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%{
#include "../dynlibsrc/hsp.h"
#include "sequencestream.h"
%}
%{
#include "hspstream.h"
%func
untyped linear hsp manager to stream
%%
void untyped_LinearHSPmanager_to_Stream(void * lm,Wise2WriteStreamInterface * ws)
{
return typed_LinearHSPmanager_to_Stream((void*)lm,ws);
}
%func
typed linear hsp manager to stream
writes out sequneces first, with query as first
sequence and then each target in turn, and then all the
hsps in turn, only writing down the target name
%%
void typed_LinearHSPmanager_to_Stream(LinearHSPmanager * lm,Wise2WriteStreamInterface * ws)
{
int i,j;
SequenceSet * out;
char buffer[512];
/* assumme that each HSPset has only one target sequence */
out = SequenceSet_alloc_len(lm->len+1);
/* query goes in first */
add_SequenceSet(out,hard_link_Sequence(lm->query));
for(i=0;i<lm->len;i++) {
if( lm->set[i]->len > 0 ) {
if( lm->set[i]->hsp[0]->target == NULL) {
warn("Unable to transport HSP at position %d, as no linked target sequence",i);
} else {
add_SequenceSet(out,hard_link_Sequence(lm->set[i]->hsp[0]->target));
}
}
}
typed_write_SequenceSet_to_Stream(out,ws);
free_SequenceSet(out);
/* now write the hsps */
for(i=0;i<lm->len;i++) {
if( lm->set[i]->len > 0 && lm->set[i]->hsp[0]->target != NULL ) {
for(j=0;j<lm->set[i]->len;j++) {
sprintf(buffer,"%s %d %d %d %d %d\n",
lm->set[i]->hsp[j]->target->name,
lm->set[i]->hsp[j]->query_start,
lm->set[i]->hsp[j]->target_start,
lm->set[i]->hsp[j]->length,
lm->set[i]->hsp[j]->score,
lm->set[i]->hsp[j]->target_reverse);
/* fprintf(stderr,"%s %d %d %d %d %d\n",
lm->set[i]->hsp[j]->target->name,
lm->set[i]->hsp[j]->query_start,
lm->set[i]->hsp[j]->target_start,
lm->set[i]->hsp[j]->length,
lm->set[i]->hsp[j]->score,
lm->set[i]->hsp[j]->target_reverse);
*/
WISE2_WRITE_STRING(buffer,ws);
}
}
}
WISE2_WRITE_STRING("//\n",ws);
}
%func
untyped read
%%
void * untyped_LinearHSPmanager_from_Stream(Wise2ReadStreamInterface * rs)
{
return (void*) typed_LinearHSPmanager_from_Stream(rs);
}
%func
typed linear hsp manager from stream
assummes sequences coming in first, with query as first sequence
and then hsps one after the other
%%
LinearHSPmanager * typed_LinearHSPmanager_from_Stream(Wise2ReadStreamInterface * rs)
{
SequenceSet * set;
LinearHSPmanager * lm;
HSPset * curr;
HSP * h;
int seq_pos;
int dummy;
int i;
char buffer[MAXLINE];
set = typed_SequenceSet_from_Stream(rs);
/*
for(i=0;i<set->len;i++) {
fprintf(stderr,"Got %d, %s with %s\n",i,set->set[i]->name,set->set[i]->desc);
}
*/
lm = LinearHSPmanager_alloc_std();
lm->query = hard_link_Sequence(set->set[0]);
if( set->len == 1 ) {
WISE2_READ_BUFFER(buffer,MAXLINE,rs);
/* should check it is // */
return lm;
}
seq_pos = 1;
curr = HSPset_alloc_std();
add_LinearHSPmanager(lm,curr);
while( WISE2_READ_BUFFER(buffer,MAXLINE,rs) != NULL ) {
auto int k;
auto int temp_len = strlen(set->set[seq_pos]->name);
if( strncmp(buffer,"//",2) == 0 ) {
break;
}
/* is space is because we can have partial matching
at the start of the of an identifier, in particular with
uniprot alternative splice -X names
*/
for(k=0;k < MAXLINE;k++) {
if( isspace(buffer[k]) ) {
buffer[k] = '\0';
break;
}
}
/*fprintf(stderr,"Comparing %s to %s with %d (%d) %d %d\n",buffer,set->set[seq_pos]->name,strncmp(buffer,set->set[seq_pos]->name,temp_len),temp_len,isspace(buffer[temp_len]),(int)(buffer[temp_len]) );
*/
if( strcmp(buffer,set->set[seq_pos]->name) != 0 ) {
seq_pos++;
if( seq_pos >= set->len ) {
warn("Overrun set sequences\n");
break;
}
curr = HSPset_alloc_std();
add_LinearHSPmanager(lm,curr);
if( strncmp(buffer,set->set[seq_pos]->name,temp_len) != 0 ) {
warn("Unable to match hsp name of [%s] to sequence name of %s, skipping\n",buffer,set->set[seq_pos]->name);
continue;
}
}
/* parse this hsp */
h = HSP_alloc();
h->query = hard_link_Sequence(set->set[0]);
h->target = hard_link_Sequence(set->set[seq_pos]);
sscanf(buffer+strlen(set->set[seq_pos]->name)+1,"%d %d %d %d %d",&h->query_start,&h->target_start,&h->length,&h->score,&dummy);
if( dummy == 0 ) {
h->target_reverse = 0;
} else {
h->target_reverse = 1;
}
add_HSPset(curr,h);
}
free_SequenceSet(set);
return lm;
}
%}
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