static int write_trailer(AVFormatContext *s)
{
int i;
write_tags(s->pb, s->metadata);
for (i = 0; i < s->nb_streams; i++) {
put_tag(s->pb, ID_STREAM);
put_byte(s->pb, '\n');
write_tags(s->pb, s->streams[i]->metadata);
}
for (i = 0; i < s->nb_chapters; i++) {
AVChapter *ch = s->chapters[i];
put_tag(s->pb, ID_CHAPTER);
put_byte(s->pb, '\n');
url_fprintf(s->pb, "TIMEBASE=%d/%d\n", ch->time_base.num, ch->time_base.den);
url_fprintf(s->pb, "START=%"PRId64"\n", ch->start);
url_fprintf(s->pb, "END=%"PRId64"\n", ch->end);
write_tags(s->pb, ch->metadata);
}
put_flush_packet(s->pb);
return 0;
}
ErrorCode WriteVtk::write_file(const char *file_name,
const bool overwrite,
const FileOptions& opts,
const EntityHandle *output_list,
const int num_sets,
const std::vector<std::string>& /* qa_list */,
const Tag* tag_list,
int num_tags,
int /* export_dimension */)
{
ErrorCode rval;
// Get precision for node coordinates
int precision;
if (MB_SUCCESS != opts.get_int_option("PRECISION", precision))
precision = DEFAULT_PRECISION;
if (MB_SUCCESS == opts.get_null_option("STRICT"))
mStrict = true;
else if (MB_SUCCESS == opts.get_null_option("RELAXED"))
mStrict = false;
else
mStrict = DEFAULT_STRICT;
// Get entities to write
Range nodes, elems;
rval = gather_mesh(output_list, num_sets, nodes, elems);
if (MB_SUCCESS != rval)
return rval;
// Honor overwrite flag
if (!overwrite) {
rval = writeTool->check_doesnt_exist(file_name);
if (MB_SUCCESS != rval)
return rval;
}
// Create file
std::ofstream file(file_name);
if (!file) {
MB_SET_ERR(MB_FILE_WRITE_ERROR, "Could not open file: " << file_name);
}
file.precision(precision);
// Write file
if ((rval = write_header(file )) != MB_SUCCESS ||
(rval = write_nodes( file, nodes )) != MB_SUCCESS ||
(rval = write_elems( file, nodes, elems)) != MB_SUCCESS ||
(rval = write_tags ( file, true, nodes, tag_list, num_tags)) != MB_SUCCESS ||
(rval = write_tags ( file, false, elems, tag_list, num_tags)) != MB_SUCCESS) {
file.close();
remove(file_name);
return rval;
}
return MB_SUCCESS;
}
void relation(const osmium::Relation& relation) {
if (m_write_change_ops) {
open_close_op_tag(relation.visible() ? (relation.version() == 1 ? operation::op_create : operation::op_modify) : operation::op_delete);
}
write_prefix();
m_out += "<relation";
write_meta(relation);
if (relation.tags().empty() && relation.members().empty()) {
m_out += "/>\n";
return;
}
m_out += ">\n";
for (const auto& member : relation.members()) {
write_prefix();
m_out += " <member type=\"";
m_out += item_type_to_name(member.type());
oprintf(m_out, "\" ref=\"%" PRId64 "\" role=\"", member.ref());
xml_string(m_out, member.role());
m_out += "\"/>\n";
}
write_tags(relation.tags());
write_prefix();
m_out += "</relation>\n";
}
void way(const osmium::Way& way) {
if (m_write_change_ops) {
open_close_op_tag(way.visible() ? (way.version() == 1 ? operation::op_create : operation::op_modify) : operation::op_delete);
}
write_prefix();
m_out += "<way";
write_meta(way);
if (way.tags().empty() && way.nodes().empty()) {
m_out += "/>\n";
return;
}
m_out += ">\n";
for (const auto& node_ref : way.nodes()) {
write_prefix();
oprintf(m_out, " <nd ref=\"%" PRId64 "\"/>\n", node_ref.ref());
}
write_tags(way.tags());
write_prefix();
m_out += "</way>\n";
}
void node(const osmium::Node& node) {
if (m_write_change_ops) {
open_close_op_tag(node.visible() ? (node.version() == 1 ? operation::op_create : operation::op_modify) : operation::op_delete);
}
write_prefix();
m_out += "<node";
write_meta(node);
if (node.location()) {
m_out += " lat=\"";
osmium::util::double2string(std::back_inserter(m_out), node.location().lat_without_check(), 7);
m_out += "\" lon=\"";
osmium::util::double2string(std::back_inserter(m_out), node.location().lon_without_check(), 7);
m_out += "\"";
}
if (node.tags().empty()) {
m_out += "/>\n";
return;
}
m_out += ">\n";
write_tags(node.tags());
write_prefix();
m_out += "</node>\n";
}
static int write_trailer(AVFormatContext *s)
{
int i;
write_tags(s->pb, s->metadata);
for (i = 0; i < s->nb_streams; i++) {
avio_write(s->pb, ID_STREAM, sizeof(ID_STREAM) - 1);
avio_w8(s->pb, '\n');
write_tags(s->pb, s->streams[i]->metadata);
}
for (i = 0; i < s->nb_chapters; i++) {
AVChapter *ch = s->chapters[i];
avio_write(s->pb, ID_CHAPTER, sizeof(ID_CHAPTER) - 1);
avio_w8(s->pb, '\n');
avio_printf(s->pb, "TIMEBASE=%d/%d\n", ch->time_base.num, ch->time_base.den);
avio_printf(s->pb, "START=%"PRId64"\n", ch->start);
avio_printf(s->pb, "END=%"PRId64"\n", ch->end);
write_tags(s->pb, ch->metadata);
}
return 0;
}
void changeset(const osmium::Changeset& changeset) {
write_prefix();
m_out += "<changeset";
oprintf(m_out, " id=\"%" PRId32 "\"", changeset.id());
if (changeset.created_at()) {
m_out += " created_at=\"";
m_out += changeset.created_at().to_iso();
m_out += "\"";
}
oprintf(m_out, " num_changes=\"%" PRId32 "\"", changeset.num_changes());
if (changeset.closed_at()) {
m_out += " closed_at=\"";
m_out += changeset.closed_at().to_iso();
m_out += "\" open=\"false\"";
} else {
m_out += " open=\"true\"";
}
if (changeset.bounds()) {
oprintf(m_out, " min_lon=\"%.7f\"", changeset.bounds().bottom_left().lon_without_check());
oprintf(m_out, " min_lat=\"%.7f\"", changeset.bounds().bottom_left().lat_without_check());
oprintf(m_out, " max_lon=\"%.7f\"", changeset.bounds().top_right().lon_without_check());
oprintf(m_out, " max_lat=\"%.7f\"", changeset.bounds().top_right().lat_without_check());
}
if (!changeset.user_is_anonymous()) {
m_out += " user=\"";
xml_string(m_out, changeset.user());
oprintf(m_out, "\" uid=\"%d\"", changeset.uid());
}
if (changeset.tags().empty()) {
m_out += "/>\n";
return;
}
m_out += ">\n";
write_tags(changeset.tags());
write_prefix();
m_out += "</changeset>\n";
}
void relation(const osmium::Relation& relation) {
m_out << "r";
write_meta(relation);
m_out << " M";
int n=0;
for (const auto& member : relation.members()) {
if (n++ != 0) {
m_out << ",";
}
m_out << item_type_to_char(member.type())
<< member.ref()
<< "!"
<< member.role();
}
write_tags(relation.tags());
m_out << "\n";
::write(this->fd(), m_out.str().c_str(), m_out.str().size());
m_out.str("");
}
char
load(ImlibImage * im, ImlibProgressFunction progress,
char progress_granularity, char immediate_load)
{
ImlibLoader *loader;
lopt opt;
int res;
struct stat st;
assert(im);
if (stat(im->real_file, &st) < 0)
return 0;
if (!get_options(&opt, im))
return 0;
if (!get_loader(&opt, &loader))
goto fail_context;
if (loader)
{
char *ofile, tmp[] = "/tmp/imlib2_loader_id3-XXXXXX";
int dest;
if ((dest = mkstemp(tmp)) < 0)
{
fprintf(stderr, "Unable to create a temporary file\n");
goto fail_context;
}
res = extract_pic(id3_tag_get_frame(opt.ctx->tag, opt.index - 1), dest);
close(dest);
if (!res)
{
unlink(tmp);
goto fail_context;
}
ofile = im->real_file;
im->real_file = strdup(tmp);
res = loader->load(im, progress, progress_granularity, immediate_load);
free(im->real_file);
im->real_file = ofile;
unlink(tmp);
}
else
{
/* The tag actually provides a image url rather than image data.
* Practically, dunno if such a tag exists on earth :)
* Here's the code anyway...
*/
union id3_field *field;
id3_length_t length;
char const *data;
char *url, *file, *ofile;
field = id3_frame_field
(id3_tag_get_frame(opt.ctx->tag, opt.index - 1), 4);
data = (char const *)id3_field_getbinarydata(field, &length);
if (!data || !length)
{
fprintf(stderr, "No link image URL present\n");
goto fail_context;
}
url = (char *)malloc((length + 1) * sizeof(char));
strncpy(url, data, length);
url[length] = '\0';
file = (strncmp(url, "file://", 7) ? url : url + 7);
if (!(loader = __imlib_FindBestLoaderForFile(file, 0)))
{
fprintf(stderr, "No loader found for file %s\n", file);
free(url);
goto fail_context;
}
ofile = im->real_file;
im->real_file = file;
res = loader->load(im, progress, progress_granularity, immediate_load);
if (!im->loader)
__imlib_AttachTag(im, "id3-link-url", 0, url, destructor_data);
else
free(url);
im->real_file = ofile;
}
if (!im->loader)
write_tags(im, &opt);
#ifdef DEBUG
if (!im->loader)
{
ImlibImageTag *cur = im->tags;
fprintf(stderr, "Tags for file %s:\n", im->file);
while (cur)
{
fprintf(stderr, "\t%s: (%d) %s\n", cur->key,
cur->val, (char *)cur->data);
cur = cur->next;
}
}
#endif
context_delref(opt.ctx);
return res;
fail_context:
context_delref(opt.ctx);
return 0;
}
int
find_repeats(GapIO *io,
int handle, /*del */
int mode,
int min_match,
int mask,
float percd, /* del */
int num_contigs,
contig_list_t *contig_array,
char *out_name)
{
int *cends, *nends;
int *sav1, *sav2, *sav3, *sav4, *sav5;
char *consensus;
int max_consensus, max_read_length, database_size, number_of_contigs;
int consensus_length, ret, task_mask;
int max_matches;
int i,j;
int num_f_matches, num_r_matches;
Contig_parms *contig_list;
Hidden_params p;
p.min = p.max = p.verbose = p.use_conf = p.qual_val = p.window_len =0;
p.test_mode = 0;
p.start = 0;
p.lwin1 = 0;
p.lcnt1 = 0;
p.rwin1 = 0;
p.rcnt1 = 0;
p.do_it = 0;
max_consensus = maxseq; /* global! */
max_matches = max_consensus / 20;
consensus = NULL;
contig_list = NULL;
cends = nends = sav1 = sav2 = sav3 = sav4 = sav5 = NULL;
if ((cends = (int *)xmalloc(max_consensus * sizeof(int)))==NULL){
goto bail_out;
}
if ((nends = (int *)xmalloc(max_consensus * sizeof(int)))==NULL){
goto bail_out;
}
if ((sav2 = (int *)xmalloc(max_matches * sizeof(int)))==NULL){
goto bail_out;
}
if ((sav4 = (int *)xmalloc(max_matches * sizeof(int)))==NULL){
goto bail_out;
}
if ((sav5 = (int *)xmalloc(max_matches * sizeof(int)))==NULL){
goto bail_out;
}
max_read_length = find_max_gel_len(io, 0, 0);
if ((consensus = (char *)xmalloc(max_consensus * sizeof(char)))==NULL){
goto bail_out;
}
database_size = io_dbsize(io);
number_of_contigs = num_contigs;
if ( ! (contig_list = get_contig_list ( database_size, io,
number_of_contigs, contig_array ))) {
goto bail_out;
}
task_mask = ADDTITLE | NORMALCONSENSUS;
if ( mask == 3 ) task_mask |= MASKING;
consensus_length = 0;
/* printf("TASK mask %d mask %d mode %d\n",task_mask,mask,mode); */
if ( ret = make_consensus ( task_mask, io, consensus, NULL,
contig_list, number_of_contigs,
&consensus_length,
max_read_length,
max_consensus,
p,
consensus_cutoff ) ) {
goto bail_out;
}
ret = repeat_search (
mode, min_match, &sav4, &sav2, &sav5, max_matches,
consensus, consensus_length, &num_f_matches, &num_r_matches );
if( ret < 0 ) {
goto bail_out;
}
/* get the output arrays filled in to fit with old routines!!*/
if ((sav1 = (int *)xmalloc((num_f_matches + num_r_matches + 1) * sizeof(int)))==NULL){
goto bail_out;
}
if ((sav3 = (int *)xmalloc((num_f_matches + num_r_matches + 1) * sizeof(int)))==NULL){
goto bail_out;
}
for ( i=0;i<num_f_matches; i++ ) {
if ( -1 != (j = (contig_listel_from_con_pos ( contig_list, number_of_contigs,
sav2[i] )))) {
sav1[i] = contig_list[j].contig_left_gel;
sav2[i] = sav2[i] + contig_list[j].contig_start - contig_list[j].contig_start_offset - 1;
}
else {
goto bail_out;
}
if ( -1 != (j = (contig_listel_from_con_pos ( contig_list, number_of_contigs,
sav4[i] )))) {
sav3[i] = contig_list[j].contig_left_gel;
sav4[i] = sav4[i] + contig_list[j].contig_start - contig_list[j].contig_start_offset - 1;
}
else {
goto bail_out;
}
}
for ( i=num_f_matches; i<num_f_matches+num_r_matches;i++ ) {
if ( -1 != (j = (contig_listel_from_con_pos ( contig_list, number_of_contigs,
sav2[i] )))) {
sav1[i] = -contig_list[j].contig_left_gel;
sav2[i] = sav2[i] + contig_list[j].contig_start - contig_list[j].contig_start_offset - 1;;
}
else {
goto bail_out;
}
if ( -1 != (j = (contig_listel_from_con_pos ( contig_list, number_of_contigs,
sav4[i] )))) {
sav3[i] = contig_list[j].contig_left_gel;
sav4[i] = sav4[i] + contig_list[j].contig_start - contig_list[j].contig_start_offset - 1;
}
else {
goto bail_out;
}
}
/* end new */
flush2t(io);
/* FIXME write_tags needs arguments changing from f_int to int */
if (out_name) {
write_tags(io, out_name, num_f_matches+num_r_matches, sav1, sav2, sav3, sav4, sav5);
}
plot_rpt(io, num_f_matches+num_r_matches, sav1, sav2, sav3, sav4, sav5);
if ( cends ) xfree(cends);
if ( nends ) xfree(nends);
if ( sav1 ) xfree(sav1);
if ( sav2 ) xfree(sav2);
if ( sav3 ) xfree(sav3);
if ( sav4 ) xfree(sav4);
if ( sav5 ) xfree(sav5);
if ( consensus ) xfree(consensus);
if ( contig_list ) xfree(contig_list);
return 0;
bail_out:
if ( cends ) xfree(cends);
if ( nends ) xfree(nends);
if ( sav1 ) xfree(sav1);
if ( sav2 ) xfree(sav2);
if ( sav3 ) xfree(sav3);
if ( sav4 ) xfree(sav4);
if ( sav5 ) xfree(sav5);
if ( consensus ) xfree(consensus);
if ( contig_list ) xfree(contig_list);
return -1;
} /* end FindRepeats */
