void init(const fs::path &rErrEvtPath, const fs::path &rStatusPath) {
// register common attributes - ThreadID, LineID, TimeStamp etc.
logging::add_common_attributes();
// Construct the sink for the "event_log" channel
typedef sinks::synchronous_sink<sinks::text_ostream_backend> text_sink;
auto sink = boost::make_shared<text_sink>();
sink->locked_backend()->auto_flush(true);
sink->locked_backend()->add_stream(boost::make_shared<std::ofstream>(rErrEvtPath.c_str()));
sink->set_formatter(expr::format("%1% [%2%] tid[%3%] %4%") %
expr::format_date_time<boost::posix_time::ptime>("TimeStamp", "%H:%M:%S.%f") %
logging::trivial::severity % expr::attr<attrs::current_thread_id::value_type>("ThreadID") %
expr::smessage);
sink->set_filter(expr::attr<std::string>("Channel") == "event");
logging::core::get()->add_sink(sink);
// Construct the sink for the "status_log" channel
sink = boost::make_shared<text_sink>();
sink->locked_backend()->auto_flush(true);
sink->locked_backend()->add_stream(boost::make_shared<std::ofstream>(rStatusPath.c_str()));
sink->set_formatter(expr::format("%1% [%2%] tid[%3%] %4%") %
expr::format_date_time<boost::posix_time::ptime>("TimeStamp", "%H:%M:%S.%f") %
logging::trivial::severity % expr::attr<attrs::current_thread_id::value_type>("ThreadID") %
expr::smessage);
sink->set_filter(expr::attr<std::string>("Channel") == "status");
logging::core::get()->add_sink(sink);
}
void filter_init(int argc, char** argv)
{
if(argc > 0)
usage("Too many arguments.");
set_filter(CLIENT_IN, filter_client_data, 0);
set_filter(SERVER_FD, filter_server_data, 0);
(void)argv;
}
CL_FileDialog_Generic::CL_FileDialog_Generic(
CL_FileDialog *self,
const std::string &title,
const std::string &file,
const std::string &filter)
: filedialog(self)
{
behavior = CL_FileDialog::quit_always;
button = CL_FileDialog::button_none;
// TODO: Calculate proper size
int width = 400;
int height = 315;
int x = (CL_Display::get_width() - width) / 2;
int y = (CL_Display::get_height() - height) / 2;
filedialog->set_position(CL_Rect(x, y, x + width, y + height));
filedialog->set_title(title);
CL_Component *client_area = filedialog->get_client_area();
width = client_area->get_width();
label_dir = new CL_Label(CL_Point(10, 12), "Directory:", client_area);
input_dir = new CL_InputBox(CL_Rect(65, 10, width - 120, 30), client_area);
input_dir->enable(false);
button_parent = new CL_Button(CL_Rect(width - 115, 9, width - 65, 28), "Parent", client_area);
button_createdir = new CL_Button(CL_Rect(width - 60, 9, width - 10, 28), "New", client_area);
treeview_files = new CL_TreeView(CL_Rect(10, 32, width - 10, 197), client_area);
treeview_files->add_column("Filename", 200);
treeview_files->add_column("Size", 80);
treeview_files->add_column("Type", 100);
treeview_files->show_root_decoration(false);
label_file = new CL_Label(CL_Point(10, 207), "Filename:", client_area);
input_file = new CL_InputBox(CL_Rect(65, 205, width - 10, 225), client_area);
label_filter = new CL_Label(CL_Point(10, 232), "Filter:", client_area);
input_filter = new CL_InputBox(CL_Rect(65, 230, width - 10, 250), client_area);
button_ok = new CL_Button(CL_Rect(10, 260, 100, 280), "OK", client_area);
button_cancel = new CL_Button(CL_Rect(width - 110, 260, width - 10, 280), "Cancel", client_area);
slots.connect(self->sig_set_options(), this, &CL_FileDialog_Generic::on_set_options);
slots.connect(treeview_files->sig_selection_changed(), this, &CL_FileDialog_Generic::on_file_activated);
slots.connect(button_ok->sig_clicked(), this, &CL_FileDialog_Generic::on_button_quit, true);
slots.connect(button_cancel->sig_clicked(), this, &CL_FileDialog_Generic::on_button_quit, false);
slots.connect(button_parent->sig_clicked(), this, &CL_FileDialog_Generic::on_button_parent);
slots.connect(button_createdir->sig_clicked(), this, &CL_FileDialog_Generic::on_button_createdir);
slots.connect(input_file->sig_return_pressed(), this, &CL_FileDialog_Generic::on_edit_file);
slots.connect(input_filter->sig_return_pressed(), this, &CL_FileDialog_Generic::on_edit_filter);
slots.connect(input_dir->sig_return_pressed(), this, &CL_FileDialog_Generic::on_edit_dir);
set_file(file, false);
set_filter(filter, false);
show_hidden = false;
read_dir();
}
/**
Switch On the wind noise filter
*/
void Filter_On(void)
{
DEBUG_FILTER(("[FILTER] ON\n"));
MessageSinkTask(theHeadset.sco_sink, &theHeadset.task);
voice_activity = VOICE_ACTIVITY_OFF;
set_filter();
}
void set_filter_level(std::string const &level) {
// The return type depends on whether compilation is whith threads.
auto logger = boost::log::core::get();
if (level == "all" || level == "trace") {
logger->set_filter(trivial::severity >= trivial::trace);
LOG(info) << "Log level set to TRACE";
} else if (level == "debug") {
logger->set_filter(trivial::severity >= trivial::debug);
LOG(info) << "Log level set to DEBUG";
} else if (level == "info") {
logger->set_filter(trivial::severity >= trivial::info);
LOG(info) << "Log level set to INFO";
} else if (level == "warn") {
logger->set_filter(trivial::severity >= trivial::warning);
} else if (level == "error") {
logger->set_filter(trivial::severity >= trivial::error);
} else if (level == "fatal") {
logger->set_filter(trivial::severity >= trivial::fatal);
} else if ((level == "off") || (level == "none")) {
logger->set_logging_enabled(false);
} else {
logger->set_filter(trivial::severity >= trivial::fatal);
}
}
void BaseSniffer::init(pcap_t *phandle, const std::string &filter,
bpf_u_int32 if_mask)
{
handle = phandle;
mask = if_mask;
if(!filter.empty() && !set_filter(filter))
throw runtime_error("Invalid filter");
}
void init_filters(void)
{
for(int i=0; i<8; i++)
{ //set sensible default values
//lowpass filter where everything passes with no resonance
set_filter(i,FLT_LOWPASS,i2fp(1),i2fp(0),i2fp(0),false);
}
fp_inv_255=fl2fp(1.0f/255) ;
filters_inited=true;
}
int ingest_pcap(char *file) {
int rc = -1;
strncpy(&cfg.path[cfg.path_file_idx], file, PATH_MAX-cfg.path_file_idx);
if (cfg.verbose) fprintf(stderr,"reading file %s\n", cfg.path);
cfg.pcap = pcap_open_offline(cfg.path, cfg.err);
if (cfg.pcap==NULL) {fprintf(stderr,"can't open %s: %s\n", cfg.path, cfg.err); goto done;}
if (set_filter()) goto done;
rc = pcap_loop(cfg.pcap, 0, cb, NULL);
done:
return rc;
}
static void determine_mode_from_name (const char *argv0)
{
/* This is filterdiff, unless it is named 'lsdiff' or 'grepdiff'. */
const char *p = strrchr (argv0, '/');
if (!p++)
p = argv0;
if (strstr (p, "lsdiff"))
set_list ();
else if (strstr (p, "grepdiff"))
set_grep ();
else
set_filter ();
}
/**
Energy changed handler
*/
void Filter_EnergyChanged(Message message) {
MessageEnergyChanged* m;
m = (MessageEnergyChanged*) message;
if (m->over_threshold) {
DEBUG_FILTER(("[FILTER] VOICE_ACTIVITY_ON\n"));
voice_activity = VOICE_ACTIVITY_ON;
} else {
DEBUG_FILTER(("[FILTER] VOICE_ACTIVITY_OFF\n"));
voice_activity = VOICE_ACTIVITY_OFF;
}
set_filter();
}
void CL_FileDialog_Generic::on_set_options(const CL_DomElement &options)
{
if (options.has_attribute("file"))
set_file(options.get_attribute("file"), false);
if (options.has_attribute("filter"))
set_filter(options.get_attribute("filter"), false);
if (options.has_attribute("show_hidden"))
show_hidden = CL_String::to_bool(options.get_attribute("show_hidden"));
read_dir();
}
int YARPMEIDeviceDriver::setIntLimit(void *cmd)
{
int16 rc = 0;
SingleAxisParameters *tmp = (SingleAxisParameters *) cmd;
int axis = tmp->axis;
double val = *((double *) tmp->parameters);
_filter_coeffs[axis][DF_I_LIMIT] = (int16) round(val);
rc = set_filter(axis, _filter_coeffs[axis]);
return rc;
}
int YARPMEIDeviceDriver::setIntLimits(void *lmts)
{
int16 rc = 0;
double *cmd = (double *) lmts;
for(int i = 0; i<_njoints; i++)
{
_filter_coeffs[i][DF_I_LIMIT] = (int16) round(cmd[i]);
rc = set_filter(i, _filter_coeffs[i]);
}
return rc;
}
int
do_lvm_clear_filter (void)
{
if (deactivate () == -1)
return -1;
if (set_filter ("\"a/.*/\"") == -1)
return -1;
if (rescan () == -1)
return -1;
return reactivate ();
}
int YARPMEIDeviceDriver::setOffsets(void *offs)
{
int16 rc = 0;
double *cmd = (double *) offs;
for(int i = 0; i<_njoints; i++)
{
_filter_coeffs[i][DF_OFFSET] = (int16) round(cmd[i]);
rc = set_filter(i, _filter_coeffs[i]);
}
return rc;
}
/* Makes a new filter */
static void on_filter_entry_changed(GtkComboBoxEntry * cbox, gpointer user_data)
{
gchar *str;
/* TODO should make sure that for each mode the filter is set up
* correctly */
str = gtk_combo_box_get_active_text(GTK_COMBO_BOX(cbox));
if (pref.filter)
g_free (pref.filter);
pref.filter = g_strdup (str);
/* TODO We should look at the error code from set_filter and pop
* up a window accordingly */
set_filter (pref.filter, NULL);
g_free (str);
cbox_add_select(cbox, pref.filter);
} /* on_filter_entry_changed */
static int need_a_filter(pam_handle_t *pamh
, int flags, int argc, const char **argv
, const char *name, int which_run)
{
int ctrl;
char **evp;
const char *filterfile;
int retval;
ctrl = process_args(pamh, argc, argv, name, &evp, &filterfile);
if (ctrl == -1) {
return PAM_AUTHINFO_UNAVAIL;
}
/* set the tty to the old or the new one? */
if (!(ctrl & NON_TERM) && !(ctrl & NEW_TERM)) {
retval = set_the_terminal(pamh);
if (retval != PAM_SUCCESS) {
_pam_log(LOG_ERR, "tried and failed to set PAM_TTY");
}
} else {
retval = PAM_SUCCESS; /* nothing to do which is always a success */
}
if (retval == PAM_SUCCESS && (ctrl & which_run)) {
retval = set_filter(pamh, flags, ctrl
, (const char **)evp, filterfile);
}
if (retval == PAM_SUCCESS
&& !(ctrl & NON_TERM) && (ctrl & NEW_TERM)) {
retval = set_the_terminal(pamh);
if (retval != PAM_SUCCESS) {
_pam_log(LOG_ERR
, "tried and failed to set new terminal as PAM_TTY");
}
}
free_evp(evp);
if (ctrl & FILTER_DEBUG) {
_pam_log(LOG_DEBUG, "filter/%s, returning %d", name, retval);
_pam_log(LOG_DEBUG, "[%s]", pam_strerror(pamh, retval));
}
return retval;
}
int caraca_init(void)
{
signal_length = hw.code_length * 1000000 / 1200;
if ((hw.fd = caraca_open(PACKAGE)) < 0) {
logprintf(LOG_ERR, "could not open lirc");
logperror(LOG_ERR, "caraca_init()");
return (0);
}
/*accept IR-Messages (16 : RC5 key code) for all nodes on the bus */
if (set_filter(hw.fd, 0x400, 0x7c0, 0) <= 0) {
logprintf(LOG_ERR, "could not set filter for IR-Messages");
caraca_deinit();
return (0);
}
return (1);
}
void Db_table_View::set_table(QString tabla)
{
this->tabla = tabla;
model->setTable(tabla);
if(!model->select())
qDebug () << model->lastError();
// ui->resultado_list->hideColumn(0);
colums = model->columnCount();
//-----------------------
// Formateo forzado
//-----------------------
if (tabla =="vistaart_tarifa"){
QString filtro ="tarifa=";
filtro.append(QString::number(tarifa));
set_filter(filtro);
ui->resultado_list->setColumnWidth(0,100);
ui->resultado_list->setColumnWidth(1,100);
ui->resultado_list->setColumnWidth(2,100);
ui->resultado_list->setColumnWidth(3,300);
ui->resultado_list->setColumnWidth(4,180);
ui->resultado_list->setColumnWidth(5,50);
ui->resultado_list->setColumnWidth(6,90);
ui->resultado_list->setColumnWidth(7,90);
ui->resultado_list->setColumnHidden(8,true);
ui->resultado_list->setColumnHidden(9,true);
ui->resultado_list->setColumnHidden(11,true);
ui->resultado_list->setColumnWidth(10,50);
ui->resultado_list->setColumnWidth(12,50);
ui->resultado_list->setColumnHidden(13,true);
model->setHeaderData(0,Qt::Horizontal,tr("Código"));
model->setHeaderData(1,Qt::Horizontal,tr("C.Barras"));
model->setHeaderData(2,Qt::Horizontal,tr("C.Proveedor"));
model->setHeaderData(3,Qt::Horizontal,tr("Descripción"));
model->setHeaderData(4,Qt::Horizontal,tr("Desc. Resumida"));
model->setHeaderData(5,Qt::Horizontal,tr("IVA"));
model->setHeaderData(6,Qt::Horizontal,tr("Coste"));
model->setHeaderData(7,Qt::Horizontal,tr("PVP"));
model->setHeaderData(10,Qt::Horizontal,tr("St.R"));
model->setHeaderData(12,Qt::Horizontal,tr("St.F"));
ui->resultado_list->setItemDelegateForColumn(6,new MonetaryDelegate);
ui->resultado_list->setItemDelegateForColumn(7, new MonetaryDelegate);
}
}
/*
* db_col_filter() - This function examines each element in the collection for
* references to objects that have been deleted. If any such elements are
* found, they are removed. If the collection type is DB_TYPE_SEQUENCE, then
* the elements containing deleted object references will be changed to have
* a DB_TYPE_NULL value. DB_TYPE_MULTISET or DB_TYPE_SET, elements containing
* deleted object references are first converted to elements containing a
* DB_TYPE_NULL value. After all deleted object references have been
* converted to null values, all but one of the null values are then removed
* from the collection.
* return : error status
* col(in): collection to filter
*/
int
db_col_filter (DB_COLLECTION * col)
{
int error;
CHECK_CONNECT_ERROR ();
CHECK_1ARG_ERROR (col);
/* Check if modifications are disabled only if the set is owned */
if (col->owner != NULL)
{
CHECK_MODIFICATION_ERROR ();
}
error = set_filter (col);
return error;
}
/*
* db_seq_filter() - This function causes set elements containing references
* to deleted objects to be completely removed from the designated set.
* The system does not automatically filter sets containing references to
* deleted objects; if you do not call this function, make sure that your
* application code is prepared to encounter deleted objects.
* return : error code
* set(in): set to filter
*/
int
db_seq_filter (DB_SET * set)
{
int retval;
CHECK_CONNECT_ERROR ();
CHECK_1ARG_ERROR (set);
/* Check if modifications are disabled only if the set is owned */
if (set->owner != NULL)
{
CHECK_MODIFICATION_ERROR ();
}
retval = (set_filter (set));
return (retval);
}
int
do_lvm_set_filter (char *const *devices)
{
CLEANUP_FREE char *filter = make_filter_string (devices);
if (filter == NULL)
return -1;
if (deactivate () == -1)
return -1;
int r = set_filter (filter);
if (r == -1)
return -1;
if (rescan () == -1)
return -1;
return reactivate ();
}
logger& logger::init()
{
typedef sinks::debug_output_backend backend_t;
auto pDebugBackend = boost::make_shared< backend_t >();
auto pDebugSink = boost::make_shared< sinks::synchronous_sink< backend_t > >(pDebugBackend);
pDebugSink->set_filter(expr::attr<severity_level>("Severity") >= trace);
pDebugSink->set_formatter(
expr::stream
<< "[" << expr::attr<UINT>("RecordID")
<< "][" << expr::format_date_time(_timestamp, "%Y-%m-%d %H:%M:%S.%f")
<< "][" << _severity
<< "]" << expr::message
<< std::endl);
logging::core::get()->add_sink(pDebugSink);
sink_ = logging::add_file_log(
keywords::open_mode = std::ios::app, // append write
keywords::file_name = file_name_ + "%Y-%m-%d.log",
keywords::rotation_size = rotation_size_,
keywords::time_based_rotation = sinks::file::rotation_at_time_point(0, 0, 0),
keywords::min_free_space = min_free_space_,
keywords::format = (
expr::stream
<< "[" << expr::attr<UINT>("RecordID")
<< "][" << expr::format_date_time(_timestamp, "%Y-%m-%d %H:%M:%S.%f")
<< "][" << _severity
<< "]" << expr::message)
);
sink_->locked_backend()->auto_flush(auto_flush_);
logging::add_common_attributes();
attrs::counter<UINT> RecordID(1);
logging::core::get()->add_global_attribute("RecordID", RecordID);
this->set_filter_trace();
return *this;
}
int YARPMEIDeviceDriver::setPid(void *cmd)
{
int16 rc = 0;
SingleAxisParameters *tmp = (SingleAxisParameters *) cmd;
LowLevelPID *pid = (LowLevelPID *) tmp->parameters;
// these are stored to be used later in the setOffsets/setOffset functions
_filter_coeffs[tmp->axis][DF_P] = (int16) round(pid->KP);
_filter_coeffs[tmp->axis][DF_I] = (int16) round(pid->KI);
_filter_coeffs[tmp->axis][DF_D] = (int16) round(pid->KD);
_filter_coeffs[tmp->axis][DF_ACCEL_FF] = (int16) round (pid->AC_FF);
_filter_coeffs[tmp->axis][DF_VEL_FF] = (int16) round(pid->VEL_FF);
_filter_coeffs[tmp->axis][DF_I_LIMIT] = (int16) round(pid->I_LIMIT);
_filter_coeffs[tmp->axis][DF_OFFSET] = (int16) round(pid->OFFSET);
_filter_coeffs[tmp->axis][DF_DAC_LIMIT] = (int16) round(pid->T_LIMIT);
_filter_coeffs[tmp->axis][DF_SHIFT] = (int16) round(pid->SHIFT);
_filter_coeffs[tmp->axis][DF_FRICT_FF] = (int16) round(pid->FRICT_FF);
rc = set_filter(tmp->axis, _filter_coeffs[tmp->axis]);
return rc;
}
void kvdb_catch_table(u16 pid, u16 table_id)
{
adv_demux_filter_t *sn_filter = NULL;
dmx_filter_setting_t param;
KVDB_DRV_DEBUG("%s, %d \n", __FUNCTION__, __LINE__);
KVDB_DRV_DEBUG("pid = %d , table_id = %d \n", pid, table_id);
memset(¶m,0x0, sizeof(dmx_filter_setting_t) );
sn_filter = alloc_filter(pid);
if(!sn_filter)
{
KVDB_DRV_DEBUG("sn_filter is NULL \n");
return;
}
param.continuous = FALSE;
param.en_crc = TRUE;
param.req_mode = DMX_REQ_MODE_SINGLE_SECTION;
param.value[0] = table_id;
param.mask[0] = 0xff,
set_filter( sn_filter, ¶m, call_back_data_procee);
KVDB_DRV_DEBUG("start_filter ----\n");
start_filter(sn_filter);
return;
}
BOOST_LOG_GLOBAL_LOGGER_INIT(__logger, bl::sources::severity_logger_mt)
{
bl::sources::severity_logger_mt<boost::log::trivial::severity_level> logger;
logger.add_attribute("TimeStamp", bl::attributes::local_clock());
using text_sink = bl::sinks::asynchronous_sink<bl::sinks::text_ostream_backend>;
auto consoleSink = boost::make_shared<text_sink>();
consoleSink->locked_backend()->add_stream(boost::shared_ptr<std::ostream>(&std::cout, boost::null_deleter()));
consoleSink->set_filter(severity >= boost::log::trivial::severity_level::warning);
using file_sink = bl::sinks::asynchronous_sink<bl::sinks::text_file_backend>;
auto logfileSink = boost::make_shared<file_sink>();
{
auto logfileBackend = logfileSink->locked_backend();
logfileBackend->set_time_based_rotation(bl::sinks::file::rotation_at_time_point(0, 0, 0));
logfileBackend->set_file_name_pattern("Logs\\ashbot_%Y%m%d.log");
logfileBackend->auto_flush();
logfileBackend->set_file_collector(
bl::sinks::file::make_collector(bl::keywords::target = "Logs\\Archive")
);
}
namespace expr = bl::expressions;
bl::formatter fmt = expr::stream
<< format_date_time(timestamp, "%Y-%m-%d %H:%M:%S.%f")
<< " [" << boost::log::trivial::severity << "] "
<< expr::smessage;
logfileSink->set_formatter(fmt);
bl::core::get()->add_sink(consoleSink);
bl::core::get()->add_sink(logfileSink);
return logger;
}
void on_container_start(proton::container &c) override {
proton::source_options opts;
set_filter(opts, "colour = 'green'");
proton::connection conn = c.connect(url);
conn.open_receiver(url.path(), proton::receiver_options().source(opts));
}
/**
* @brief Main entry point for R
*
* @param bamfilenameR Filename of read container
* @param aRgvals Vector containing the user arguments
* @param filterList passed from R in the form list("chr1"=c(100,200,3000,3010...start,end...))
* @return R list in the form list("chr1"=c(1,2,1,2,1,1,...),"chr1_gind"=c(1100,1200...),"chr1_lind"=c(0,112,...),"chrX"=NA,...) and a Statistics vector
* @details All chromosome of the filter or all chromosomes in the file header will be scanned and passed to an R list
* @note
* @todo high_cov not yet implemented.
*/
SEXP construct_dc(SEXP bamfilenameR, SEXP aRgvals, SEXP filterList) {
double *statsp;//resulting statistics in the order "total reads" "coverage" "local coverage" "max score"
uint32_t upcounter=0,i=0;
time_t tstart,tstop;
global_densities_t gd={0};
user_arguments_t user_args;
filter_t ft;
SEXP histogram,stats;
int *argvalsp;
signal(SIGINT,SIG_DFL);//make this thing stop on CTRL+C
time(&tstart);
/* Set user defined values */
PROTECT(aRgvals=AS_INTEGER(aRgvals));upcounter++;
if(LENGTH(aRgvals)!=10)error("Invalid amount of arguments - arguments[%d] / should be %d!\n",LENGTH(aRgvals),9);
argvalsp=INTEGER_POINTER(aRgvals);
user_args.bamfilename = STRING_VALUE(bamfilenameR);
user_args.READTHROUGH = argvalsp[0];//bool. read from start to end and 0 take whole read whithout CIGAR splice info
user_args.PAIRED = argvalsp[1];
user_args.STRANDED = argvalsp[2];//Set to 1 / -1 it will use only forward / reverse reads respectively. 0 means all reads are processed
user_args.TMAPQ = argvalsp[3];//Minimum MPAQ score. Lower scored reads will be skipped
user_args.COLLAPSE = argvalsp[4];
user_args.EXTEND = argvalsp[5];//extend each read in its direction by this amount of BPs
user_args.HWINDOW = argvalsp[6];
user_args.COMPRESSION = argvalsp[7];//minimum BPs needed between data blocks to collapse the gap and index it
user_args.VERBOSE = argvalsp[8];
user_args.UNIQUE = argvalsp[9];
/* Try to open the file */
samfile_t *bam_file;
bam_file=open_samtools(user_args.bamfilename);
if(!bam_file){
warning("sam/bam file not found!\n");
UNPROTECT(upcounter);
return(R_NilValue);
}
if(user_args.HWINDOW>user_args.COMPRESSION){
warning("HWINDOW has to be smaller than COMPRESSION! HWINDOW updated to %d\n",user_args.COMPRESSION);
user_args.HWINDOW=user_args.COMPRESSION;
}
PROTECT(histogram = NEW_INTEGER(UINT16_MAX));upcounter++;//initialize compressed scores
gd.histogramp = (uint32_t*) INTEGER_POINTER(histogram);
for(i = 0; i < UINT16_MAX; i++) gd.histogramp[i] = 0;
gd.total_elements=bam_file->header->n_targets;//one vector per chromosome needed
/* #### CHECK IF THERE IS AN ACTIVE FILTER IN PLACE */
user_args.FILTER=isNewList(filterList) ? 1 : 0;
if(user_args.FILTER){
upcounter+=set_filter(filterList,&ft);
gd.total_elements=ft.seqn;//overwrite total elements if filter is passed, since one density is returned per slice
}
// Creating a list with vector elements as many as sequences plus a character string vector:
PROTECT(gd.list = allocVector(VECSXP, (gd.total_elements*3)+2));upcounter++;//3x for the two indexes and scores per chromosome
PROTECT(gd.list_names = allocVector(STRSXP,(gd.total_elements*3)+2));upcounter++;//+1 for statistics vector +1 for the histogram
/* PASS EVERYTHING */
write_density(&gd,&user_args,bam_file,&ft);
if(!gd.total_reads)goto NO_READS_FOUND;
// 1 total_reads 2 gcoverage 3 lcoverage 4 maxscore 5 lmaxscore 6 lowqual 7 filtered 8 collapsed 9 paired 10 proper_pairs 11 pos 12 neg 13 fmapmass 14 lsize 15 gsize
SET_STRING_ELT(gd.list_names,gd.total_elements*3,mkChar("Statistics"));
PROTECT(stats = NEW_NUMERIC(15));upcounter++;
statsp = NUMERIC_POINTER(stats);
*statsp++=(double)gd.total_reads;
*statsp++=(double)gd.mapmass/(double)gd.gsize;
*statsp++=(double)gd.lmapmass/(double)gd.lsize;
*statsp++=(double)gd.maxscore;
*statsp++=(double)gd.lmaxScore;
*statsp++=(double)gd.lowqual;
*statsp++=(double)gd.filtered_reads;
*statsp++=(double)gd.collapsed;
*statsp++=(double)gd.paired;
*statsp++=(double)gd.ppairs/2;
*statsp++=(double)gd.pos_strand;
*statsp++=(double)gd.neg_strand;
*statsp=(double)gd.mapmass;
*statsp++=(double)gd.lsize;
*statsp++=(double)gd.gsize;
if(gd.lmaxScore>=umaxof(usersize)-1){
warning("\nThe maximum pile up is exceeding the maximal value of UINT16_MAX=%d. Reads have been capped to that value.\nConsider to rerun using the maxDups option!\n",UINT16_MAX);
}
SET_VECTOR_ELT(gd.list,gd.total_elements*3, stats);
SET_STRING_ELT(gd.list_names,(gd.total_elements*3)+1,mkChar("Histogram"));
SET_VECTOR_ELT(gd.list,(gd.total_elements*3)+1,histogram);
setAttrib(gd.list, R_NamesSymbol, gd.list_names);
NO_READS_FOUND:
time(&tstop);
if(user_args.VERBOSE>0)printf("About %.0f seconds passed. %llu reads processed \n", difftime(tstop, tstart),gd.total_reads);
close_bamfile(bam_file);
if(user_args.FILTER)destroy_filter(&ft);
UNPROTECT(upcounter+gd.upcounter);
if(!gd.total_reads)return(R_NilValue);
else return(gd.list);
}
char *uilib_select_file_autostart(const char *title,
unsigned int filterlist, unsigned int type,
int style, int *autostart,
char *resource_readonly)
{
char *name = NULL;
char *initialdir = NULL;
char *initialfile = NULL;
// char *filter = NULL;
// unsigned int filterindex;
// OPENFILENAME ofn;
// int result;
char *ret = NULL;
if (styles[style].initialdir_resource != NULL)
resources_get_value(styles[style].initialdir_resource,
(void *)&initialdir);
initialfile = ui_file_selector_initialfile[style];
if (styles[style].file_resource != NULL)
resources_get_value(styles[style].file_resource,
(void *)&initialfile);
#if 0
if (fontfile == NULL) {
fontfile = util_concat(archdep_boot_path(),
"\\fonts\\cbm-directory-charset.fon", NULL);
font_loaded = 0;
EnumFontFamilies(GetDC(NULL), "cbm-directory-charset/ck!",
(FONTENUMPROC)EnumFontProc, (LPARAM)&font_loaded);
if (font_loaded == 0) {
font_loaded = AddFontResource(fontfile);
}
}
filter = set_filter(filterlist, &filterindex);
memset(&ofn, 0, sizeof(ofn));
ofn.lStructSize = sizeof(ofn);
ofn.hwndOwner = hwnd;
ofn.hInstance = winmain_instance;
ofn.lpstrFilter = filter;
ofn.lpstrCustomFilter = NULL;
ofn.nMaxCustFilter = 0;
ofn.nFilterIndex = filterindex;
ofn.lpstrFile = st_name;
ofn.nMaxFile = sizeof(st_name);
ofn.lpstrFileTitle = NULL;
ofn.nMaxFileTitle = 0;
ofn.lpstrInitialDir = initialdir;
ofn.lpstrTitle = title;
ofn.Flags = OFN_EXPLORER | OFN_HIDEREADONLY | OFN_NOTESTFILECREATE
| OFN_SHAREAWARE | OFN_ENABLESIZING;
if (styles[style].TemplateID != 0) {
ofn.Flags |= OFN_ENABLEHOOK | OFN_ENABLETEMPLATE;
ofn.lpfnHook = styles[style].hook_proc;
ofn.lpTemplateName = MAKEINTRESOURCE(styles[style].TemplateID);
} else {
ofn.lpfnHook = NULL;
ofn.lpTemplateName = NULL;
}
if (type == UILIB_SELECTOR_TYPE_FILE_LOAD)
ofn.Flags |= OFN_FILEMUSTEXIST;
ofn.nFileOffset = 0;
ofn.nFileExtension = 0;
ofn.lpstrDefExt = NULL;
read_content_func = styles[style].content_read_function;
autostart_result = autostart;
res_readonly = resource_readonly;
vsync_suspend_speed_eval();
if (type == UILIB_SELECTOR_TYPE_FILE_SAVE)
result = GetSaveFileName(&ofn);
else
result = GetOpenFileName(&ofn);
update_filter_history(ofn.nFilterIndex);
#endif
name = ui_filereq(title, styles[style].TemplateID, initialdir, initialfile, styles[style].content_read_function, autostart, resource_readonly);
if (name != NULL) {
char newdir[1024], *ptr = PathPart(name);
memcpy(newdir, name, (int)(ptr - name));
newdir[(int)(ptr - name)] = '\0';
if (ui_file_selector_initialfile[style] != NULL)
lib_free(ui_file_selector_initialfile[style]);
if (styles[style].file_resource != NULL)
resources_set_value(styles[style].file_resource, FilePart(name));
ui_file_selector_initialfile[style] = lib_stralloc(FilePart(name));
resources_set_value(styles[style].initialdir_resource, newdir);
ret = lib_stralloc(name);
}
// lib_free(filter);
return ret;
}
int action_set_filter(MENU_ITEM *self)
{
int p=(int)self->user_data;
set_filter(p);
return 2;
}
