FieldDescription* UnionMetaClass::get_proper_field_description(const Address address,const LString& field_name ) const
{
int index = get_tag_num( address );
if ((index >= 0) && ((*_union_fields)[ index ]->get_member_name() == field_name))
return (*_union_fields)[ index ];
return(NULL);
}
Walker::ApplyStatus UnionMetaClass::walk(const Address instance,Walker &walk) const {
AggregateWrapper agg_obj(instance, this);
AggregateMetaClass::walk_fields(instance,walk);
int index = get_tag_num( instance );
if ( index == -1 ) {
return Walker::Continue;
}
FieldDescription* field_description = (*_union_fields)[ index ];
ObjectWrapper obj = field_description->build_object(agg_obj);
return field_description->get_meta_class()->walk(obj.get_address(), walk);
}
int main()
{
char key[] = "key1,key2,key3";
char tag[32];
int num = get_tag_num(key,',');
// for(int i=0;i<num+1;i++) {
get_tag_by_index(key,tag,2);
printf("tag %d: %s\n",2,tag);
// }
return 0;
}
FieldDescription* UnionMetaClass::
get_proper_field_description(const Address address,
size_t i) const {
// This used to be an INT. Just to make sure no one really
// tried to get the -1 field assert here.
kernel_assert(i < (unsigned)-10);
// if (i < 0)
// return NULL;
int index = get_tag_num( address );
if ( index > 0 ) {
if (i == 0) {
FieldDescription* field_description = (*_union_fields)[ index ];
return field_description;
}
i--;
}
return(NULL);
}
void UnionMetaClass::initialize( const ObjectWrapper &obj,
InputStream* inputStream ) const {
Address address = obj.get_address();
kernel_assert(obj.get_meta_class() == this);
// debugit("initializing union ",address);
AggregateWrapper agg_obj(address, this);
AggregateMetaClass::initialize( obj, inputStream );
int index = get_tag_num( address );
if (index < 0)
zero_field(address);
else {
FieldDescription* field_description = (*_union_fields)[ index ];
ObjectWrapper field = field_description->build_object(agg_obj);
//Address instance_address = (Address)( ( (Byte*)address ) + field_description->offset );
field.initialize(inputStream);
// field_description->get_meta_class()->initialize( field.get_address() ,inputStream );
}
}
void UnionMetaClass::write( const ObjectWrapper &obj,
OutputStream* outputStream ) const {
Address instance = obj.get_address();
kernel_assert(obj.get_meta_class() == this);
AggregateWrapper agg_obj(instance, this);
AggregateMetaClass::write( obj, outputStream );
int index = get_tag_num( instance );
// if the tag number is not stored in a field that was already
// written out => write out the tag number
if ( _tag_offset == -1 ) {
outputStream->write_unsigned_int( index );
}
if ( index >= 0 ) {
FieldDescription* field_description = (*_union_fields)[ index ];
ObjectWrapper field = field_description->build_object(agg_obj);
outputStream->write( field, false );
}
}
int
display_cs_tags(Tcl_Interp *interp, /* in */
GapIO *io, /* in */
obj_cs *cs) /* in */
{
GAnnotations *annotation; /* annotation structure */
char **tag_types = NULL;
int num_tags;
int tag_pos; /* tag LH position */
int whole_reading = 0; /* if TRUE display entire reading */
int r_pos, r_len; /* reading LH position and length */
int c_num;
int r_num;
GContigs contig;
GReadings reading;
int x1, x2;
int tag_num = 0;
/* get template display tag list */
/* HACK - put in registration structure ? */
if (TCL_ERROR == Tcl_VarEval(interp, "GetDefaultTags ", "CONTIG_SEL.TAGS ", NULL)) {
printf("ERROR %s\n", Tcl_GetStringResult(interp));
}
if (SetActiveTags2(Tcl_GetStringResult(interp), &num_tags, &tag_types) == -1) {
return -1;
}
if (num_tags == 0) {
if (tag_types)
Tcl_Free((char *)tag_types);
return 0;
}
for (c_num = 1; c_num <= NumContigs(io); c_num++) {
/* reading tags */
contig_read(io, c_num, contig);
for (r_num=contig.left; r_num; r_num=reading.right) {
gel_read(io, r_num, reading);
/* like vtagget except also returns tag_num */
annotation = get_tag_num(io, r_num, num_tags,
tag_types, &tag_num);
while (annotation && annotation != (GAnnotations *)-1){
/* if reading has been complemented, find new pos of tag */
if (reading.sense) {
tag_pos = (reading.position - reading.start) +
(reading.length - annotation->position -
annotation->length + 1);
tag_pos = find_position_in_DB(io, c_num, tag_pos);
} else {
tag_pos = annotation->position - (reading.start -
reading.position +1);
tag_pos = find_position_in_DB(io, c_num, tag_pos);
} /* end if */
/*
printf("num %d tag_pos %d len %d \n",
c_num, tag_pos, annotation->length);
*/
SetReadingPosLen(whole_reading, io, r_num, &r_pos, &r_len);
r_pos = find_position_in_DB(io, c_num, r_pos);
CalcXCoords(tag_pos, annotation->length, &x1, &x2);
/* clip tag at cutoff data */
x1 = MAX(x1, r_pos);
x2 = MIN(x2, r_pos + r_len - 1);
if (x2 >= x1) {
DrawCSTags(interp, x1, x2, tag_num, annotation,
cs->tag.offset,
cs->hori, cs->tag.width, c_num, r_num);
}
annotation = get_tag_num(io, 0, num_tags, tag_types, &tag_num);
} /* end while */
} /* end for each reading */
/* consensus tags */
annotation = get_tag_num(io, -c_num, num_tags, tag_types, &tag_num);
while (annotation && annotation != (GAnnotations *)-1){
tag_pos = annotation->position;
tag_pos = find_position_in_DB(io, c_num, tag_pos);
CalcXCoords(tag_pos, annotation->length, &x1, &x2);
DrawCSTags(interp, x1, x2, tag_num, annotation, cs->tag.offset+20,
cs->hori, cs->tag.width, c_num, 0);
annotation = get_tag_num(io, 0, num_tags, tag_types, &tag_num);
} /* end while */
} /* end for each contig */
if (tag_types)
Tcl_Free((char *)tag_types);
return 0;
}
size_t UnionMetaClass::get_proper_field_count(const Address address) const {
int index = get_tag_num( address );
if ( index >= 0 )
return(1);
return(0); // -1 is used to mark an empty union
}
