Constant Field Values


Contents
<Unnamed>.*

Constants
protected static final double big 4.503599627370496E15
protected static final double biginv 2.220446049250313E-16
protected static final double LOGPI 1.1447298858494002
protected static final double MACHEP 1.1102230246251565E-16
protected static final double MAXGAM 171.6243769563027
protected static final double MAXLOG 709.782712893384
protected static final double MINLOG -745.1332191019412
protected static final double SQRTH 0.7071067811865476
protected static final double SQTPI 2.5066282746310007

Forward_alt
final int BI 14
final int PO 13
final int U 12

Forward_std
final int BI 14
final int PO 13
final int U 12

HMM
public static final int AMINO 1
public static final int AMINO_DOUBLE_GAP 4
public static final int AMINO_GAP 3
public static final int CLUSTER 100
public static final int DELETE 4
public static final int DNA 2
public static final int END 99
public static final int ENDNODE 2
public static final int EVEN 0
public static final int FORWARD_ALT 104
public static final int FORWARD_STD 103
public static final int HIGHWAY 107
public static final int INSERT 3
public static final int LOCKED 5
public static final int LOCKED_EVEN 4
public static final int LOCKED_MANUAL 5
public static final int MANUAL 3
public static final int NOTYPE -1
public static final int OWN 100
public static final int PROFILE7 101
public static final int PROFILE9 105
public static final int RANDOM 2
public static final int SILENT 2
public static final int SINGLELOOP 102
public static final int SINGLENODE 0
public static final int STANDARD 1
public static final int START 0
public static final int STARTNODE 1
public static final int U_TURN 106
public static final int ZERO 1

Profile7
final double INIT_A_OPEN_PROB 0.99
final double INIT_DD_PROB 0.8
final double INIT_DM_PROB 0.2
final double INIT_EXIT_PROB 0.025
final double INIT_II_PROB 0.8
final double INIT_IM_PROB 0.2
final double INIT_MD_PROB 0.025
final double INIT_MI_PROB 0.025
final double INIT_MM_PROB 0.925
final double INIT_NA_CLOSE_PROB 0.01
final double INIT_NA_LOOP_PROB 0.99
final double INIT_NA_OPEN_PROB 0.01

Profile9
final double INIT_A_OPEN_PROB 0.99
final double INIT_DD_PROB 0.8
final double INIT_DI_PROB 0.01
final double INIT_DM_PROB 0.19
final double INIT_EXIT_PROB 0.025
final double INIT_ID_PROB 0.01
final double INIT_II_PROB 0.8
final double INIT_IM_PROB 0.19
final double INIT_MD_PROB 0.025
final double INIT_MI_PROB 0.025
final double INIT_MM_PROB 0.925
final double INIT_NA_CLOSE_PROB 0.01
final double INIT_NA_LOOP_PROB 0.99
final double INIT_NA_OPEN_PROB 0.01