// File: /workspace/github_c_makefile_star2_O0/dapogon[P]cellcoal/src/cellcoal.c
// Function: HKYmodel
void HKYmodel (double Pij[4][4], double branchLength)
	{
	int			i, j;
	double		AA, t, PIj;

	t = branchLength;

	for (i=0; i<4; i++)
		{
		for (j=0; j<4; j++)
			{
			if (j == A || j == G)	/* purine */
				PIj = freqR;
			else
				PIj = freqY; /* pyrimidine */
				
			AA = 1 + PIj*(kappa-1.0);
			
			if (i==j)
				Pij[i][j] = freq[j] + freq[j]*(1/PIj - 1)*exp(-beta*t) + ((PIj-freq[j])/PIj)*exp(-beta*t*AA);
			else if ((i==A && j==G) || (i==C && j==T) || (i==G && j==A) || (i==T && j==C)) /* transition */
				Pij[i][j] = freq[j] + freq[j]*(1/PIj - 1)*exp(-beta*t) - (freq[j]/PIj)*exp(-beta*t*AA);
			else /* transversion */
				Pij[i][j] = freq[j]*(1-exp(-beta*t));
			}
		}
	}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x80, %rsp
movq %rdi, -0x8(%rbp)
movsd %xmm0, -0x10(%rbp)
movsd -0x10(%rbp), %xmm0
movsd %xmm0, -0x28(%rbp)
movl $0x0, -0x14(%rbp)
cmpl $0x4, -0x14(%rbp)
jge 0x1cb3b
movl $0x0, -0x18(%rbp)
cmpl $0x4, -0x18(%rbp)
jge 0x1cb2b
cmpl $0x0, -0x18(%rbp)
je 0x1c7fc
cmpl $0x2, -0x18(%rbp)
jne 0x1c80b
movsd 0x33214(%rip), %xmm0    # 0x4fa18
movsd %xmm0, -0x30(%rbp)
jmp 0x1c818
movsd 0x3320d(%rip), %xmm0    # 0x4fa20
movsd %xmm0, -0x30(%rbp)
movsd -0x30(%rbp), %xmm0
movsd 0x33213(%rip), %xmm1    # 0x4fa38
movsd 0x227f3(%rip), %xmm2    # 0x3f020
subsd %xmm2, %xmm1
mulsd %xmm1, %xmm0
movsd 0x227e3(%rip), %xmm1    # 0x3f020
addsd %xmm1, %xmm0
movsd %xmm0, -0x20(%rbp)
movl -0x14(%rbp), %eax
cmpl -0x18(%rbp), %eax
jne 0x1c95b
movslq -0x18(%rbp), %rcx
leaq 0x319f3(%rip), %rax     # 0x4e250
movsd (%rax,%rcx,8), %xmm0
movsd %xmm0, -0x50(%rbp)
movslq -0x18(%rbp), %rcx
leaq 0x319de(%rip), %rax     # 0x4e250
movsd (%rax,%rcx,8), %xmm0
movsd 0x227a1(%rip), %xmm1    # 0x3f020
divsd -0x30(%rbp), %xmm1
movsd 0x22794(%rip), %xmm2    # 0x3f020
subsd %xmm2, %xmm1
mulsd %xmm1, %xmm0
movsd %xmm0, -0x48(%rbp)
movsd 0x3316f(%rip), %xmm0    # 0x4fa10
movq %xmm0, %rax
movabsq $-0x8000000000000000, %rcx # imm = 0x8000000000000000
xorq %rcx, %rax
movq %rax, %xmm0
mulsd -0x28(%rbp), %xmm0
callq 0x22b0
movsd -0x50(%rbp), %xmm1
movaps %xmm0, %xmm2
movsd -0x48(%rbp), %xmm0
mulsd %xmm2, %xmm0
addsd %xmm1, %xmm0
movsd %xmm0, -0x40(%rbp)
movsd -0x30(%rbp), %xmm0
movslq -0x18(%rbp), %rcx
leaq 0x31964(%rip), %rax     # 0x4e250
subsd (%rax,%rcx,8), %xmm0
divsd -0x30(%rbp), %xmm0
movsd %xmm0, -0x38(%rbp)
movsd 0x3310d(%rip), %xmm0    # 0x4fa10
movq %xmm0, %rax
movabsq $-0x8000000000000000, %rcx # imm = 0x8000000000000000
xorq %rcx, %rax
movq %rax, %xmm0
mulsd -0x28(%rbp), %xmm0
mulsd -0x20(%rbp), %xmm0
callq 0x22b0
movsd -0x40(%rbp), %xmm1
movaps %xmm0, %xmm2
movsd -0x38(%rbp), %xmm0
mulsd %xmm2, %xmm0
addsd %xmm1, %xmm0
movq -0x8(%rbp), %rax
movslq -0x14(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movslq -0x18(%rbp), %rcx
movsd %xmm0, (%rax,%rcx,8)
jmp 0x1cb1b
cmpl $0x0, -0x14(%rbp)
jne 0x1c967
cmpl $0x2, -0x18(%rbp)
je 0x1c993
cmpl $0x1, -0x14(%rbp)
jne 0x1c973
cmpl $0x3, -0x18(%rbp)
je 0x1c993
cmpl $0x2, -0x14(%rbp)
jne 0x1c97f
cmpl $0x0, -0x18(%rbp)
je 0x1c993
cmpl $0x3, -0x14(%rbp)
jne 0x1caab
cmpl $0x1, -0x18(%rbp)
jne 0x1caab
movslq -0x18(%rbp), %rcx
leaq 0x318b2(%rip), %rax     # 0x4e250
movsd (%rax,%rcx,8), %xmm0
movsd %xmm0, -0x70(%rbp)
movslq -0x18(%rbp), %rcx
leaq 0x3189d(%rip), %rax     # 0x4e250
movsd (%rax,%rcx,8), %xmm0
movsd 0x22660(%rip), %xmm1    # 0x3f020
divsd -0x30(%rbp), %xmm1
movsd 0x22653(%rip), %xmm2    # 0x3f020
subsd %xmm2, %xmm1
mulsd %xmm1, %xmm0
movsd %xmm0, -0x68(%rbp)
movsd 0x3302e(%rip), %xmm0    # 0x4fa10
movq %xmm0, %rax
movabsq $-0x8000000000000000, %rcx # imm = 0x8000000000000000
xorq %rcx, %rax
movq %rax, %xmm0
mulsd -0x28(%rbp), %xmm0
callq 0x22b0
movsd -0x70(%rbp), %xmm1
movaps %xmm0, %xmm2
movsd -0x68(%rbp), %xmm0
mulsd %xmm2, %xmm0
addsd %xmm1, %xmm0
movsd %xmm0, -0x60(%rbp)
movslq -0x18(%rbp), %rcx
leaq 0x31828(%rip), %rax     # 0x4e250
movsd (%rax,%rcx,8), %xmm0
divsd -0x30(%rbp), %xmm0
movsd %xmm0, -0x58(%rbp)
movsd 0x32fd1(%rip), %xmm0    # 0x4fa10
movq %xmm0, %rax
movabsq $-0x8000000000000000, %rcx # imm = 0x8000000000000000
xorq %rcx, %rax
movq %rax, %xmm0
mulsd -0x28(%rbp), %xmm0
mulsd -0x20(%rbp), %xmm0
callq 0x22b0
movsd -0x60(%rbp), %xmm1
movaps %xmm0, %xmm2
movsd -0x58(%rbp), %xmm0
movq %xmm0, %rax
movabsq $-0x8000000000000000, %rcx # imm = 0x8000000000000000
xorq %rcx, %rax
movq %rax, %xmm0
mulsd %xmm2, %xmm0
addsd %xmm1, %xmm0
movq -0x8(%rbp), %rax
movslq -0x14(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movslq -0x18(%rbp), %rcx
movsd %xmm0, (%rax,%rcx,8)
jmp 0x1cb19
movslq -0x18(%rbp), %rcx
leaq 0x3179a(%rip), %rax     # 0x4e250
movsd (%rax,%rcx,8), %xmm0
movsd %xmm0, -0x78(%rbp)
movsd 0x32f48(%rip), %xmm0    # 0x4fa10
movq %xmm0, %rax
movabsq $-0x8000000000000000, %rcx # imm = 0x8000000000000000
xorq %rcx, %rax
movq %rax, %xmm0
mulsd -0x28(%rbp), %xmm0
callq 0x22b0
movaps %xmm0, %xmm2
movsd -0x78(%rbp), %xmm0
movsd 0x22527(%rip), %xmm1    # 0x3f020
subsd %xmm2, %xmm1
mulsd %xmm1, %xmm0
movq -0x8(%rbp), %rax
movslq -0x14(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movslq -0x18(%rbp), %rcx
movsd %xmm0, (%rax,%rcx,8)
jmp 0x1cb1b
jmp 0x1cb1d
movl -0x18(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x18(%rbp)
jmp 0x1c7e6
jmp 0x1cb2d
movl -0x14(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x14(%rbp)
jmp 0x1c7d5
addq $0x80, %rsp
popq %rbp
retq
nopw %cs:(%rax,%rax)