/* Display information about the currently selected file or folder. */
void
on_info_clicked (GtkToolButton *item)
{
GtkWidget *dialog, *name, *loc, *type, *size, *mod, *access, *treeview;
gchar *file, *location, *modified, *accessed;
GtkTreeSelection *selection;
GtkTreeModel *model;
GtkTreeIter iter;
struct stat st;
gfloat file_size;
gint i;
treeview = glade_xml_get_widget (xml, "treeview");
selection = gtk_tree_view_get_selection (GTK_TREE_VIEW (treeview));
if (gtk_tree_selection_get_selected (selection, &model, &iter))
{
dialog = glade_xml_get_widget (xml, "dialog");
name = glade_xml_get_widget (xml, "name");
loc = glade_xml_get_widget (xml, "filelocation");
type = glade_xml_get_widget (xml, "type");
size = glade_xml_get_widget (xml, "size");
mod = glade_xml_get_widget (xml, "modified");
access = glade_xml_get_widget (xml, "accessed");
gtk_tree_model_get (model, &iter, FILENAME, &file, -1);
/* Set the file name, location and whether it is a file or directory. */
location = path_to_string ();
gtk_label_set_text (GTK_LABEL (name), file);
gtk_label_set_text (GTK_LABEL (loc), location);
file = g_strconcat (location, "/", file, NULL);
if (g_file_test (file, G_FILE_TEST_IS_DIR))
gtk_label_set_text (GTK_LABEL (type), "Directory");
else
gtk_label_set_text (GTK_LABEL (type), "File");
/* Set the file size, last modified date and last accessed date. */
if (g_stat (file, &st) == 0)
{
i = 0;
file_size = (gfloat) st.st_size;
while (file_size >= 1024.0)
{
file_size = file_size / 1024.0;
i++;
}
modified = g_strndup (ctime (&st.st_mtime), strlen (ctime (&st.st_mtime))-1);
accessed = g_strndup (ctime (&st.st_atime), strlen (ctime (&st.st_atime))-1);
gtk_label_set_text (GTK_LABEL (mod), modified);
gtk_label_set_text (GTK_LABEL (access), accessed);
gtk_label_set_text (GTK_LABEL (size),
g_strdup_printf ("%.1f %s", file_size, size_type[i]));
}
gtk_dialog_run (GTK_DIALOG (dialog));
gtk_widget_hide (dialog);
}
}
char *HIDGetDataItem(const HIDData_t *hiddata, usage_tables_t *utab)
{
/* TODO: not thread safe! */
static char itemPath[128];
path_to_string(itemPath, sizeof(itemPath), &hiddata->Path, utab);
return itemPath;
}
/* When a row is activated, either move to the desired location or show
* more information if the file is not a directory. */
void
on_row_activated (GtkTreeView *treeview,
GtkTreePath *path,
GtkTreeViewColumn *column)
{
GtkTreeModel *model;
GtkTreeIter iter;
gchar *file;
model = gtk_tree_view_get_model (treeview);
if (gtk_tree_model_get_iter (model, &iter, path))
{
gtk_tree_model_get (model, &iter, FILENAME, &file, -1);
/* Move to the parent directory. */
if (g_ascii_strcasecmp ("..", file) == 0)
{
GList *last = g_list_last (current_path);
store_history ();
current_path = g_list_remove_link (current_path, last);
g_list_free_1 (last);
populate_tree_model (GTK_WIDGET (treeview));
}
/* Move to the chosen directory or show more information about the file. */
else
{
gchar *location = path_to_string ();
if (g_file_test (g_strconcat (location, "/", file, NULL), G_FILE_TEST_IS_DIR))
{
store_history ();
current_path = g_list_append (current_path, file);
populate_tree_model (GTK_WIDGET (treeview));
}
else
on_info_clicked (NULL);
}
}
}
void Deconstructor::sb2vcf(string outfile){
Header h;
h.set_date();
h.set_source("VG");
h.set_reference("");
h.set_version("VCF4.2");
cout << h << endl;
// for each superbubble:
// Fill out a vcflib Variant
// Check if it is masked by an input vcf
// if not, print it to stdout
map<id_t, vcflib::Variant> node_to_var;
vcflib::VariantCallFile mask;
if (!mask_file.empty()){
//node_to_var = my_vg->get_node_to_variant(mask);
}
for (auto s : my_sbs){
vcflib::Variant var;
// Make subgraphs out of the superbubble:
// Operating on a pair<id_t, id_t>, vector<id_t>
// then enumerate k_paths through the SuperBubbles
set<Node*> nodes;
set<Edge*> edges;
for (int i = 0; i < s.second.size(); i++){
id_t n_id = s.second[i];
//cerr << n_id << endl;
Node* n_node = my_vg->get_node(n_id);
vector<Edge*> e_end = my_vg->edges_from(n_node);
nodes.insert(n_node);
if (i < s.second.size() - 1){
edges.insert(e_end.begin(), e_end.end());
}
}
vg::VG t_graph = vg::VG(nodes, edges);
vector<Path> paths;
std::function<void(NodeTraversal)> no_op = [](NodeTraversal n){};
std::function<void(size_t, Path&)> extract_path = [&paths](size_t x_size, Path& path){
paths.push_back(path);
};
t_graph.for_each_kpath(10000, false, 100, no_op, no_op, extract_path);
std::function<std::vector<Path>(vector<Path>)> uniquify = [](vector<Path> v){
map<string, Path> unqs;
vector<Path> ret;
for (auto x: v){
unqs[path_to_string(x)] = x;
}
for (auto y : unqs){
ret.push_back(y.second);
}
return ret;
};
paths = uniquify(paths);
std::function<bool(Path)> all_ref = [&](Path p){
for (int i = 0; i < p.mapping_size(); i++){
Mapping m = p.mapping(i);
Position pos = m.position();
vg::id_t pos_id = pos.node_id();
map<string, set<Mapping*> > path_to_mappings = my_vg->paths.get_node_mapping(pos_id);
if (path_to_mappings.size() <= 0){
return false;
}
}
return true;
};
/*
* This means we now have vectors for the superbubble
* that have the paths through the nodes within it (including end nodes)
* however, these paths are repeated several times.
* We should find a way to prevent them being inserted once for each node.
*
* Next on the agenda: use the get_path_dist thing from vg call / vg stats
* to get the distance to the head node.
* Might need an XG index for this.
*
* Also need a way to deal with GAMs for this i.e. a way to
* count the number of times we see something come up in the gam
*/
int first_len = (my_vg->get_node(1))->sequence().size();
map<string, set<Mapping*> > p_to_mappings = my_vg->paths.get_node_mapping(s.first.first);
for (auto p_name : p_to_mappings){
var.sequenceName = p_name.first;
}
var.position = my_xg->approx_path_distance(var.sequenceName, 1, s.first.first) + (s.first.first == 1 ? 0 : first_len);
//var.sequenceName = my_vg->paths.get_node_mapping(pos_id);
//
for (auto x : paths){
//cerr << path_to_string(x) << endl;
stringstream ref_seq;
stringstream alt_seq;
bool is_ref = true;
for (int m_i = 1; m_i < x.mapping_size() -1 ; m_i++){
Mapping m = x.mapping(m_i);
id_t pos_id = m.position().node_id();
Node* n = my_vg->get_node(pos_id);
string n_seq = n->sequence();
map<string, set<Mapping*> > path_to_mappings = my_vg->paths.get_node_mapping(pos_id);
if (path_to_mappings.size() == 0){
is_ref = false;
}
if (is_ref){
ref_seq << n_seq;
}
alt_seq << n_seq;
//cerr << " REF: " << ref_seq.str() << " ALT: " << alt_seq.str() << endl;
}
if (is_ref){
if(var.ref.empty()){
string ref_str = ref_seq.str();
var.ref = ref_str; //(ref_str.size() > 0) ? ref_str : (my_vg->get_node(s.first.first))->sequence();
var.alleles.insert(var.alleles.begin(), var.ref);
}
}
else{
string alt_string = alt_seq.str();
var.alt.push_back(alt_string);
var.alleles.push_back(alt_string);
}
}
if (! (var.ref.empty() && var.alt.empty()) ){
cout << var << endl;
}
}
}
/* Setup the content of the tree model. */
void
populate_tree_model (GtkWidget *treeview)
{
GtkWidget *entry, *statusbar;
GdkPixbuf *pixbuf_file, *pixbuf_dir;
GtkListStore *store;
GtkTreeIter iter;
GdkPixbuf *directory;
struct stat st;
gchar *location, *file, *message;
gfloat size, total_size = 0;
gint i, items = 0;;
GDir *dir;
store = GTK_LIST_STORE (gtk_tree_view_get_model (GTK_TREE_VIEW (treeview)));
gtk_list_store_clear (store);
location = path_to_string ();
/* If the current location is not the root directory, add the '..' entry. */
if (g_list_length (current_path) > 0)
{
directory = gdk_pixbuf_new_from_file ("directory.png", NULL);
gtk_list_store_append (store, &iter);
gtk_list_store_set (store, &iter, ICON, directory, FILENAME, "..", -1);
}
/* Return if the path does not exist. */
if (!g_file_test (location, G_FILE_TEST_IS_DIR))
{
file_manager_error ("The path %s does not exist!");
g_free (location);
return;
}
/* Display the new location in the address bar. */
entry = glade_xml_get_widget (xml, "location");
gtk_entry_set_text (GTK_ENTRY (entry), location);
/* Add each file to the list along with the file size and modified date. */
pixbuf_dir = gdk_pixbuf_new_from_file ("directory.png", NULL);
pixbuf_file = gdk_pixbuf_new_from_file ("file.png", NULL);
dir = g_dir_open (location, 0, NULL);
while ((file = (gchar*) g_dir_read_name (dir)))
{
gchar *fn, *filesize, *modified;
fn = g_strconcat (location, "/", file, NULL);
if (g_stat (fn, &st) == 0)
{
/* Calculate the file size and order of magnitude. */
i = 0;
size = (gfloat) st.st_size;
total_size += size;
while (size >= 1024.0)
{
size = size / 1024.0;
i++;
}
/* Create strings for the file size and last modified date. */
filesize = g_strdup_printf ("%.1f %s", size, size_type[i]);
modified = g_strdup (ctime (&st.st_mtime));
modified[strlen(modified)-1] = '\0';
}
/* Add the file and its properties as a new tree view row. */
gtk_list_store_append (store, &iter);
if (g_file_test (fn, G_FILE_TEST_IS_DIR))
gtk_list_store_set (store, &iter, ICON, pixbuf_dir, FILENAME, file,
SIZE, filesize, MODIFIED, modified, -1);
else
gtk_list_store_set (store, &iter, ICON, pixbuf_file, FILENAME, file,
SIZE, filesize, MODIFIED, modified, -1);
items++;
g_free (fn);
}
/* Calculate the total size of the directory content. */
i = 0;
while (total_size >= 1024.0)
{
total_size = total_size / 1024.0;
i++;
}
/* Add the number of items and the total size of the directory content
* to the status bar. */
statusbar = glade_xml_get_widget (xml, "statusbar");
message = g_strdup_printf ("%d items, Total Size: %.1f %s", items,
total_size, size_type[i]);
gtk_statusbar_pop (GTK_STATUSBAR (statusbar), context_id);
gtk_statusbar_push (GTK_STATUSBAR (statusbar), context_id, message);
g_object_unref (pixbuf_dir);
g_object_unref (pixbuf_file);
g_free (message);
}
int _file_text_open_read(const boost::filesystem::path& filename, filestream_organizer::encoding enc, bool forced)
{
os_string_type fname_string = path_to_string(filename);
return _file_text_open_read(fname_string, enc, forced);
}
