static DiaObject *
image_load(ObjectNode obj_node, int version, DiaContext *ctx)
{
Image *image;
Element *elem;
DiaObject *obj;
int i;
AttributeNode attr;
char *diafile_dir;
image = g_malloc0(sizeof(Image));
elem = &image->element;
obj = &elem->object;
obj->type = &image_type;
obj->ops = &image_ops;
element_load(elem, obj_node, ctx);
image->border_width = 0.1;
attr = object_find_attribute(obj_node, "border_width");
if (attr != NULL)
image->border_width = data_real(attribute_first_data(attr), ctx);
image->border_color = color_black;
attr = object_find_attribute(obj_node, "border_color");
if (attr != NULL)
data_color(attribute_first_data(attr), &image->border_color, ctx);
image->line_style = LINESTYLE_SOLID;
attr = object_find_attribute(obj_node, "line_style");
if (attr != NULL)
image->line_style = data_enum(attribute_first_data(attr), ctx);
image->dashlength = DEFAULT_LINESTYLE_DASHLEN;
attr = object_find_attribute(obj_node, "dashlength");
if (attr != NULL)
image->dashlength = data_real(attribute_first_data(attr), ctx);
image->draw_border = TRUE;
attr = object_find_attribute(obj_node, "draw_border");
if (attr != NULL)
image->draw_border = data_boolean(attribute_first_data(attr), ctx);
image->keep_aspect = TRUE;
attr = object_find_attribute(obj_node, "keep_aspect");
if (attr != NULL)
image->keep_aspect = data_boolean(attribute_first_data(attr), ctx);
attr = object_find_attribute(obj_node, "file");
if (attr != NULL) {
image->file = data_filename(attribute_first_data(attr), ctx);
} else {
image->file = g_strdup("");
}
element_init(elem, 8, NUM_CONNECTIONS);
for (i=0;i<NUM_CONNECTIONS;i++) {
obj->connections[i] = &image->connections[i];
image->connections[i].object = obj;
image->connections[i].connected = NULL;
}
image->connections[8].flags = CP_FLAGS_MAIN;
image->image = NULL;
if (strcmp(image->file, "")!=0) {
diafile_dir = get_directory(dia_context_get_filename(ctx));
if (g_path_is_absolute(image->file)) { /* Absolute pathname */
image->image = dia_image_load(image->file);
if (image->image == NULL) {
/* Not found as abs path, try in same dir as diagram. */
char *temp_string;
const char *image_file_name = image->file;
const char *psep;
psep = strrchr(image->file, G_DIR_SEPARATOR);
/* try the other G_OS as well */
if (!psep)
psep = strrchr(image->file, G_DIR_SEPARATOR == '/' ? '\\' : '/');
if (psep)
image_file_name = psep + 1;
temp_string = g_build_filename(diafile_dir, image_file_name, NULL);
image->image = dia_image_load(temp_string);
if (image->image != NULL) {
/* Found file in same dir as diagram. */
message_warning(_("The image file '%s' was not found in the specified directory.\n"
"Using the file '%s' instead.\n"), image->file, temp_string);
g_free(image->file);
image->file = temp_string;
} else {
g_free(temp_string);
image->image = dia_image_load((char *)image_file_name);
if (image->image != NULL) {
char *tmp;
/* Found file in current dir. */
message_warning(_("The image file '%s' was not found in the specified directory.\n"
"Using the file '%s' instead.\n"), image->file, image_file_name);
tmp = image->file;
image->file = g_strdup(image_file_name);
g_free(tmp);
} else {
message_warning(_("The image file '%s' was not found.\n"),
image_file_name);
}
}
}
} else { /* Relative pathname: */
char *temp_string;
temp_string = g_build_filename (diafile_dir, image->file, NULL);
image->image = dia_image_load(temp_string);
if (image->image != NULL) {
/* Found file in same dir as diagram. */
g_free(image->file);
image->file = temp_string;
} else {
g_free(temp_string);
image->image = dia_image_load(image->file);
if (image->image == NULL) {
/* Didn't find file in current dir. */
message_warning(_("The image file '%s' was not found.\n"),
image->file);
}
}
}
g_free(diafile_dir);
}
/* if we don't have an image yet try to recover it from inlined data */
if (!image->image) {
attr = object_find_attribute(obj_node, "pixbuf");
if (attr != NULL) {
GdkPixbuf *pixbuf = data_pixbuf (attribute_first_data(attr));
if (pixbuf) {
image->image = dia_image_new_from_pixbuf (pixbuf);
image->inline_data = TRUE; /* avoid loosing it */
/* FIXME: should we reset the filename? */
g_object_unref (pixbuf);
}
}
}
/* update mtime */
{
struct stat st;
if (g_stat (image->file, &st) != 0)
st.st_mtime = 0;
image->mtime = st.st_mtime;
}
image_update_data(image);
return &image->element.object;
}
static DiaObject *
image_load(ObjectNode obj_node, int version, const char *filename)
{
EImage *image;
Element *elem;
DiaObject *obj;
int i;
AttributeNode attr;
char *diafile_dir;
Diagram *dia;
GList *list;
image = g_malloc0(sizeof(EImage));
elem = &image->element;
obj = &elem->object;
obj->type = &eimage_type;
obj->ops = &eimage_ops;
element_load(elem, obj_node);
image->border_width = 0.1;
attr = object_find_attribute(obj_node, "border_width");
if (attr != NULL)
image->border_width = data_real( attribute_first_data(attr) );
image->border_color = color_black;
attr = object_find_attribute(obj_node, "border_color");
if (attr != NULL)
data_color(attribute_first_data(attr), &image->border_color);
image->line_style = LINESTYLE_SOLID;
attr = object_find_attribute(obj_node, "line_style");
if (attr != NULL)
image->line_style = data_enum( attribute_first_data(attr) );
image->dashlength = DEFAULT_LINESTYLE_DASHLEN;
attr = object_find_attribute(obj_node, "dashlength");
if (attr != NULL)
image->dashlength = data_real(attribute_first_data(attr));
image->draw_border = TRUE;
attr = object_find_attribute(obj_node, "draw_border");
if (attr != NULL)
image->draw_border = data_boolean( attribute_first_data(attr) );
image->keep_aspect = TRUE;
attr = object_find_attribute(obj_node, "keep_aspect");
if (attr != NULL)
image->keep_aspect = data_boolean( attribute_first_data(attr) );
image->keep_orig_aspect = TRUE;
attr = object_find_attribute(obj_node, "keep_orig_aspect");
if (attr != NULL)
image->keep_orig_aspect = data_boolean( attribute_first_data(attr) );
attr = object_find_attribute(obj_node, "file");
if (attr != NULL) {
image->file = data_filename( attribute_first_data(attr) );
} else {
image->file = g_strdup("");
}
attr = object_find_attribute(obj_node, "embed_id");
if (attr) {
image->embed_id =
dtree_conv_longname_from_xml(data_string(attribute_first_data(attr)));
} else {
image->embed_id = get_default_embed_id("embed_image");
}
register_embed_id(image->embed_id);
element_init(elem, 8, NUM_CONNECTIONS);
for (i=0;i<NUM_CONNECTIONS;i++) {
obj->connections[i] = &image->connections[i];
image->connections[i].object = obj;
image->connections[i].connected = NULL;
}
image->connections[8].flags = CP_FLAGS_MAIN;
image->image = NULL;
if (strcmp(image->file, "")!=0) {
diafile_dir = get_directory(filename);
if (g_path_is_absolute(image->file)) { /* Absolute pathname */
image->image = dia_image_load(image->file);
if (image->image == NULL) {
/* Not found as abs path, try in same dir as diagram. */
char *temp_string;
const char *image_file_name = image->file;
const char *psep;
psep = strrchr(image->file, G_DIR_SEPARATOR);
/* try the other G_OS as well */
if (!psep)
psep = strrchr(image->file, G_DIR_SEPARATOR == '/' ? '\\' : '/');
if (psep)
image_file_name = psep + 1;
temp_string = g_build_filename(diafile_dir, image_file_name, NULL);
image->image = dia_image_load(temp_string);
if (image->image != NULL) {
/* Found file in same dir as diagram. */
message_warning(_("The image file '%s' was not found in that directory.\n"
"Using the file '%s' instead\n"), image->file, temp_string);
g_free(image->file);
image->file = temp_string;
} else {
g_free(temp_string);
image->image = dia_image_load((char *)image_file_name);
if (image->image != NULL) {
char *tmp;
/* Found file in current dir. */
message_warning(_("The image file '%s' was not found in that directory.\n"
"Using the file '%s' instead\n"), image->file, image_file_name);
tmp = image->file;
image->file = g_strdup(image_file_name);
g_free(tmp);
} else {
message_warning(_("The image file '%s' was not found.\n"),
image_file_name);
}
}
}
} else { /* Relative pathname: */
char *temp_string;
temp_string = g_build_filename (diafile_dir, image->file, NULL);
image->image = dia_image_load(temp_string);
if (image->image != NULL) {
/* Found file in same dir as diagram. */
g_free(image->file);
image->file = temp_string;
} else {
g_free(temp_string);
image->image = dia_image_load(image->file);
if (image->image == NULL) {
/* Didn't find file in current dir. */
message_warning(_("The image file '%s' was not found.\n"),
image->file);
}
}
}
g_free(diafile_dir);
}
/* update mtime */
{
struct stat st;
if (g_stat (image->file, &st) != 0)
st.st_mtime = 0;
image->mtime = st.st_mtime;
}
image_update_data(image);
obj->node = NULL;
list = dia_open_diagrams();
while (list != NULL) {
dia = (Diagram *)list->data;
if (!g_strcmp0(dia->filename,filename)) {
obj->node = dtree_set_data_by_longname(DIA_DIAGRAM_DATA(dia)->dtree,
image->embed_id,&image->element.object);
}
list = g_list_next(list);
}
return &image->element.object;
}
int main(int argc, const char **argv) {
Parameters par(argc, argv);
#ifdef HHSEARCH
HHsearch::ProcessAllArguments(par);
#elif HHALIGN
HHalign::ProcessAllArguments(par);
#else
HHblits::ProcessAllArguments(par);
#endif
// hhblits_mpi will be parallelized with openmpi, no other parallelization
par.threads = 1;
#ifdef OPENMP
omp_set_num_threads(1);
#endif
std::string data_filename(par.infile);
data_filename.append(".ffdata");
std::string index_filename(par.infile);
index_filename.append(".ffindex");
FFindexDatabase reader(data_filename.c_str(), index_filename.c_str(), false);
reader.ensureLinearAccess();
int mpq_status = MPQ_Init(argc, argv, reader.db_index->n_entries);
if (mpq_status == MPQ_SUCCESS) {
if (MPQ_rank == MPQ_MASTER) {
MPQ_Master(1);
} else {
std::vector<OutputFFIndex> outputDatabases;
makeOutputFFIndex(par.outfile, MPQ_rank, &HHblits::writeHHRFile,
outputDatabases);
makeOutputFFIndex(par.scorefile, MPQ_rank, &HHblits::writeScoresFile,
outputDatabases);
makeOutputFFIndex(par.pairwisealisfile, MPQ_rank,
&HHblits::writePairwiseAlisFile, outputDatabases);
makeOutputFFIndex(par.alitabfile, MPQ_rank, &HHblits::writeAlitabFile,
outputDatabases);
makeOutputFFIndex(par.psifile, MPQ_rank, &HHblits::writePsiFile,
outputDatabases);
makeOutputFFIndex(par.hhmfile, MPQ_rank, &HHblits::writeHMMFile,
outputDatabases);
makeOutputFFIndex(par.alnfile, MPQ_rank, &HHblits::writeA3MFile,
outputDatabases);
makeOutputFFIndex(par.matrices_output_file, MPQ_rank, &HHblits::writeMatricesFile,
outputDatabases);
makeOutputFFIndex(par.m8file, MPQ_rank, &HHblits::writeM8,
outputDatabases);
std::vector<HHblitsDatabase*> databases;
#ifdef HHSEARCH
HHsearch::prepareDatabases(par, databases);
HHblits app(par, databases);
#elif HHalign
HHalign app(par);
#else
HHblits::prepareDatabases(par, databases);
HHblits app(par, databases);
#endif
HHblits_MPQ_Wrapper wrapper(reader.db_data, reader.db_index, app, outputDatabases);
MPQ_Worker(payload, &wrapper);
for (size_t i = 0; i < outputDatabases.size(); i++) {
outputDatabases[i].close();
}
}
MPI_Barrier(MPI_COMM_WORLD);
if (MPQ_rank == MPQ_MASTER) {
merge_splits(par.outfile);
merge_splits(par.scorefile);
merge_splits(par.pairwisealisfile);
merge_splits(par.alitabfile);
merge_splits(par.psifile);
merge_splits(par.hhmfile);
merge_splits(par.alnfile);
merge_splits(par.matrices_output_file);
merge_splits(par.m8file);
}
} else {
if (mpq_status == MPQ_ERROR_NO_WORKERS) {
fprintf(stderr, "MPQ_Init: Needs at least one worker process.\n");
exit(EXIT_FAILURE);
}
}
MPI_Finalize();
return EXIT_SUCCESS;
}
