Ejemplo n.º 1
0
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;
}
Ejemplo n.º 2
0
//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();
	
	
}
Ejemplo n.º 3
0
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();
}
Ejemplo n.º 4
0
    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;
    }
Ejemplo n.º 5
0
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;
		}
	}
}