std::string pretty_print() const
{
std::ostringstream ss;
ss << what();
if (call_stack.size() > 0) {
ss << "during evaluation at (" << fname(call_stack[0]) << " " << startpos(call_stack[0]) << ")" << std::endl;
ss << std::endl << detail << std::endl;
ss << " " << fname(call_stack[0]) << " (" << startpos(call_stack[0]) << ") '" << pretty(call_stack[0]) << "'";
for (size_t j = 1; j < call_stack.size(); ++j) {
if (id(call_stack[j]) != chaiscript::AST_Node_Type::Block
&& id(call_stack[j]) != chaiscript::AST_Node_Type::File)
{
ss << std::endl;
ss << " from " << fname(call_stack[j]) << " (" << startpos(call_stack[j]) << ") '" << pretty(call_stack[j]) << "'";
}
}
}
ss << std::endl;
return ss.str();
}
GraphSize OperationDrawer::drawOrSizeDiagram(DiagramDrawer &drawer,
OperationGraph &graph, const OperationDrawOptions &options, bool draw)
{
mCharHeight = static_cast<int>(drawer.getTextExtentHeight("W"));
int pad = mCharHeight / 3;
if(pad < 1)
pad = 1;
mPad = pad;
GraphPoint startpos(mCharHeight, mCharHeight);
GraphPoint pos = startpos;
GraphSize size;
GraphSize diagramSize;
int maxy = 0;
std::vector<int> classEndY;
for(size_t i=0; i<graph.mOpClasses.size(); i++)
{
OperationClass &opClass = graph.mOpClasses[i];
opClass.setPosition(pos);
size = drawClass(drawer, opClass, options, draw);
size_t condDepth = graph.getNestDepth(i);
size.x += static_cast<int>(condDepth) * mPad;
opClass.setSize(size);
pos.x += size.x + mCharHeight;
classEndY.push_back(startpos.y + size.y);
if(size.y > maxy)
maxy = size.y;
}
diagramSize.x = pos.x;
pos = startpos;
pos.y = startpos.y + maxy; // space between class rect and operations
std::set<const OperationDefinition*> drawnOperations;
for(const auto &oper : graph.mOperations)
{
if(drawnOperations.find(oper) == drawnOperations.end())
{
size = drawOperation(drawer, pos, *oper, graph, options,
drawnOperations, draw);
pos.y += size.y;
}
}
if(draw)
{
drawLifeLines(drawer, graph.mOpClasses, classEndY, pos.y);
}
diagramSize.y = pos.y + mCharHeight;
return diagramSize;
}
void DispInfo::rotate(const Vertex& point, const Matrix3d& rotmat)
{
//mictimer rotatetimer("ms Side::rotate()", 1000.0);
if (keyvals.size() == 0) return;
Vertex startpos((*this)["startposition"]);
startpos = startpos.rotate(point, rotmat);
(*this)["startposition"] = std::string("[") + startpos.toStr() + "]";
for (auto& vec : info)
for (auto& disp : vec)
disp.offset_normal = disp.offset_normal.rotate(rotmat);
}
bool OptionsWrapper::loadOptions(Enum::GameOption modmapFlag, const std::string& name)
{
unLoadOptions(modmapFlag);
GameOptions opt;
switch (modmapFlag) {
default:
break;
case Enum::MapOption:
try {
opt = usync().GetMapOptions(name);
} catch (...) {
LslError("Could not load map options");
usync().FetchUnitsyncErrors(name);
return false;
}
break;
case Enum::ModOption:
try {
opt = usync().GetGameOptions(name);
} catch (...) {
LslError("Could not load game options");
usync().FetchUnitsyncErrors(name);
return false;
}
break;
case Enum::EngineOption: {
//TODO Fixed,random and so forth are intls
mmOptionList startpos("Start Position Type", "startpostype", "How players will select where to be spawned in the map\n0: fixed map positions\n1: random map positions\n2: choose in game\n3: choose in the lobby before starting", "0");
startpos.addItem("0", "Fixed", "Use the start positions defined in the map, the positions will be assigned incrementally from the team with lowest number to highest");
startpos.addItem("1", "Random", "Use the start positions defined in the map, the positions will be assigned randomly");
startpos.addItem("2", "Choose in-game", "Players will be able to pick their own starting point right before the game starts, optionally limited by a bounding box defined by the host");
startpos.addItem("3", "Choose before game", "The host will place each player's start position in the map preview before the game is launched");
opt.list_map["startpostype"] = startpos;
break;
}
case Enum::PrivateOptions: {
opt.string_map["restrictions"] = mmOptionString("List of restricted units", "restrictedunits", "Units in this list won't be available in game", "", 0); // tab separated list
opt.string_map["mapname"] = mmOptionString("Map name", "mapname", "Map name", "", 0);
break;
}
}
m_opts[modmapFlag] = opt;
return true;
}
int main(int argc, char *argv[])
{
char instructions;
//Alloc memory for robot
ROBOT *bot = malloc(sizeof(ROBOT));
while(1) {
startpos(bot);
location(bot);
printf("Please give the robot some instructions\n"
"t for turn, m for move +5 in current facing\n");
read_instructions(bot);
printf("Bot after moving\n");
location(bot);
//Check they want to play again
if(move_again()==1) break;
}
free(bot);
return 0;
}
void LevelFinished::setPosition(){
sf::Vector2f startpos(285,300);
float distance = 96;
float ydist = 96;
bool overflow = false;
int n = 0;
for(int i = 0; i<mAliveVector.size(); i++){
if(n > 6){
overflow = true;
n=0;
}
mAliveVector[i]->setPosition(startpos.x + distance * n, startpos.y + ydist*overflow);
n++;
}
for(int i = 0; i<mDeadVector.size(); i++){
mDeadVector[i]->setPosition(startpos.x + distance * i, startpos.y + ydist + ydist*overflow);
}
}
void
SectorParser::parse_old_format(const ReaderMapping& reader)
{
m_sector.name = "main";
reader.get("gravity", m_sector.gravity);
std::string backgroundimage;
if (reader.get("background", backgroundimage) && (backgroundimage != "")) {
if (backgroundimage == "arctis.png") backgroundimage = "arctis.jpg";
if (backgroundimage == "arctis2.jpg") backgroundimage = "arctis.jpg";
if (backgroundimage == "ocean.png") backgroundimage = "ocean.jpg";
backgroundimage = "images/background/" + backgroundimage;
if (!PHYSFS_exists(backgroundimage.c_str())) {
log_warning << "Background image \"" << backgroundimage << "\" not found. Ignoring." << std::endl;
backgroundimage = "";
}
}
float bgspeed = .5;
reader.get("bkgd_speed", bgspeed);
bgspeed /= 100;
Color bkgd_top, bkgd_bottom;
int r = 0, g = 0, b = 128;
reader.get("bkgd_red_top", r);
reader.get("bkgd_green_top", g);
reader.get("bkgd_blue_top", b);
bkgd_top.red = static_cast<float> (r) / 255.0f;
bkgd_top.green = static_cast<float> (g) / 255.0f;
bkgd_top.blue = static_cast<float> (b) / 255.0f;
reader.get("bkgd_red_bottom", r);
reader.get("bkgd_green_bottom", g);
reader.get("bkgd_blue_bottom", b);
bkgd_bottom.red = static_cast<float> (r) / 255.0f;
bkgd_bottom.green = static_cast<float> (g) / 255.0f;
bkgd_bottom.blue = static_cast<float> (b) / 255.0f;
if(backgroundimage != "") {
auto background = std::make_shared<Background>();
background->set_image(backgroundimage, bgspeed);
m_sector.add_object(background);
} else {
auto gradient = std::make_shared<Gradient>();
gradient->set_gradient(bkgd_top, bkgd_bottom);
m_sector.add_object(gradient);
}
std::string particlesystem;
reader.get("particle_system", particlesystem);
if(particlesystem == "clouds")
m_sector.add_object(std::make_shared<CloudParticleSystem>());
else if(particlesystem == "snow")
m_sector.add_object(std::make_shared<SnowParticleSystem>());
else if(particlesystem == "rain")
m_sector.add_object(std::make_shared<RainParticleSystem>());
Vector startpos(100, 170);
reader.get("start_pos_x", startpos.x);
reader.get("start_pos_y", startpos.y);
auto spawn = std::make_shared<SpawnPoint>();
spawn->pos = startpos;
spawn->name = "main";
m_sector.spawnpoints.push_back(spawn);
m_sector.music = "chipdisko.ogg";
// skip reading music filename. It's all .ogg now, anyway
/*
reader.get("music", music);
*/
m_sector.music = "music/" + m_sector.music;
int width = 30, height = 15;
reader.get("width", width);
reader.get("height", height);
std::vector<unsigned int> tiles;
if(reader.get("interactive-tm", tiles)
|| reader.get("tilemap", tiles)) {
auto tileset = TileManager::current()->get_tileset(m_sector.level->get_tileset());
auto tilemap = std::make_shared<TileMap>(tileset);
tilemap->set(width, height, tiles, LAYER_TILES, true);
// replace tile id 112 (old invisible tile) with 1311 (new invisible tile)
for(size_t x=0; x < tilemap->get_width(); ++x) {
for(size_t y=0; y < tilemap->get_height(); ++y) {
uint32_t id = tilemap->get_tile_id(x, y);
if(id == 112)
tilemap->change(x, y, 1311);
}
}
if (height < 19) tilemap->resize(width, 19);
m_sector.add_object(tilemap);
}
if(reader.get("background-tm", tiles)) {
auto tileset = TileManager::current()->get_tileset(m_sector.level->get_tileset());
auto tilemap = std::make_shared<TileMap>(tileset);
tilemap->set(width, height, tiles, LAYER_BACKGROUNDTILES, false);
if (height < 19) tilemap->resize(width, 19);
m_sector.add_object(tilemap);
}
if(reader.get("foreground-tm", tiles)) {
auto tileset = TileManager::current()->get_tileset(m_sector.level->get_tileset());
auto tilemap = std::make_shared<TileMap>(tileset);
tilemap->set(width, height, tiles, LAYER_FOREGROUNDTILES, false);
// fill additional space in foreground with tiles of ID 2035 (lightmap/black)
if (height < 19) tilemap->resize(width, 19, 2035);
m_sector.add_object(tilemap);
}
// read reset-points (now spawn-points)
ReaderMapping resetpoints;
if(reader.get("reset-points", resetpoints)) {
auto iter = resetpoints.get_iter();
while(iter.next()) {
if(iter.get_key() == "point") {
Vector sp_pos;
if(reader.get("x", sp_pos.x) && reader.get("y", sp_pos.y))
{
auto sp = std::make_shared<SpawnPoint>();
sp->name = "main";
sp->pos = sp_pos;
m_sector.spawnpoints.push_back(sp);
}
} else {
log_warning << "Unknown token '" << iter.get_key() << "' in reset-points." << std::endl;
}
}
}
// read objects
ReaderCollection objects;
if(reader.get("objects", objects)) {
for(auto const& obj : objects.get_objects())
{
auto object = parse_object(obj.get_name(), obj.get_mapping());
if(object) {
m_sector.add_object(object);
} else {
log_warning << "Unknown object '" << obj.get_name() << "' in level." << std::endl;
}
}
}
// add a camera
auto camera_ = std::make_shared<Camera>(&m_sector, "Camera");
m_sector.add_object(camera_);
m_sector.update_game_objects();
if (m_sector.solid_tilemaps.empty()) {
log_warning << "sector '" << m_sector.name << "' does not contain a solid tile layer." << std::endl;
}
fix_old_tiles();
m_sector.update_game_objects();
}
/** Object packs are our own custom format for simple, fixed, object tests. The file format is
* a simple binary dump of each objects information:
*
* struct ObjectInformation {
* uint64 object_id;
* double x;
* double y;
* double z;
* double radius;
* };
*
* This gives the minimal information for a static object and allows you to seek directly to any
* object in the file, making it easy to split the file across multiple object hosts.
*/
void ObjectFactory::generatePackObjects(const BoundingBox3f& region, const Duration& duration) {
bool dump_pack = GetOptionValue<bool>(OBJECT_PACK_DUMP);
if (dump_pack) return; // If we're dumping objects, don't load
// from a pack
Time start(Time::null());
uint32 nobjects = GetOptionValue<uint32>(OBJECT_PACK_NUM);
if (nobjects == 0) return;
String pack_filename = GetOptionValue<String>(OBJECT_PACK);
assert(!pack_filename.empty());
String pack_dir = GetOptionValue<String>(OBJECT_PACK_DIR);
pack_filename = pack_dir + pack_filename;
FILE* pack_file = fopen(pack_filename.c_str(), "rb");
if (pack_file == NULL) {
SILOG(objectfactory,error,"Couldn't open object pack file, not generating any objects.");
assert(false);
return;
}
// First offset ourselves into the file
uint32 pack_offset = GetOptionValue<uint32>(OBJECT_PACK_OFFSET);
uint32 obj_pack_size =
8 + // objid
8 + // radius
8 + // x
8 + // y
8 + // z
0;
int seek_success = fseek( pack_file, obj_pack_size * pack_offset, SEEK_SET );
if (seek_success != 0) {
SILOG(objectfactory,error,"Couldn't seek to appropriate offset in object pack file.");
fclose(pack_file);
return;
}
for(uint32 i = 0; i < nobjects; i++) {
ObjectInputs* inputs = new ObjectInputs;
uint64 pack_objid = 0;
double x = 0, y = 0, z = 0, rad = 0;
fread( &pack_objid, sizeof(uint64), 1, pack_file );
fread( &x, sizeof(double), 1, pack_file );
fread( &y, sizeof(double), 1, pack_file );
fread( &z, sizeof(double), 1, pack_file );
fread( &rad, sizeof(double), 1, pack_file );
UUID id = pack2UUID(pack_objid);
Vector3f startpos((float)x, (float)y, (float)z);
float bounds_radius = (float)rad;
//SILOG(oh,error,"Preating "<<id.toString()<<" radius "<<bounds_radius);
inputs->localID = mLocalIDSource++;
inputs->motion = new StaticMotionPath(start, startpos);
inputs->bounds = BoundingSphere3f( Vector3f(0, 0, 0), bounds_radius );
inputs->registerQuery = false;
inputs->queryAngle = SolidAngle::Max;
inputs->connectAt = Duration::seconds(0.f);
inputs->startTimer = Network::IOTimer::create(mContext->ioService);
mObjectIDs.insert(id);
mInputs[id] = inputs;
}
fclose(pack_file);
}
bool OptionsWrapper::loadOptions( GameOption modmapFlag, const wxString& name, const wxString& extra_filename )
{
unLoadOptions(modmapFlag);
GameOptions opt;
switch (modmapFlag)
{
default:
break;
case MapOption:
try
{
opt = usync().GetMapOptions(name);
ParseSectionMap( m_sections[modmapFlag], opt.section_map );
}
catch(...)
{
wxLogError(_T("Could not load map options"));
return false;
}
break;
case ModOption:
try
{
opt = usync().GetModOptions(name);
ParseSectionMap( m_sections[modmapFlag], opt.section_map );
}
catch(...)
{
wxLogError(_T("Could not load game options"));
return false;
}
break;
case EngineOption: {
mmOptionList startpos( _("Start Position Type"),_T("startpostype"), _("How players will select where to be spawned in the map\n0: fixed map positions\n1: random map positions\n2: choose in game\n3: choose in the lobby before starting"), _T("0") );
startpos.addItem( _T("0"), _("Fixed"), _T("Use the start positions defined in the map, the positions will be assigned incrementally from the team with lowest number to highest") );
startpos.addItem( _T("1"), _("Random"), _T("Use the start positions defined in the map, the positions will be assigned randomly") );
startpos.addItem( _T("2"), _("Choose in-game"), _T("Players will be able to pick their own starting point right before the game starts, optionally limited by a bounding box defined by the host") );
startpos.addItem( _T("3"), _("Choose before game"), _T("The host will place each player's start position in the map preview before the game is launched") );
opt.list_map[_T("startpostype")] = startpos;
break;
}
case PrivateOptions: {
opt.string_map[_T("restrictions")] = mmOptionString(_("List of restricted units"), _T("restrictedunits"), _T("Units in this list won't be available in game"), _T(""), 0 ); // tab separated list
opt.string_map[_T("mapname")] = mmOptionString(_("Map name"), _T("mapname"), _T("Map name"), _T(""), 0 );
break;
}
case ModCustomizations: {
try {
opt = usync().GetModCustomizations( name );
}
catch(...) {
wxLogError(_T("Could not load mod customizations"));
return false;
}
break;
}
case SkirmishOptions: {
try {
opt = usync().GetSkirmishOptions( name, extra_filename );
}
catch(...) {
wxLogError(_T("Could not load skirmish options"));
return false;
}
break;
}
}
m_opts[modmapFlag] = opt;
return true;
}
void ITEMS::render_projectile(const NETOBJ_PROJECTILE *current, int itemid)
{
// get positions
float curvature = 0;
float speed = 0;
if(current->type == WEAPON_GRENADE)
{
curvature = gameclient.tuning.grenade_curvature;
speed = gameclient.tuning.grenade_speed;
}
else if(current->type == WEAPON_SHOTGUN)
{
curvature = gameclient.tuning.shotgun_curvature;
speed = gameclient.tuning.shotgun_speed;
}
else if(current->type == WEAPON_GUN)
{
curvature = gameclient.tuning.gun_curvature;
speed = gameclient.tuning.gun_speed;
}
float ct = (client_prevtick()-current->start_tick)/(float)SERVER_TICK_SPEED + client_ticktime();
if(ct < 0)
return; // projectile havn't been shot yet
vec2 startpos(current->x, current->y);
vec2 startvel(current->vx/100.0f, current->vy/100.0f);
vec2 pos = calc_pos(startpos, startvel, curvature, speed, ct);
vec2 prevpos = calc_pos(startpos, startvel, curvature, speed, ct-0.001f);
gfx_texture_set(data->images[IMAGE_GAME].id);
gfx_quads_begin();
select_sprite(data->weapons.id[clamp(current->type, 0, NUM_WEAPONS-1)].sprite_proj);
vec2 vel = pos-prevpos;
//vec2 pos = mix(vec2(prev->x, prev->y), vec2(current->x, current->y), client_intratick());
// add particle for this projectile
if(current->type == WEAPON_GRENADE)
{
gameclient.effects->smoketrail(pos, vel*-1);
gameclient.flow->add(pos, vel*1000*client_frametime(), 10.0f);
gfx_quads_setrotation(client_localtime()*pi*2*2 + itemid);
}
else
{
gameclient.effects->bullettrail(pos);
gameclient.flow->add(pos, vel*1000*client_frametime(), 10.0f);
if(length(vel) > 0.00001f)
gfx_quads_setrotation(get_angle(vel));
else
gfx_quads_setrotation(0);
}
gfx_quads_draw(pos.x, pos.y, 32, 32);
///--- Added by Tigra
// Draw shadows of grenades
bool local_player_in_game =
gameclient.clients[gameclient.snap.local_cid].team != -1;
if(config.cl_antiping && current->type == WEAPON_GRENADE && local_player_in_game)
{
// Calculate average prediction offset, because client_predtick() gets varial values :(((
// Must be there is a normal way to realize it, but I'm too lazy to find it. ^)
if (gameclient.average_prediction_offset == -1)
{
int offset = client_predtick() - client_tick();
gameclient.prediction_offset_summ += offset;
gameclient.prediction_offset_count++;
if (gameclient.prediction_offset_count >= 100)
{
gameclient.average_prediction_offset =
round((float)gameclient.prediction_offset_summ / gameclient.prediction_offset_count);
}
}
// Draw shadow only if grenade directed to local player
int local_cid = gameclient.snap.local_cid;
NETOBJ_CHARACTER& cur_char = gameclient.snap.characters[local_cid].cur;
NETOBJ_CHARACTER& prev_char = gameclient.snap.characters[local_cid].prev;
vec2 server_pos = mix(vec2(prev_char.x, prev_char.y), vec2(cur_char.x, cur_char.y), client_intratick());
float d1 = distance(pos, server_pos);
float d2 = distance(prevpos, server_pos);
if (d1 < 0) d1 *= -1;
if (d2 < 0) d2 *= -1;
bool grenade_directed_to_local_player = d1 < d2;
if (gameclient.average_prediction_offset != -1 && grenade_directed_to_local_player)
{
int predicted_tick = client_prevtick() + gameclient.average_prediction_offset;
float predicted_ct = (predicted_tick - current->start_tick)/(float)SERVER_TICK_SPEED + client_ticktime();
if (predicted_ct >= 0)
{
int shadow_type = WEAPON_GUN; // Pistol bullet sprite is used for marker of shadow. TODO: use something custom.
select_sprite(data->weapons.id[clamp(shadow_type, 0, NUM_WEAPONS-1)].sprite_proj);
vec2 predicted_pos = calc_pos(startpos, startvel, curvature, speed, predicted_ct);
gfx_quads_draw(predicted_pos.x, predicted_pos.y, 32, 32);
}
}
}
///---
gfx_quads_setrotation(0);
gfx_quads_end();
}
void stratifysites::run () {
cout << "# Parameters\n";
cout << "# thresh1=" << thresh1 << "\n";
cout << "# thresh2=" <<thresh2 << "\n";
cout << "# tlength="<<tlength << "h\n";
cout << "# genpos="<<usegenpos << "\n";
cout << "# strict="<<strict << "\n";
cout << "# bin="<<bins << "\n";
cout << "# predfile="<<predfile << "\n";
cout << "# snpfile="<<snpfile << "\n";
cout << "# genofile="<<genofile << "\n";
cout << "## SNP id\n";
cout << "## Chromosome \n";
cout << "## Genetic position\n";
cout << "## Physical position\n";
cout << "## Average posterior probability of N on derived alleles \n";
cout << "## Average posterior probability of N on ancestral alleles \n";
cout << "## Number of derived alleles that are predicted to be Neandertal \n";
cout << "## Total number of derived alleles \n";
cout << "## Number of ancestral alleles that are predicted to be Neandertal \n";
cout << "## Total number of ancestral alleles \n";
if (givenprefix) {
cout.setf(ios::fixed,ios::floatfield);
cout.precision(3);
}
for (int c = 0 ; c < nchr; c++) {
vector<snp> snps = geno->snps[geno->chrs[c]];
vector<int> tmppred (nind, 0);
vector<double> reg (nind,0);
vector<double> reg2 (nind,0);
vector<double> st1 (nind,0);
vector<double> st2 (nind,0);
vector<int> startpos (nind, 0);
vector<double> maxlengths(snps.size(), 0 );
vector<double> avglengths(snps.size(), 0 );
vector<double> maxglengths(snps.size(), 0 );
vector<double> avgglengths(snps.size(), 0 );
vector<int> denomlengths(snps.size(), 0 );
unordered_map <string, double> plmap ;
unordered_map <string, double> glmap ;
int incontig = 0 ;
int contigsnps = 0;
string contigchr;
double contigstart = 0;
double contigend = 0 ;
double contigl = 0 ;
double contigavganc = 0;
double avgpredanc = 0;
for (int i = 0 ; i < snps.size() ; i++) {
for (int j = 0 ; j < nind; j++) {
double p = (*predanc).get(c,i,j);
tmppred [j] = (p>thresh1)?1:0;
avgpredanc += p;
}
string id = snps[i].id;
string chr = snps[i].chr;
if (nind>0)
avgpredanc /= nind ;
if (i==0) {
for (int j = 0 ; j < nind ; j++) {
reg[j] =reg2[j] = 0;
st1[j] = st2[j] = tmppred[j];
startpos[j] = 0;
}
} else {
int count1 = 0 ;
int count2 = 0;
for (int j = 0 ; j < nind; j++) {
int flag1 = 0;
int flag2 = 0;
int len1 = 0 ;
double len2 = 0;
double avgconf = 0 ;
double trueconf = 0 ;
int denom = 0 ;
int start = 0 ;
int end = 0 ;
if (st1[j] == 0 && tmppred[j] > 0) {
st1[j] = 1;
startpos[j] = i;
} else if (st1[j]==1 && tmppred[j]==0) {
len1 = reg[j];
for (int k = i - 1; k >= 0 && k >= startpos[j] ; k--) {
if ( maxlengths[k] < len1) {
maxlengths[k] = len1;
}
avglengths[k] += len1;
denomlengths[k]++;
start = snps[k].physpos;
avgconf += (*predanc).get (c,k,j);
if (giventrue)
trueconf += (*trueanc)(c,k,j);
denom ++;
string key = chr + ":" + tostring(k) +":"+ tostring(j);
plmap[key] = len1;
}
avgconf = (denom>0)?avgconf/denom:0;
trueconf = (denom>0)?trueconf/denom:0;
reg[j] = 0;
st1[j] = 0;
flag1 = 1;
end = snps[i-1].physpos;
if (len1 > 0) count1++;
} else if (st1[j]==1 && tmppred[j] > 0 ) {
reg[j] += tmppred[j] *(snps[i].physpos - snps[i-1].physpos);
count2 ++;
} else {
}
if (st2[j] == 0 && tmppred[j] > 0)
st2[j] = 1;
else if (st2[j]==1 && tmppred[j]==0) {
len2 = reg2[j];
for (int k = i - 1; k >= 0 && k >= startpos[j] ; k--) {
if (maxglengths[k] < len2) {
maxglengths[k] = len2;
}
avgglengths[k] += len2;
string key = chr + ":" + tostring(k) +":"+ tostring(j);
glmap[key] = len2;
}
reg2[j] = 0;
st2[j] = 0 ;
flag2 = 1;
} else if (st2[j]==1 && tmppred[j] > 0 ) {
reg2[j] += tmppred[j] *(snps[i].genpos - snps[i-1].genpos);
} else {
}
if (flag1 && flag2) {
if (givenprefix) {
len2 *= 100;
}
}
}
if (count2 > 0 ) {
if (incontig) {
contigsnps ++;
contigavganc += avgpredanc;
} else {
contigchr = geno->chrs[c];
contigstart = snps[i-1].physpos;
incontig = 1;
}
contigl += (snps[i].physpos - snps[i-1].physpos);
} else if (count2 == 0 && count1 > 0) {
contigend = snps[i].physpos;
if (contigsnps > 0)
contigavganc /= contigsnps;
long cs = contigstart;
long ce = contigend;
contigl = 0 ;
incontig = 0 ;
contigsnps = 0 ;
contigavganc = 0 ;
}
}
}
for (int i = 0 ; i < snps.size() ; i++) {
string id = snps[i].id;
string chr = snps[i].chr;
double pos = snps[i].physpos;
double gpos = snps[i].genpos;
int n1 = 0;
int n2 = 0;
double n3 = 0;
double n3a = 0 ;
double n4 = 0;
double g = 0 ;
double f = 0 ;
double f2 = 0 ;
int denom2 = 0 ;
double f1 = 0 ;
int denom1 = 0 ;
int d = 0 ;
int a = 0 ;
int dn = 0 ;
int an = 0;
double maxl = 0 ;
double maxgl = 0;
for (int j = 0 ; j < nind ; j++) {
string key = chr + ":" + tostring(i) + ":" + tostring(j);
double panc = (*predanc).get(c,i,j);
if (io::debug >= 1)
cout << "panc ( " << c <<","<<i<<","<<j<<") = " << panc << endl;
int predn = 0 ;
int predh = 0 ;
double predl = 0 ;
if (usegenpos) {
if ( glmap.find(key) != glmap.end())
predl = glmap[key] * 100;
if (maxgl < predl)
maxgl = predl;
} else {
if ( plmap.find(key) != plmap.end())
predl = plmap[key];
if (maxl < predl)
maxl = predl;
}
if ( panc >= thresh1 && predl >= tlength)
predn = 1;
if (panc <= thresh2)
predh = 1;
int allele = (*geno)(c,i,j);
f += allele;
if (allele==1) {
d ++;
n1 += predn;
n2 += predh;
n3 += panc;
if (predn )
dn ++;
}
if (allele==0) {
n3a += panc;
a ++;
if (predn )
an ++;
}
n4 += panc;
if (predn) {
f1 += allele;
denom1++;
}
if (predh) {
f2 += allele;
denom2 ++;
}
}
f /= nind;
g /= nind;
f1 = denom1>0?(f1/denom1):0;
f2 = denom2>0?(f2/denom2):0;
if (d>0) {
n1/=d; n2/=d; n3/=d;
}
if (a>0) {
n3a /= a;
}
if (nind > 0)
n4 /= nind;
int m1 = (n1>=1)?1:0;
int m2 = ( (n1>0)&&(n2>0))?1:0;
cout << id << "\t" << chr << "\t" << gpos*100 << "\t" << snps[i].getphyspos ();
cout << "\t" << n3 << "\t" << n3a ;
cout << "\t" << dn << "\t" << d << "\t" << an << "\t" << a;
cout << endl;
if (denomlengths[i]>0) {
avglengths[i] /= denomlengths[i];
avgglengths[i] /= denomlengths[i];
}
if (givenprefix) {
maxglengths[i] *= 100;
avgglengths[i] *= 100;
long ml = maxlengths[i];
long al = avglengths[i];
}
}
}
}