode * )(*pw) );
}
return rc;
}
static rc_t make_spot_group( spot_group ** sg, DLList * list, const char * name, size_t len )
{
rc_t rc = 0;
*sg = calloc( 1, sizeof ** sg );
if ( *sg == NULL )
rc = RC( rcAlign, rcIterator, rcConstructing, rcMemory, rcExhausted );
else
{
if ( len > 0 && name != NULL )
{
(*sg)->name = string_dup( name, len );
if ( (*sg)->name != NULL )
{
(*sg)->len = len;
}
}
/* if name is NULL, the spot-group is initialized with 0 via calloc() */
DLListInit( &( (*sg)->records ) );
DLListPushTail ( list, ( DLNode * )(*sg) );
}
return rc;
}
static rc_t add_to_pi_window( pi_window * pw, PlacementIterator *pi )
{
rc_t rc = 0;
pi_entry * pie = calloc( 1, sizeof *pie );
if ( pie == NULL )
rc = RC( rcAlign, rcIterator, rcConstructing, rcMemory, rcExhausted );
else
{
rc = PlacementIteratorNextAvailPos ( pi, &(pie->nxt_avail.first), &(pie->nxt_avail.len) );
if ( rc == 0 )
{
pie->pi = pi; /* store the placement-iterator in it's entry-struct */
DLListPushTail ( &pw->pi_entries, ( DLNode * )pie );
pw->count += 1;
}
else
{
free( pie );
ALIGN_DBG( "PlacementIter has no placements...", 0 );
}
}
return rc;
}
