ThreeStateModel * read_TSM_ThreeStateDB(ThreeStateDB * mdb,int * return_status)
{
ThreeStateModel * tsm;
Protein * pro;
Sequence * seq;
if( mdb->hmm_model_end != -1 && mdb->current_no == mdb->hmm_model_end ) {
*return_status = DB_RETURN_END;
return NULL;
}
mdb->current_no++;
switch( mdb->dbtype ) {
case TSMDB_SINGLE :
*return_status = DB_RETURN_END;
if( mdb->single->rm == NULL ) {
warn("Threestate model without an internal random model!");
mdb->single->rm = hard_link_RandomModel(mdb->rm);
}
return hard_link_ThreeStateModel(mdb->single);
case TSMDB_HMMER1PFAM :
tsm= read_next_TSM_PfamHmmer1DB(mdb->phdb,return_status);
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
return tsm;
case TSMDB_PROTEIN :
if( mdb->seq_cache != NULL ) {
/* just after an open. Should actually use this sequence, and flush the cache */
pro = Protein_from_Sequence(hard_link_Sequence(mdb->seq_cache));
mdb->seq_cache = free_Sequence(mdb->seq_cache);
*return_status = DB_RETURN_OK;
} else {
/* reload a sequence from a database */
seq = reload_SequenceDB(NULL,mdb->sdb,return_status);
/* exit now if error */
if( *return_status == DB_RETURN_ERROR ) {
return NULL; /* might have leaked memory. Ugh! */
}
/* if we get NULL... for the moment, silent flag end */
if( seq == NULL ) {
*return_status = DB_RETURN_END;
return NULL;
}
pro = Protein_from_Sequence(seq);
}
if( pro == NULL ) {
warn("Could not convert sequence to a protein. Exiting!");
*return_status = DB_RETURN_ERROR;
return NULL;
}
/* convert protein to threestatemodel */
tsm = ThreeStateModel_from_half_bit_Sequence(pro,mdb->comp,mdb->rm,mdb->gap,mdb->ext);
if( tsm == NULL ) {
warn("Could not convert protein to threestatemode. Exiting!");
free_Protein(pro);
*return_status = DB_RETURN_ERROR;
return NULL;
}
/* DB status already set by seqdb */
return tsm;
case TSMDB_GENERIC :
tsm = ((*mdb->reload_generic)(mdb,return_status));
if( tsm == NULL ) {
return NULL; /* means end of database */
}
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
return tsm;
default :
warn("Got an unrecognisable tsm db type in read-load");
return NULL;
}
}
boolean build_objects(void)
{
boolean ret = TRUE;
Protein * pro_temp;
SequenceDB * psdb;
startend = threestatemodel_mode_from_string(startend_string);
if( startend == TSM_unknown ) {
warn("String %s was unable to converted into a start/end policy\n",startend_string);
ret = FALSE;
}
if( use_single_dna == TRUE ) {
cdna = read_fasta_file_cDNA(dna_seq_file);
if( cdna == NULL ) {
warn("Could not open single dna sequence in %s",dna_seq_file);
ret = FALSE;
}
} else {
sdb = single_fasta_SequenceDB(dna_seq_file);
if( sdb == NULL ) {
warn("Could not build a sequence database on %s",dna_seq_file);
ret = FALSE;
}
}
rm = default_RandomModel();
if( (mat = read_Blast_file_CompMat(matrix_file)) == NULL) {
if( use_tsm == TRUE ) {
info("I could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.",matrix_file);
} else {
warn("Could not read Comparison matrix file in %s",matrix_file);
ret = FALSE;
}
}
if( is_integer_string(gap_str,&gap) == FALSE ) {
warn("Could not get gap string number %s",gap_str);
ret = FALSE;
}
if( is_integer_string(ext_str,&ext) == FALSE ) {
warn("Could not get ext string number %s",ext_str);
ret = FALSE;
}
if( qstart_str != NULL ) {
if( is_integer_string(qstart_str,&qstart) == FALSE || qstart < 0) {
warn("Could not make %s out as query start",qstart);
ret = FALSE;
}
}
if( qend_str != NULL ) {
if( is_integer_string(qend_str,&qend) == FALSE || qend < 0) {
warn("Could not make %s out as query end",qend);
ret = FALSE;
}
}
if( aln_number_str != NULL ) {
if( is_integer_string(aln_number_str,&aln_number) == FALSE || aln_number < 0) {
warn("Weird aln number string %s...\n",aln_number_str);
ret = FALSE;
}
}
if( report_str != NULL ) {
if( is_integer_string(report_str,&report_stagger) == FALSE ) {
warn("Weird report stagger asked for %s",report_str);
ret = FALSE;
}
}
if( use_pfam1 == TRUE ) {
tsmdb = new_PfamHmmer1DB_ThreeStateDB(protein_file);
if( set_search_type_ThreeStateDB(tsmdb,startend_string) == FALSE) {
warn("Unable to set global/local switch on threestatedb");
ret = FALSE;
}
} else if ( use_pfam2 == TRUE ) {
tsmdb = HMMer2_ThreeStateDB(protein_file);
if( set_search_type_ThreeStateDB(tsmdb,startend_string) == FALSE) {
warn("Unable to set global/local switch on threestatedb");
ret = FALSE;
}
} else if ( use_tsm == TRUE) {
/** using a HMM **/
tsm = HMMer2_read_ThreeStateModel(protein_file);
if( tsm == NULL ) {
warn("Could not read hmm from %s\n",protein_file);
ret = FALSE;
} else {
display_char_in_ThreeStateModel(tsm);
if( hmm_name != NULL ) {
if( tsm->name != NULL )
ckfree(tsm->name);
tsm->name = stringalloc(hmm_name);
} else {
if( tsm->name == NULL ) {
tsm->name = stringalloc(protein_file);
}
}
/** have to set start/end **/
set_startend_policy_ThreeStateModel(tsm,startend,15,0.2);
tsmdb = new_single_ThreeStateDB(tsm,rm);
if( tsmdb == NULL ) {
warn("Could not build a threestatemodel database from a single tsm. Weird!");
ret = FALSE;
}
} /* end of else tsm != NULL */
} /* end of else is tsm */
else if( use_single_pro ) {
if( startend != TSM_default && startend != TSM_global && startend != TSM_local ) {
warn("Proteins can only have local/global startend policies set, not %s",startend_string);
ret = FALSE;
}
if( (pro = read_fasta_file_Protein(protein_file)) == NULL ) {
ret = FALSE;
warn("Could not read Protein sequence in %s",protein_file);
} else {
if( qstart != -1 || qend != -1 ) {
if( qstart == -1 )
qstart = 0;
if( qend == -1 )
qend = pro->baseseq->len;
pro_temp = truncate_Protein(pro,qstart-1,qend);
if( pro_temp == NULL ){
ret = FALSE;
} else {
free_Protein(pro);
pro = pro_temp;
}
}
if( startend == TSM_global)
tsm = global_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,-gap,-ext);
else
tsm = ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,-gap,-ext);
if( tsm == NULL ) {
warn("Could not build ThreeStateModel from a single protein sequence...");
ret = FALSE;
} else {
tsmdb = new_single_ThreeStateDB(tsm,rm);
if( tsmdb == NULL ) {
warn("Could not build a threestatemodel database from a single tsm. Weird!");
ret = FALSE;
}
} /* end of could build a TSM */
} /* else is a real protein */
} /* end of else is single protein */
else if (use_db_pro == TRUE ) {
psdb = single_fasta_SequenceDB(protein_file);
tsmdb = new_proteindb_ThreeStateDB(psdb,mat,-gap,-ext);
free_SequenceDB(psdb);
}
else {
warn("No protein input file! Yikes!");
}
/***
if( use_tsm == FALSE ) {
} else {
****/
if( main_block_str != NULL ) {
if( is_integer_string(main_block_str,&main_block) == FALSE ) {
warn("Could not get maximum main_block number %s",main_block_str);
ret = FALSE;
}
}
if( evalue_search_str != NULL && is_double_string(evalue_search_str,&evalue_search_cutoff) == FALSE ) {
warn("Could not convert %s to a double",evalue_search_str);
ret = FALSE;
}
if( is_double_string(search_cutoff_str,&search_cutoff) == FALSE ) {
warn("Could not convert %s to a double",search_cutoff_str);
ret = FALSE;
}
if( is_double_string(subs_string,&subs_error) == FALSE ) {
warn("Could not convert %s to a double",subs_error);
ret = FALSE;
}
if( is_double_string(indel_string,&indel_error) == FALSE ) {
warn("Could not convert %s to a double",indel_error);
ret = FALSE;
}
if( is_double_string(allN_string,&allN) == FALSE ) {
warn("Could not convert %s to a double",allN_string);
ret = FALSE;
}
if( strcmp(null_string,"syn") == 0 ) {
use_syn = TRUE;
} else if ( strcmp(null_string,"flat") == 0 ) {
use_syn = FALSE;
} else {
warn("Cannot interpret [%s] as a null model string\n",null_string);
ret = FALSE;
}
if( alg_str != NULL ) {
alg = alg_estwrap_from_string(alg_str);
} else {
alg_str = "312";
alg = alg_estwrap_from_string(alg_str);
}
if( aln_alg_str != NULL ) {
aln_alg = alg_estwrap_from_string(aln_alg_str);
} else {
/* if it is a protein, don't loop */
if( use_single_pro == TRUE || use_db_pro == TRUE )
aln_alg_str = "333";
else
aln_alg_str = "333L";
aln_alg = alg_estwrap_from_string(aln_alg_str);
}
if( (rm = default_RandomModel()) == NULL) {
warn("Could not make default random model\n");
ret = FALSE;
}
if( (ct = read_CodonTable_file(codon_file)) == NULL) {
ret = FALSE;
warn("Could not read codon table file in %s",codon_file);
}
if( (ofp = openfile(output_file,"W")) == NULL) {
warn("Could not open %s as an output file",output_file);
ret = FALSE;
}
rmd = RandomModelDNA_std();
cps = flat_cDNAParser(indel_error);
cm = flat_CodonMapper(ct);
sprinkle_errors_over_CodonMapper(cm,subs_error);
return ret;
}
ThreeStateModel * indexed_ThreeStateModel_ThreeStateDB(ThreeStateDB * mdb,DataEntry * en)
{
Sequence * seq;
Protein * pro;
ThreeStateModel * tsm;
switch(mdb->dbtype) {
case TSMDB_SINGLE :
return hard_link_ThreeStateModel(mdb->single);
case TSMDB_HMMER1PFAM :
tsm = ThreeStateModel_from_name_PfamHmmer1DB(mdb->phdb,en->name);
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
return tsm;
case TSMDB_PROTEIN :
seq = get_Sequence_from_SequenceDB(mdb->sdb,en);
if( seq == NULL ) {
warn("could not retrieve %s as a sequence from database",en->name);
return NULL;
}
pro = Protein_from_Sequence(seq);
if( pro == NULL ) {
warn("Could not convert sequence to a protein. Exiting!");
return NULL;
}
/* convert protein to threestatemodel */
tsm = ThreeStateModel_from_half_bit_Sequence(pro,mdb->comp,mdb->rm,mdb->gap,mdb->ext);
if( tsm == NULL ) {
warn("Could not convert protein to threestatemode. Exiting!");
free_Protein(pro);
return NULL;
}
free_Protein(pro);
/* DB status already set by seqdb */
return tsm;
case TSMDB_GENERIC :
tsm = ((*mdb->index_generic)(mdb,en));
if( tsm == NULL ) {
return NULL;
}
/* fprintf(stdout,"Setting %d as policy\n",mdb->type); */
set_startend_policy_ThreeStateModel(tsm,mdb->type,30,0.2);
return tsm;
default :
warn("Unknown threestatedb type");
return NULL;
}
warn("Should never get here - in threestatedb reload!");
return NULL;
}
