static void xml_showgthgenomicinformation(GthSA *sa,
GthInput *input,
unsigned int indentlevel,
GtFile *outfp)
{
gt_assert(gth_sa_gen_file_num(sa) != GT_UNDEF_ULONG);
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<gDNA_segment>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<template temp_file=\"%s\" temp_id=\"%s\" "
"temp_strand=\"%c\" temp_description=\"",
gth_input_get_genomic_filename(input,
gth_sa_gen_file_num(sa)),
gth_sa_gen_id(sa),
gth_sa_gen_strand_char(sa));
gth_input_echo_genomic_description(input, gth_sa_gen_file_num(sa),
gth_sa_gen_seq_num(sa), outfp);
gt_file_xprintf(outfp, "\">\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<position start=\"%lu\" stop=\"%lu\"/>\n",
gth_sa_gen_dp_start_show(sa),
gth_sa_gen_dp_end_show(sa));
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</template>\n");
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</gDNA_segment>\n");
}
static bool cluster_is_consistent(GtArray *pgls)
{
GtUword i, j, maxright = GT_UNDEF_UWORD, gen_file_num = GT_UNDEF_UWORD;
GthPGL *pgl;
bool strandsign = GT_UNDEF_BOOL;
GthSA *sa;
GtRange range;
for (i = 0; i < gt_array_size(pgls); i++) {
pgl = *(GthPGL**) gt_array_get(pgls, i);
for (j = 0; j < gt_array_size(pgl->alignments); j++) {
sa = *(GthSA**) gt_array_get(pgl->alignments, j);
if (j == 0) {
/* save genomic file number of this cluster */
gen_file_num = gth_sa_gen_file_num(sa);
/* save strand sign of this cluster */
strandsign = gth_sa_gen_strand_forward(sa);
/* set maxright to right border of first SA */
range = gth_sa_range_forward(sa);
maxright = range.end;
}
else {
/* check if all genomic file numbers are the same */
if (gth_sa_gen_file_num(sa) != gen_file_num)
return false;
/* check if all strand signs of this cluster are equal */
if (gth_sa_gen_strand_forward(sa) != strandsign)
return false;
/* check for cluster condition */
range = gth_sa_range_forward(sa);
if (range.start > maxright)
return false;
if (range.end > maxright)
maxright = range.end;
}
}
}
return true;
}
static void saveSAtoPGLs(GtUword *gen_file_num, GtUword *maxright,
GtUword *currentPGLindex, GtArray *pgls,
GthSA *sa)
{
GtRange range;
/* in this case save SA */
range = gth_sa_range_forward(sa);
if ((*gen_file_num == GT_UNDEF_UWORD) ||
(gth_sa_gen_file_num(sa) != *gen_file_num) ||
(range.start > *maxright)) {
storeSAinnewPGL(pgls, currentPGLindex, sa);
*gen_file_num = gth_sa_gen_file_num(sa);
*maxright = range.end;
}
else {
storeSAincurrentPGL(pgls, *currentPGLindex, sa);
if (range.end > *maxright)
*maxright = range.end;
}
}
static void showgthgenomicinformation(GthSA *sa, GthInput *input,
bool showseqnums, GtFile *outfp)
{
gt_assert(gth_sa_gen_file_num(sa) != GT_UNDEF_UWORD);
gt_file_xprintf(outfp, "Genomic Template: file=%s, strand=%c, from="GT_WU", "
"to="GT_WU", description=",
gth_input_get_genomic_filename(input,
gth_sa_gen_file_num(sa)),
gth_sa_gen_strand_char(sa),
gth_sa_gen_dp_start_show(sa),
gth_sa_gen_dp_end_show(sa));
gth_sa_echo_genomic_description(sa, input, outfp);
if (showseqnums)
gt_file_xprintf(outfp, ", seqnum="GT_WU"", gth_sa_gen_seq_num(sa));
gt_file_xfputc('\n', outfp);
gt_file_xfputc('\n', outfp);
}
static void showgenomicfilename(GthSA *sa, GthInput *input,
unsigned int indentlevel, GtFile *outfp)
{
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomicfile>\n");
indentlevel++;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomicfilename>%s</genomicfilename>\n",
gth_input_get_genomic_filename(input,
gth_sa_gen_file_num(sa)));
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "<genomicfilehash>%s</genomicfilehash>\n",
GTH_UNDEFINED_HASH);
indentlevel--;
gth_indent(outfp, indentlevel);
gt_file_xprintf(outfp, "</genomicfile>\n");
}
GtUword gth_sa_get_alignment_lines(const GthSA *sa,
unsigned char **first_line,
unsigned char **second_line,
unsigned char **third_line,
GtUword translationtable,
GthInput *input)
{
GtUword genomicstartcutoff, genomicendcutoff, genomictotalcutoff,
referencestartcutoff, referenceendcutoff, referencetotalcutoff;
GT_UNUSED bool reverse_subject_pos = false;
gt_assert(sa && first_line && second_line && third_line && input);
/* only for cosmetic reasons */
genomicstartcutoff = gth_sa_genomiccutoff_start(sa);
genomicendcutoff = gth_sa_genomiccutoff_end(sa);
genomictotalcutoff = genomicstartcutoff + genomicendcutoff;
referencestartcutoff = gth_sa_referencecutoff_start(sa);
referenceendcutoff = gth_sa_referencecutoff_end(sa);
referencetotalcutoff = referencestartcutoff + referenceendcutoff;
/* sequences */
unsigned char *gen_seq_orig, *ref_seq_orig;
GtUword cols = 0;
GthSeqCon *ref_seq_con;
/* make sure that the correct files are loaded */
gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
ref_seq_con = gth_input_current_ref_seq_con(input);
/* If the reverse complement of the genomic DNA is considered, this
opition is needed for correct output of the genomic sequence positions
by the function showalignmentgeneric() */
if (!gth_sa_gen_strand_forward(sa))
reverse_subject_pos = true;
/* get genomic sequence */
gen_seq_orig = (unsigned char*)
gth_input_original_genomic_sequence(input, gth_sa_gen_file_num(sa),
gth_sa_gen_strand_forward(sa))
+ gth_sa_gen_dp_start(sa);
/* get reference sequence */
if (gth_sa_ref_strand_forward(sa)) {
ref_seq_orig =
gth_seq_con_get_orig_seq(ref_seq_con, gth_sa_ref_seq_num(sa));
}
else {
ref_seq_orig =
gth_seq_con_get_orig_seq_rc(ref_seq_con, gth_sa_ref_seq_num(sa));
}
switch (gth_sa_alphatype(sa)) {
case DNA_ALPHA:
/* compute the two alignment lines */
cols = gthfillthetwoalignmentlines(first_line,
second_line,
gen_seq_orig +
genomicstartcutoff,
gth_sa_gen_dp_length(sa) -
genomictotalcutoff,
ref_seq_orig +
referencestartcutoff,
gth_sa_ref_total_length(sa) -
referencetotalcutoff,
gth_sa_get_editoperations(sa),
gth_sa_get_editoperations_length(sa),
0, /* linewidth not important here */
0, /* no short introns here */
NULL,/* therefore no shortintroninfo */
gth_sa_indelcount(sa));
*third_line = NULL;
break;
case PROTEIN_ALPHA:
/* compute the three alignment lines */
cols = gthfillthethreealignmentlines(first_line,
second_line,
third_line,
gth_sa_get_editoperations(sa),
gth_sa_get_editoperations_length(sa),
gth_sa_indelcount(sa),
gen_seq_orig +
genomicstartcutoff,
gth_sa_gen_dp_length(sa) -
genomictotalcutoff,
ref_seq_orig +
referencestartcutoff,
gth_sa_ref_total_length(sa) -
referencetotalcutoff,
translationtable);
break;
default: gt_assert(0);
}
return cols;
}
