mvec< mvec<int>* > Genome::GetGenicDNA()
{
mvec<mvec<int>*> dna(genes.size());
for (int i=0;i<genes.size();i++)
dna[i] = new mvec<int>(dna::nt2int(GetGeneDNA(genes[i])));
return dna;
}
//does everything to fill in all the data
void BAMUtils::_crunch_data() {
dna();
padded_alignment();
if (get_bamread().mapped_reverse_strand()) {
reverse();
}
//shift indels to 5'
if (five_prime_justify)
left_justify();
//cip soft clipped portions of read
if (total_three_prime_ignore > 0)
remove_bases_before_soft_clipped();
int startBase = 0;
int stopBase = 0;
bool calcRegionError = bam_record.get_region_base_positions(&startBase, &stopBase);
_region_clipped = false;
if(calcRegionError) adjust_region_base_positions(&startBase, &stopBase, pad_target, &_region_clipped);
score_alignments(q_scores, calcRegionError, startBase, stopBase);
calc_error();
}
void display(void)
{
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
glOrtho(0, 1000, 0.0, 650,-2000,1500);
glMatrixMode(GL_MODELVIEW);
glClearColor(0.9, 0.9, 0.9, 0.9);
glClear(GL_DEPTH_BUFFER_BIT | GL_COLOR_BUFFER_BIT);
switch(page)
{
case -1: intro(); break;
case 0: menu(); break;
case 1: dna(); break;
case 2: adenineThymine(); break;
case 3: cytosineGuanine(); break;
}
glFlush();
glutSwapBuffers();
}
std::vector<Wt::WSslCertificate::DnAttribute>
getDnAttributes(struct X509_name_st *sn)
{
std::vector<Wt::WSslCertificate::DnAttribute> retval;
if (!sn)
return retval;
int entries = X509_NAME_entry_count(sn);
for (int i = 0; i < entries; ++i) {
X509_NAME_ENTRY *entry = X509_NAME_get_entry(sn, i);
ASN1_OBJECT *obj = X509_NAME_ENTRY_get_object(entry);
ASN1_STRING *data = X509_NAME_ENTRY_get_data(entry);
int nid = OBJ_obj2nid(obj);
std::string value;
{
char *s;
ASN1_STRING_to_UTF8((unsigned char **)(&s), data);
value = s;
OPENSSL_free(s);
}
Wt::WSslCertificate::DnAttributeName name;
bool knownAttribute = true;
switch (nid) {
case NID_commonName:
name = Wt::WSslCertificate::CommonName; break;
case NID_countryName:
name = Wt::WSslCertificate::CountryName; break;
case NID_localityName:
name = Wt::WSslCertificate::LocalityName; break;
case NID_stateOrProvinceName:
name = Wt::WSslCertificate::StateOrProvinceName; break;
case NID_organizationName:
name = Wt::WSslCertificate::OrganizationName; break;
case NID_organizationalUnitName:
name = Wt::WSslCertificate::OrganizationalUnitName; break;
case NID_givenName:
name = Wt::WSslCertificate::GivenName; break;
case NID_surname:
name = Wt::WSslCertificate::Surname; break;
case NID_initials:
name = Wt::WSslCertificate::Initials; break;
case NID_serialNumber:
name = Wt::WSslCertificate::SerialNumber; break;
case NID_title:
name = Wt::WSslCertificate::Title; break;
default:
// extra unknown attributes; ignore them
knownAttribute = false;
break;
}
if (knownAttribute) {
Wt::WSslCertificate::DnAttribute dna(name, value);
retval.push_back(dna);
}
}
return retval;
}
void display_loop(){
// mcuf_serial_mode();
mode = setjmp(newmode_jmpbuf);
#ifdef JOYSTICK_SUPPORT
// in case we get here via mode jump, we (re)enable joystick queries
waitForFire = 1;
#endif
oldOldmode = oldMode;
#ifdef JOYSTICK_SUPPORT
waitForFire = 1;
#endif
for(;;){
#ifndef MENU_SUPPORT
clear_screen(0);
#endif
oldMode = mode;
switch(mode++) {
#ifdef ANIMATION_SCROLLTEXT
case 1:
scrolltext(scrolltext_text);
#ifdef RANDOM_SUPPORT
{
char a[28];
sprintf(a,"</# counter == %lu ",
(unsigned long)percnt_get(&g_reset_counter, &g_reset_counter_idx));
scrolltext(a);
}
#endif
#endif
#ifdef ANIMATION_TIME
#ifndef ANIMATION_SCROLLTEXT
case 1:
#endif
time_anim();
break;
#else
#ifdef ANIMATION_SCROLLTEXT
break;
#endif
#endif
#ifdef ANIMATION_SPIRAL
# ifndef SPIRAL_DELAY
# define SPIRAL_DELAY 5
# endif
case 2:
spiral(SPIRAL_DELAY);
break;
#endif
#ifdef ANIMATION_JOERN1
case 3:
joern1();
break;
#endif
#ifdef ANIMATION_SNAKE
case 4:
snake_animation();
break;
#endif
#ifdef ANIMATION_CHECKERBOARD
case 5:
checkerboard(20);
break;
#endif
#ifdef ANIMATION_FIRE
case 6:
fire();
break;
#endif
#ifdef ANIMATION_TIME
case 7:
time_anim();
break;
#endif
#ifdef ANIMATION_MATRIX
case 8:
matrix();
break;
#endif
#ifdef ANIMATION_RANDOM_BRIGHT
case 9:
random_bright(30);
break;
#endif
#ifdef ANIMATION_STONEFLY
case 10:
stonefly();
break;
#endif
#ifdef ANIMATION_GAMEOFLIFE
case 11:
gameoflife();
break;
#endif
#ifdef ANIMATION_FLYINGDOTS
case 12:
flyingdots();
break;
#endif
#ifdef ANIMATION_BREAKOUT
case 13:
breakout_demo();
break;
#endif
#ifdef ANIMATION_MHERWEG
case 14:
mherweg();
break;
#endif
#ifdef ANIMATION_MOIRE
case 15:
moire();
break;
#endif
#ifdef ANIMATION_TIME
case 16:
time_anim();
break;
#endif
#ifdef ANIMATION_LTN_ANT
case 17:
ltn_ant();
break;
#endif
#ifdef ANIMATION_LABORLOGO
case 18:
laborlogo();
break;
#endif
#ifdef ANIMATION_AMPHIBIAN
case 19:
amphibian();
break;
#endif
#ifdef ANIMATION_LOGO_OOS
case 20:
logo_OutOfSpec();
break;
#endif
#ifdef ANIMATION_FAIRYDUST
case 21:
fairydust();
break;
#endif
#ifdef ANIMATION_PLASMA
case 22:
plasma();
break;
#endif
#ifdef ANIMATION_PSYCHEDELIC
case 23:
psychedelic();
break;
#endif
#ifdef ANIMATION_BLACKHOLE
case 24:
blackhole();
break;
#endif
#ifdef ANIMATION_SQUARES
case 25:
squares();
break;
#endif
#ifdef ANIMATION_DNA
case 26:
dna();
break;
#endif
#ifdef ANIMATION_TESTS
case 31:
test_level(1, false);
break;
case 32:
test_level(2, false);
break;
case 33:
test_level(3, false);
break;
case 35:
test_palette(false);
test_palette2(false);
break;
#endif
#ifdef SMALLANIMATION_ROWWALK
case 36:
rowwalk(SMALLANIMATION_ROWWALK_COUNT,SMALLANIMATION_ROWWALK_SPEED);
break;
#endif
#ifdef SMALLANIMATION_COLWALK
case 37:
colwalk(SMALLANIMATION_COLWALK_COUNT,SMALLANIMATION_COLWALK_SPEED);
break;
#endif
#ifdef SMALLANIMATION_COLBOUNCE
case 38:
colbounce(SMALLANIMATION_COLBOUNCE_COUNT,SMALLANIMATION_COLBOUNCE_SPEED);
break;
#endif
#ifdef SMALLANIMATION_ROWBOUNCE
case 39:
rowbounce(SMALLANIMATION_ROWBOUNCE_COUNT,SMALLANIMATION_ROWBOUNCE_SPEED);
break;
#endif
#ifdef MENU_SUPPORT
case 0xFDu:
mode = 1;
break;
case 0xFEu:
menu();
mode = oldOldmode;
break;
#else
case 0xFDu:
#ifdef JOYSTICK_SUPPORT
if (JOYISFIRE)
mode = 0xFEu;
else
#endif
mode = 1;
break;
case 0xFEu:
#ifdef JOYSTICK_SUPPORT
waitForFire = 0; // avoid circular jumps
while (JOYISFIRE); // wait until user released the fire button
#endif
wait(25); // wait for button to settle
# ifdef GAME_TETRIS
tetris();
# endif
# ifdef GAME_BASTET
tetris_bastet();
# endif
# ifdef GAME_TETRIS_FP
tetris_fp();
# endif
# ifdef GAME_SPACE_INVADERS
borg_invaders();
# endif
# ifdef GAME_SNAKE
snake_game();
# endif
# ifdef GAME_BREAKOUT
borg_breakout(0);
# endif
#ifdef JOYSTICK_SUPPORT
while (JOYISFIRE); // avoid an unwanted restart of the game loop
#endif
wait(25); // wait for button to settle
mode = oldOldmode; // restore old animation mode
#ifdef JOYSTICK_SUPPORT
waitForFire = 1; // reenable joystick query of the wait() function
#endif
break;
#endif
#ifdef ANIMATION_OFF
case 0xFFu:
off();
break;
#endif
default:
if (reverseMode) {
if (reverseMode-- == (mode - 1)) {
mode -= 2;
} else {
reverseMode = 0;
}
}
break;
}
}
}
