LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addChromosome(Chromosome)
void Model::addChromosome(Chromosome chr) {
  assert ( find(chromosomes.begin(), chromosomes.end(), chr) == chromosomes.end() ); // Chromosomes must be unique
  // Assert that all Bead IDS ARE UNIQUE HERE AND NOT FOUND ON ANY CHR HERE
  chromosomes.push_back(chr);  
  this->updateBeadMap();
  //hasUpdatedHashMap = false;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
movq 0xa78(%rdi), %rdi
movq 0xa80(%rbx), %rsi
movq %r14, %rdx
callq 0x17ac5
cmpq 0xa80(%rbx), %rax
jne 0xe3f9
leaq 0xa78(%rbx), %rdi
movq %r14, %rsi
callq 0x16a98
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0xe2ba
leaq 0x1bf60(%rip), %rdi     # 0x2a360
leaq 0x1bfa0(%rip), %rsi     # 0x2a3a7
leaq 0x1bfa7(%rip), %rcx     # 0x2a3b5
movl $0x29, %edx
callq 0x6210
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double, ConstraintType, double, double, double)
void Model::addConstraint(string beadId1, string beadId2, double targetDistance, ConstraintType ct /*=REGULAR*/, double springConstant /*=1*/, double lowerBound /*=0*/, double upperBound /*=INF*/) {
  assert(getBead.find(beadId1) != getBead.end()); 
  assert(getBead.find(beadId2) != getBead.end()); 
  Bead* b1 = getBead[beadId1];
  Bead* b2 = getBead[beadId2];
  this->addConstraint(Constraint(b1, b2, targetDistance, ct, springConstant, lowerBound, upperBound));
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x98, %rsp
movsd %xmm3, 0x58(%rsp)
movsd %xmm2, 0x50(%rsp)
movsd %xmm1, 0x48(%rsp)
movl %ecx, %ebp
movsd %xmm0, 0x40(%rsp)
movq %rdx, %r14
movq %rsi, %r12
movq %rdi, %rbx
leaq 0xaa0(%rdi), %r15
movq %r15, %rdi
callq 0x18430
leaq 0xaa8(%rbx), %r13
cmpq %r13, %rax
je 0xe5c2
movq %r15, %rdi
movq %r14, %rsi
callq 0x18430
cmpq %r13, %rax
je 0xe5e1
movq %r15, %rdi
movq %r12, %rsi
callq 0x16b76
movq (%rax), %r12
movq %r15, %rdi
movq %r14, %rsi
callq 0x16b76
movq (%rax), %rdx
leaq 0x60(%rsp), %r14
movq %r14, %rdi
movq %r12, %rsi
movsd 0x40(%rsp), %xmm0
movl %ebp, %ecx
movsd 0x48(%rsp), %xmm1
movsd 0x50(%rsp), %xmm2
movsd 0x58(%rsp), %xmm3
callq 0xde1c
movq 0x30(%r14), %rax
movq %rax, 0x30(%rsp)
movups (%r14), %xmm0
movups 0x10(%r14), %xmm1
movups 0x20(%r14), %xmm2
movups %xmm2, 0x20(%rsp)
movups %xmm1, 0x10(%rsp)
movups %xmm0, (%rsp)
movq %rbx, %rdi
callq 0xe418
addq $0x98, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1be12(%rip), %rdi     # 0x2a3db
leaq 0x1bdd7(%rip), %rsi     # 0x2a3a7
leaq 0x1be2b(%rip), %rcx     # 0x2a402
movl $0x37, %edx
callq 0x6210
leaq 0x1be74(%rip), %rdi     # 0x2a45c
leaq 0x1bdb8(%rip), %rsi     # 0x2a3a7
leaq 0x1be0c(%rip), %rcx     # 0x2a402
movl $0x38, %edx
callq 0x6210
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addInteractionConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double, ConstraintType)
void Model::addInteractionConstraint(string beadId1, string beadId2, double springConstant /*=1*/, ConstraintType interactionType/*= INTERACTION*/) {
  assert(getBead.find(beadId1) != getBead.end()); 
  assert(getBead.find(beadId2) != getBead.end());
  assert(interactionType == INTERACTION || interactionType == INTERACTION_INTRA || interactionType == INTERACTION_INTER);

  Bead* b1 = getBead[beadId1];
  Bead* b2 = getBead[beadId2];
  this->addConstraint(beadId1, beadId2, b1->getRadius()+b2->getRadius(), interactionType, springConstant);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movl %ecx, %ebx
movsd %xmm0, 0x30(%rsp)
movq %rdx, %r15
movq %rsi, %r12
movq %rdi, %r14
leaq 0xaa0(%rdi), %r13
movq %r13, %rdi
callq 0x18430
leaq 0xaa8(%r14), %rbp
cmpq %rbp, %rax
je 0xe747
movq %r13, %rdi
movq %r15, %rsi
callq 0x18430
cmpq %rbp, %rax
je 0xe766
leal -0x7(%rbx), %eax
cmpl $0x2, %eax
jb 0xe663
cmpl $0x1, %ebx
jne 0xe785
movq %r13, %rdi
movq %r12, %rsi
callq 0x16b76
movq (%rax), %rbp
movq %r13, %rdi
movq %r15, %rsi
callq 0x16b76
movq (%rax), %r13
leaq 0x18(%rsp), %rax
movq %rax, -0x10(%rax)
movq (%r12), %rsi
movq 0x8(%r12), %rdx
addq %rsi, %rdx
leaq 0x8(%rsp), %rdi
callq 0xa53a
leaq 0x48(%rsp), %r12
movq %r12, -0x10(%r12)
movq (%r15), %rsi
movq 0x8(%r15), %rdx
addq %rsi, %rdx
leaq 0x38(%rsp), %rdi
callq 0xa53a
movq %rbp, %rdi
callq 0xae12
movsd %xmm0, 0x28(%rsp)
movq %r13, %rdi
callq 0xae12
movsd 0x28(%rsp), %xmm1
addsd %xmm0, %xmm1
leaq 0x8(%rsp), %rsi
leaq 0x38(%rsp), %rdx
movsd 0x1bbfa(%rip), %xmm3    # 0x2a2e8
xorps %xmm2, %xmm2
movq %r14, %rdi
movapd %xmm1, %xmm0
movl %ebx, %ecx
movsd 0x30(%rsp), %xmm1
callq 0xe4d6
movq 0x38(%rsp), %rdi
cmpq %r12, %rdi
je 0xe71c
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0xe738
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1bc8d(%rip), %rdi     # 0x2a3db
leaq 0x1bc52(%rip), %rsi     # 0x2a3a7
leaq 0x1bd27(%rip), %rcx     # 0x2a483
movl $0x3f, %edx
callq 0x6210
leaq 0x1bcef(%rip), %rdi     # 0x2a45c
leaq 0x1bc33(%rip), %rsi     # 0x2a3a7
leaq 0x1bd08(%rip), %rcx     # 0x2a483
movl $0x40, %edx
callq 0x6210
leaq 0x1bd44(%rip), %rdi     # 0x2a4d0
leaq 0x1bc14(%rip), %rsi     # 0x2a3a7
leaq 0x1bce9(%rip), %rcx     # 0x2a483
movl $0x41, %edx
callq 0x6210
movq %rax, %rbx
jmp 0xe7c3
movq %rax, %rbx
movq 0x38(%rsp), %rdi
cmpq %r12, %rdi
je 0xe7c3
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0xe7df
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addInteractionDistanceConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double, double)
void Model::addInteractionDistanceConstraint(string beadId1, string beadId2, double beadPairDesiredDistance, double springConstant /*=1*/) {
  assert(getBead.find(beadId1) != getBead.end()); 
  assert(getBead.find(beadId2) != getBead.end());

  Bead* b1 = getBead[beadId1];
  Bead* b2 = getBead[beadId2];
  this->addConstraint(beadId1, beadId2, b1->getRadius()+b2->getRadius() + beadPairDesiredDistance, INTERACTION_DIST, springConstant);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movsd %xmm1, 0x10(%rsp)
movsd %xmm0, 0x8(%rsp)
movq %rdx, %r14
movq %rsi, %r12
movq %rdi, %rbx
leaq 0xaa0(%rdi), %r15
movq %r15, %rdi
callq 0x18430
leaq 0xaa8(%rbx), %r13
cmpq %r13, %rax
je 0xe924
movq %r15, %rdi
movq %r14, %rsi
callq 0x18430
cmpq %r13, %rax
je 0xe943
movq %r15, %rdi
movq %r12, %rsi
callq 0x16b76
movq (%rax), %r13
movq %r15, %rdi
movq %r14, %rsi
callq 0x16b76
movq (%rax), %r15
leaq 0x48(%rsp), %rbp
movq %rbp, -0x10(%rbp)
movq (%r12), %rsi
movq 0x8(%r12), %rdx
addq %rsi, %rdx
leaq 0x38(%rsp), %rdi
callq 0xa53a
leaq 0x28(%rsp), %r12
movq %r12, -0x10(%r12)
movq (%r14), %rsi
movq 0x8(%r14), %rdx
addq %rsi, %rdx
leaq 0x18(%rsp), %rdi
callq 0xa53a
movq %r13, %rdi
callq 0xae12
movsd %xmm0, (%rsp)
movq %r15, %rdi
callq 0xae12
movsd (%rsp), %xmm1
addsd %xmm0, %xmm1
addsd 0x8(%rsp), %xmm1
leaq 0x38(%rsp), %rsi
leaq 0x18(%rsp), %rdx
movsd 0x1ba1b(%rip), %xmm3    # 0x2a2e8
xorps %xmm2, %xmm2
movq %rbx, %rdi
movapd %xmm1, %xmm0
movl $0x9, %ecx
movsd 0x10(%rsp), %xmm1
callq 0xe4d6
movq 0x18(%rsp), %rdi
cmpq %r12, %rdi
je 0xe8fe
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x38(%rsp), %rdi
cmpq %rbp, %rdi
je 0xe915
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1bab0(%rip), %rdi     # 0x2a3db
leaq 0x1ba75(%rip), %rsi     # 0x2a3a7
leaq 0x1bc06(%rip), %rcx     # 0x2a53f
movl $0x49, %edx
callq 0x6210
leaq 0x1bb12(%rip), %rdi     # 0x2a45c
leaq 0x1ba56(%rip), %rsi     # 0x2a3a7
leaq 0x1bbe7(%rip), %rcx     # 0x2a53f
movl $0x4a, %edx
callq 0x6210
movq %rax, %rbx
jmp 0xe981
movq %rax, %rbx
movq 0x18(%rsp), %rdi
cmpq %r12, %rdi
je 0xe981
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x38(%rsp), %rdi
cmpq %rbp, %rdi
je 0xe998
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addInteractionLowerDistanceConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double, double)
void Model::addInteractionLowerDistanceConstraint(string beadId1, string beadId2, double beadPairDesiredDistance, double springConstant /*=1*/) {
  assert(getBead.find(beadId1) != getBead.end()); 
  assert(getBead.find(beadId2) != getBead.end());

  Bead* b1 = getBead[beadId1];
  Bead* b2 = getBead[beadId2];
  this->addConstraint(beadId1, beadId2, b1->getRadius()+b2->getRadius() + beadPairDesiredDistance, INTERACTION_DIST, springConstant, 0, b1->getRadius()+b2->getRadius() + beadPairDesiredDistance);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movsd %xmm1, 0x20(%rsp)
movsd %xmm0, 0x18(%rsp)
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbx
leaq 0xaa0(%rdi), %r14
movq %r14, %rdi
callq 0x18430
leaq 0xaa8(%rbx), %r15
cmpq %r15, %rax
je 0xeb04
movq %r14, %rdi
movq %r12, %rsi
callq 0x18430
cmpq %r15, %rax
je 0xeb23
movq %r14, %rdi
movq %r13, %rsi
callq 0x16b76
movq (%rax), %r15
movq %r14, %rdi
movq %r12, %rsi
callq 0x16b76
movq (%rax), %r14
leaq 0x58(%rsp), %rbp
movq %rbp, -0x10(%rbp)
movq (%r13), %rsi
movq 0x8(%r13), %rdx
addq %rsi, %rdx
leaq 0x48(%rsp), %rdi
callq 0xa53a
leaq 0x38(%rsp), %r13
movq %r13, -0x10(%r13)
movq (%r12), %rsi
movq 0x8(%r12), %rdx
addq %rsi, %rdx
leaq 0x28(%rsp), %rdi
callq 0xa53a
movq %r15, %rdi
callq 0xae12
movsd %xmm0, 0x10(%rsp)
movq %r14, %rdi
callq 0xae12
movsd %xmm0, 0x8(%rsp)
movq %r15, %rdi
callq 0xae12
movsd %xmm0, (%rsp)
movq %r14, %rdi
callq 0xae12
movsd 0x10(%rsp), %xmm4
addsd 0x8(%rsp), %xmm4
movsd 0x18(%rsp), %xmm1
addsd %xmm1, %xmm4
movsd (%rsp), %xmm3
addsd %xmm0, %xmm3
addsd %xmm1, %xmm3
leaq 0x48(%rsp), %rsi
leaq 0x28(%rsp), %rdx
xorps %xmm2, %xmm2
movq %rbx, %rdi
movapd %xmm4, %xmm0
movl $0x9, %ecx
movsd 0x20(%rsp), %xmm1
callq 0xe4d6
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0xeade
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0xeaf5
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1b8d0(%rip), %rdi     # 0x2a3db
leaq 0x1b895(%rip), %rsi     # 0x2a3a7
leaq 0x1ba73(%rip), %rcx     # 0x2a58c
movl $0x53, %edx
callq 0x6210
leaq 0x1b932(%rip), %rdi     # 0x2a45c
leaq 0x1b876(%rip), %rsi     # 0x2a3a7
leaq 0x1ba54(%rip), %rcx     # 0x2a58c
movl $0x54, %edx
callq 0x6210
movq %rax, %rbx
jmp 0xeb61
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0xeb61
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0xeb78
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addInteractionUpperDistanceConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double, double)
void Model::addInteractionUpperDistanceConstraint(string beadId1, string beadId2, double beadPairDesiredDistance, double springConstant /*=1*/) {
  assert(getBead.find(beadId1) != getBead.end()); 
  assert(getBead.find(beadId2) != getBead.end());

  Bead* b1 = getBead[beadId1];
  Bead* b2 = getBead[beadId2];
  this->addConstraint(beadId1, beadId2, b1->getRadius()+b2->getRadius() + beadPairDesiredDistance, INTERACTION_DIST, springConstant, b1->getRadius()+b2->getRadius() + beadPairDesiredDistance);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movsd %xmm1, 0x20(%rsp)
movsd %xmm0, 0x18(%rsp)
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbx
leaq 0xaa0(%rdi), %r14
movq %r14, %rdi
callq 0x18430
leaq 0xaa8(%rbx), %r15
cmpq %r15, %rax
je 0xece9
movq %r14, %rdi
movq %r12, %rsi
callq 0x18430
cmpq %r15, %rax
je 0xed08
movq %r14, %rdi
movq %r13, %rsi
callq 0x16b76
movq (%rax), %r15
movq %r14, %rdi
movq %r12, %rsi
callq 0x16b76
movq (%rax), %r14
leaq 0x58(%rsp), %rbp
movq %rbp, -0x10(%rbp)
movq (%r13), %rsi
movq 0x8(%r13), %rdx
addq %rsi, %rdx
leaq 0x48(%rsp), %rdi
callq 0xa53a
leaq 0x38(%rsp), %r13
movq %r13, -0x10(%r13)
movq (%r12), %rsi
movq 0x8(%r12), %rdx
addq %rsi, %rdx
leaq 0x28(%rsp), %rdi
callq 0xa53a
movq %r15, %rdi
callq 0xae12
movsd %xmm0, 0x10(%rsp)
movq %r14, %rdi
callq 0xae12
movsd %xmm0, 0x8(%rsp)
movq %r15, %rdi
callq 0xae12
movsd %xmm0, (%rsp)
movq %r14, %rdi
callq 0xae12
movsd 0x10(%rsp), %xmm4
addsd 0x8(%rsp), %xmm4
movsd 0x18(%rsp), %xmm1
addsd %xmm1, %xmm4
movsd (%rsp), %xmm2
addsd %xmm0, %xmm2
addsd %xmm1, %xmm2
leaq 0x48(%rsp), %rsi
leaq 0x28(%rsp), %rdx
movsd 0x1b653(%rip), %xmm3    # 0x2a2e8
movq %rbx, %rdi
movapd %xmm4, %xmm0
movl $0x9, %ecx
movsd 0x20(%rsp), %xmm1
callq 0xe4d6
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0xecc3
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0xecda
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1b6eb(%rip), %rdi     # 0x2a3db
leaq 0x1b6b0(%rip), %rsi     # 0x2a3a7
leaq 0x1b8e0(%rip), %rcx     # 0x2a5de
movl $0x5c, %edx
callq 0x6210
leaq 0x1b74d(%rip), %rdi     # 0x2a45c
leaq 0x1b691(%rip), %rsi     # 0x2a3a7
leaq 0x1b8c1(%rip), %rcx     # 0x2a5de
movl $0x5d, %edx
callq 0x6210
movq %rax, %rbx
jmp 0xed46
movq %rax, %rbx
movq 0x28(%rsp), %rdi
cmpq %r13, %rdi
je 0xed46
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x48(%rsp), %rdi
cmpq %rbp, %rdi
je 0xed5d
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addNucleusConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double)
void Model::addNucleusConstraint(string beadId, double springConstant /*=1*/) {
  assert(getBead.find(beadId) != getBead.end()); 
  assert(this->hasNucleus);
  Bead* b1 = getBead[beadId];  
  this->addConstraint(Constraint(b1, &(this->centerBead), this->nucleusRadius - b1->getRadius(), NUCLEUS, springConstant, this->nucleusRadius - b1->getRadius()));
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x88, %rsp
movsd %xmm0, 0x48(%rsp)
movq %rsi, %r14
movq %rdi, %rbx
leaq 0xaa0(%rdi), %r15
movq %r15, %rdi
callq 0x18430
leaq 0xaa8(%rbx), %rcx
cmpq %rcx, %rax
je 0xef43
cmpb $0x0, 0xa90(%rbx)
je 0xef62
movq %r15, %rdi
movq %r14, %rsi
callq 0x16b76
movq (%rax), %r14
leaq 0xad0(%rbx), %r15
movsd 0xa98(%rbx), %xmm0
movsd %xmm0, 0x38(%rsp)
movq %r14, %rdi
callq 0xae12
movsd 0x38(%rsp), %xmm1
subsd %xmm0, %xmm1
movsd %xmm1, 0x38(%rsp)
movsd 0xa98(%rbx), %xmm0
movsd %xmm0, 0x40(%rsp)
movq %r14, %rdi
callq 0xae12
movsd 0x40(%rsp), %xmm2
subsd %xmm0, %xmm2
leaq 0x50(%rsp), %r12
movsd 0x1b404(%rip), %xmm3    # 0x2a2e8
movq %r12, %rdi
movq %r14, %rsi
movq %r15, %rdx
movsd 0x38(%rsp), %xmm0
movl $0x3, %ecx
movsd 0x48(%rsp), %xmm1
callq 0xde1c
movq 0x30(%r12), %rax
movq %rax, 0x30(%rsp)
movups (%r12), %xmm0
movups 0x10(%r12), %xmm1
movups 0x20(%r12), %xmm2
movups %xmm2, 0x20(%rsp)
movups %xmm1, 0x10(%rsp)
movups %xmm0, (%rsp)
movq %rbx, %rdi
callq 0xe418
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
leaq 0x1b6e6(%rip), %rdi     # 0x2a630
leaq 0x1b456(%rip), %rsi     # 0x2a3a7
leaq 0x1b738(%rip), %rcx     # 0x2a690
movl $0x6e, %edx
callq 0x6210
leaq 0x1b758(%rip), %rdi     # 0x2a6c1
leaq 0x1b437(%rip), %rsi     # 0x2a3a7
leaq 0x1b719(%rip), %rcx     # 0x2a690
movl $0x6f, %edx
callq 0x6210
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addPeripheryConstraint(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, double)
void Model::addPeripheryConstraint(string beadId, double springConstant /*=1*/) {
  assert(this->hasNucleus);
  assert(getBead.find(beadId) != getBead.end()); 
  Bead* b1 = getBead[beadId];  
  this->addConstraint(Constraint(b1, &(this->centerBead), this->nucleusRadius - b1->getRadius(), PERIPHERY, springConstant));
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x88, %rsp
movsd %xmm0, 0x48(%rsp)
cmpb $0x0, 0xa90(%rdi)
je 0xf06a
movq %rsi, %r14
movq %rdi, %rbx
leaq 0xaa0(%rdi), %r15
movq %r15, %rdi
callq 0x18430
leaq 0xaa8(%rbx), %rcx
cmpq %rcx, %rax
je 0xf089
movq %r15, %rdi
movq %r14, %rsi
callq 0x16b76
movq (%rax), %r14
leaq 0xad0(%rbx), %r15
movsd 0xa98(%rbx), %xmm0
movsd %xmm0, 0x40(%rsp)
movq %r14, %rdi
callq 0xae12
movsd 0x40(%rsp), %xmm1
subsd %xmm0, %xmm1
leaq 0x50(%rsp), %r12
movsd 0x1b2de(%rip), %xmm3    # 0x2a2e8
xorps %xmm2, %xmm2
movq %r12, %rdi
movq %r14, %rsi
movq %r15, %rdx
movapd %xmm1, %xmm0
movl $0x2, %ecx
movsd 0x48(%rsp), %xmm1
callq 0xde1c
movq 0x30(%r12), %rax
movq %rax, 0x30(%rsp)
movups (%r12), %xmm0
movups 0x10(%r12), %xmm1
movups 0x20(%r12), %xmm2
movups %xmm2, 0x20(%rsp)
movups %xmm1, 0x10(%rsp)
movups %xmm0, (%rsp)
movq %rbx, %rdi
callq 0xe418
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
leaq 0x1b650(%rip), %rdi     # 0x2a6c1
leaq 0x1b32f(%rip), %rsi     # 0x2a3a7
leaq 0x1b653(%rip), %rcx     # 0x2a6d2
movl $0x75, %edx
callq 0x6210
leaq 0x1b5a0(%rip), %rdi     # 0x2a630
leaq 0x1b310(%rip), %rsi     # 0x2a3a7
leaq 0x1b634(%rip), %rcx     # 0x2a6d2
movl $0x76, %edx
callq 0x6210
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::reweightConstraints(ConstraintType, double)
void Model::reweightConstraints(ConstraintType ct, double newSpringConstant) {
  map<string,vector<Constraint> >::iterator cm_it;
  vector<Constraint>::iterator c_it;   
  for(cm_it = constraints.begin(); cm_it != constraints.end(); cm_it++) {
      for(c_it = cm_it->second.begin(); c_it != cm_it->second.end();c_it++) {
        if(c_it->constType == ct) {
	  c_it->k = newSpringConstant;
      }
    }
  }
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
movq 0xa00(%rdi), %rax
addq $0x9f0, %r14            # imm = 0x9F0
cmpq %r14, %rax
je 0xf1fa
movl %esi, %ebx
movsd %xmm0, (%rsp)
movq 0x40(%rax), %rcx
movq 0x48(%rax), %rdx
cmpq %rdx, %rcx
je 0xf1e8
cmpl %ebx, 0x10(%rcx)
jne 0xf1e2
movsd %xmm0, 0x18(%rcx)
addq $0x38, %rcx
jmp 0xf1d3
movq %rax, %rdi
callq 0x6250
movsd (%rsp), %xmm0
cmpq %r14, %rax
jne 0xf1cb
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::interactionWeightsSpecifiedSymmetricly(std::map<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>, double, std::less<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>, std::allocator<std::pair<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>> const, double>>>&)
double Model::getLossScore() {
  map<string,vector<Constraint> >::iterator it1;
  vector<Constraint>::iterator it2;  
  double res = 0;
  string constraintType;
  for(it1 = constraints.begin(); it1 != constraints.end(); it1++) {
      for(it2 = it1->second.begin(); it2 != it1->second.end(); it2++) {
	constraintType = it2->getConstraintType();
	if(constraintType == "INTERACTION" || constraintType == "INTERACTION_DIST" || constraintType == "INTERACTION_INTRA" || constraintType == "INTERACTION_INTER") {
	  res += it2->eval()/2;
	}
	else {
	  res += it2->eval();
	}
      }
  }
  return res; 
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x88, %rsp
leaq 0x18(%rsp), %rcx
movq %rcx, -0x10(%rcx)
xorl %eax, %eax
movq %rax, -0x8(%rcx)
movb %al, (%rcx)
leaq 0x38(%rsp), %rcx
movq %rcx, -0x10(%rcx)
movq %rax, -0x8(%rcx)
movb %al, (%rcx)
movq 0x18(%rsi), %r15
leaq 0x8(%rsi), %r13
cmpq %r13, %r15
sete %bl
je 0x15c1a
movq %rsi, %r14
leaq 0x48(%rsp), %rbp
leaq 0x8(%rsp), %r12
leaq 0x20(%r15), %rdx
leaq 0x40(%r15), %rsi
movq %rbp, %rdi
callq 0x1767e
movq %r12, %rdi
movq %rbp, %rsi
callq 0x63b0
leaq 0x28(%rsp), %rdi
leaq 0x68(%rsp), %rsi
callq 0x63b0
movq 0x68(%rsp), %rdi
leaq 0x78(%rsp), %rax
cmpq %rax, %rdi
je 0x15bb0
movq 0x78(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x48(%rsp), %rdi
leaq 0x58(%rsp), %rax
cmpq %rax, %rdi
je 0x15bcc
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x6310
movq %r14, %rdi
movq %r12, %rsi
callq 0x1af00
cmpq %r13, %rax
je 0x15c1a
movq %r14, %rdi
movq %r12, %rsi
callq 0x16fd2
movsd (%rax), %xmm0
subsd 0x60(%r15), %xmm0
andpd 0x14737(%rip), %xmm0    # 0x2a330
ucomisd 0x1470f(%rip), %xmm0    # 0x2a310
ja 0x15c1a
movq %r15, %rdi
callq 0x6250
movq %rax, %r15
cmpq %r13, %rax
sete %bl
jne 0x15b6a
movq 0x28(%rsp), %rdi
leaq 0x38(%rsp), %rax
cmpq %rax, %rdi
je 0x15c36
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x15c52
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
andb $0x1, %bl
movl %ebx, %eax
addq $0x88, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x15c6d
jmp 0x15c6d
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x16b40
movq %rbx, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: weightedSamplePos(std::vector<double, std::allocator<double>>, boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u>&)
uint weightedSamplePos(std::vector<double> weights, ENG &eng) {  
  std::vector<double> cumSumWeights(0, weights.size());
  double weightSum = accumulate(weights.begin(), weights.end(), 0);
  partial_sum(weights.begin(), weights.end(), weights.begin());
  double rnd = util::unif_real(0.0,weightSum, eng);
  uint pos = std::lower_bound(weights.begin(), weights.end(), rnd) - weights.begin();
  return pos;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movq (%rdi), %rcx
movq 0x8(%rdi), %rax
cmpq %rax, %rcx
je 0xfe7d
xorl %edx, %edx
movq %rcx, %rdi
xorps %xmm0, %xmm0
cvtsi2sd %edx, %xmm0
addsd (%rdi), %xmm0
cvttsd2si %xmm0, %edx
addq $0x8, %rdi
cmpq %rax, %rdi
jne 0xfe5f
cvtsi2sd %edx, %xmm1
jmp 0xfe81
xorpd %xmm1, %xmm1
cmpq %rax, %rcx
je 0xfea4
leaq 0x8(%rcx), %rdx
cmpq %rax, %rdx
je 0xfea4
movsd (%rcx), %xmm0
addsd (%rdx), %xmm0
movsd %xmm0, (%rdx)
addq $0x8, %rdx
cmpq %rax, %rdx
jne 0xfe93
xorpd %xmm0, %xmm0
movq %rsi, %rdi
callq 0x72a4
movq (%rbx), %rcx
movq 0x8(%rbx), %rdx
subq %rcx, %rdx
sarq $0x3, %rdx
movq %rcx, %rax
testq %rdx, %rdx
jle 0xfeec
movq %rcx, %rax
movq %rdx, %rsi
shrq %rsi
ucomisd (%rax,%rsi,8), %xmm0
jbe 0xfee4
leaq (%rax,%rsi,8), %rax
addq $0x8, %rax
notq %rsi
addq %rdx, %rsi
movq %rsi, %rdx
testq %rsi, %rsi
jg 0xfecc
subq %rcx, %rax
shrq $0x3, %rax
popq %rbx
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::writeCMM(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
void Model::writeCMM(string fileName) {
  std::ofstream myfile;
  myfile.open(fileName.c_str());
  myfile << this->getCMM();
  myfile.close();
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x220, %rsp            # imm = 0x220
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x20(%rsp), %r15
movq %r15, %rdi
callq 0x6540
movq (%r14), %rsi
movq %r15, %rdi
movl $0x10, %edx
callq 0x6050
movq %rsp, %rdi
movq %rbx, %rsi
callq 0x10f5e
movq (%rsp), %rsi
movq 0x8(%rsp), %rdx
leaq 0x20(%rsp), %rdi
callq 0x6370
leaq 0x10(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x116a2
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x6310
leaq 0x20(%rsp), %rdi
callq 0x6410
movq 0x26895(%rip), %rax     # 0x37f48
movq (%rax), %rcx
movq 0x18(%rax), %rax
leaq 0x28(%rsp), %rdi
movq %rcx, -0x8(%rdi)
movq -0x18(%rcx), %rcx
movq %rax, 0x20(%rsp,%rcx)
callq 0x62d0
leaq 0x118(%rsp), %rdi
callq 0x6120
addq $0x220, %rsp            # imm = 0x220
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %rbx
leaq 0x10(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x11710
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x6310
jmp 0x11710
jmp 0x1170d
movq %rax, %rbx
leaq 0x20(%rsp), %rdi
callq 0x6450
movq %rbx, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::rescaleBeadSizes(double)
void Model::rescaleBeadSizes(double occupancyFactor) {
  assert(this->hasNucleus);
  vector<Chromosome>::iterator chriter;
  boost::container::static_vector<Bead,MAXSIZE>::iterator beaditer;
  double beadVol = this->getTotalBeadVolume();
  double genomeLength = this->getTotalGenomeLength();
  for(chriter = chromosomes.begin(); chriter != chromosomes.end(); chriter++) {
    for(beaditer=chriter->begin(); beaditer!=chriter->end(); beaditer++) {
      double newRadius = pow((occupancyFactor * (beaditer->getBpSpan()) / (genomeLength)),1/3.0) * (this->nucleusRadius);
      beaditer->setRadius(newRadius);
    }
  }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x18, %rsp
movsd %xmm0, 0x10(%rsp)
cmpb $0x0, 0xa90(%rdi)
je 0x158ee
movq %rdi, %rbx
callq 0x16838
movq %rbx, %rdi
callq 0x168e8
movsd %xmm0, 0x8(%rsp)
movq 0xa78(%rbx), %r14
cmpq 0xa80(%rbx), %r14
je 0x158e2
movq %rsp, %r15
movq %r15, %rdi
movq %r14, %rsi
callq 0xb208
movq (%rsp), %r12
movq %r15, %rdi
movq %r14, %rsi
callq 0xb214
cmpq (%rsp), %r12
je 0x158d2
movq %r12, %rdi
callq 0xae18
movl %eax, %eax
xorps %xmm0, %xmm0
cvtsi2sd %rax, %xmm0
mulsd 0x10(%rsp), %xmm0
divsd 0x8(%rsp), %xmm0
movsd 0x14a51(%rip), %xmm1    # 0x2a308
callq 0x6590
mulsd 0xa98(%rbx), %xmm0
movq %r12, %rdi
callq 0xadfa
addq $0x60, %r12
jmp 0x15880
addq $0x75330, %r14          # imm = 0x75330
cmpq 0xa80(%rbx), %r14
jne 0x15871
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
leaq 0x14dcc(%rip), %rdi     # 0x2a6c1
leaq 0x14aab(%rip), %rsi     # 0x2a3a7
leaq 0x15528(%rip), %rcx     # 0x2ae2b
movl $0x3c2, %edx            # imm = 0x3C2
callq 0x6210
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addNucleusConstraints(double)
void Model::addNucleusConstraints(double springConstant /*=1*/) {
  assert(this->hasNucleus);
  vector<Chromosome>::iterator chriter;
  boost::container::static_vector<Bead,MAXSIZE>::iterator beaditer;  
  for(chriter = chromosomes.begin(); chriter != chromosomes.end(); chriter++) {
    for(beaditer=chriter->begin(); beaditer!=chriter->end(); beaditer++) {
      this->addNucleusConstraint(beaditer->getID(),springConstant);
    }
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movsd %xmm0, 0x10(%rsp)
cmpb $0x0, 0xa90(%rdi)
je 0x162ed
movq %rdi, %rbx
movq 0xa78(%rdi), %r14
cmpq 0xa80(%rdi), %r14
je 0x162de
leaq 0x28(%rsp), %rbp
leaq 0x8(%rsp), %r15
leaq 0x18(%rsp), %r12
movq %r15, %rdi
movq %r14, %rsi
callq 0xb208
movq 0x8(%rsp), %r13
movq %r15, %rdi
movq %r14, %rsi
callq 0xb214
cmpq 0x8(%rsp), %r13
je 0x162ce
movq %r12, %rdi
movq %r13, %rsi
callq 0xae24
movq %rbx, %rdi
movq %r12, %rsi
movsd 0x10(%rsp), %xmm0
callq 0xee36
movq 0x18(%rsp), %rdi
cmpq %rbp, %rdi
je 0x162c8
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x60, %r13
jmp 0x16283
addq $0x75330, %r14          # imm = 0x75330
cmpq 0xa80(%rbx), %r14
jne 0x16273
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x143cd(%rip), %rdi     # 0x2a6c1
leaq 0x140ac(%rip), %rsi     # 0x2a3a7
leaq 0x14ad6(%rip), %rcx     # 0x2add8
movl $0x372, %edx            # imm = 0x372
callq 0x6210
movq %rax, %rbx
movq 0x18(%rsp), %rdi
cmpq %rbp, %rdi
je 0x16326
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/Model.cpp
// Function: Model::addCenterConstraints(double)
void Model::addCenterConstraints(double springConstant /*=1*/) {
  assert(this->hasNucleus);
  vector<Chromosome>::iterator chriter;
  boost::container::static_vector<Bead,MAXSIZE>::iterator beaditer;  
  for(chriter = chromosomes.begin(); chriter != chromosomes.end(); chriter++) {
    for(beaditer=chriter->begin(); beaditer!=chriter->end(); beaditer++) {
      this->addCenterConstraint(beaditer->getID(), springConstant);
    }
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movsd %xmm0, 0x10(%rsp)
cmpb $0x0, 0xa90(%rdi)
je 0x163eb
movq %rdi, %rbx
movq 0xa78(%rdi), %r14
cmpq 0xa80(%rdi), %r14
je 0x163dc
leaq 0x28(%rsp), %rbp
leaq 0x8(%rsp), %r15
leaq 0x18(%rsp), %r12
movq %r15, %rdi
movq %r14, %rsi
callq 0xb208
movq 0x8(%rsp), %r13
movq %r15, %rdi
movq %r14, %rsi
callq 0xb214
cmpq 0x8(%rsp), %r13
je 0x163cc
movq %r12, %rdi
movq %r13, %rsi
callq 0xae24
movq %rbx, %rdi
movq %r12, %rsi
movsd 0x10(%rsp), %xmm0
callq 0xf0a8
movq 0x18(%rsp), %rdi
cmpq %rbp, %rdi
je 0x163c6
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x60, %r13
jmp 0x16381
addq $0x75330, %r14          # imm = 0x75330
cmpq 0xa80(%rbx), %r14
jne 0x16371
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x142cf(%rip), %rdi     # 0x2a6c1
leaq 0x13fae(%rip), %rsi     # 0x2a3a7
leaq 0x14a02(%rip), %rcx     # 0x2ae02
movl $0x38a, %edx            # imm = 0x38A
callq 0x6210
movq %rax, %rbx
movq 0x18(%rsp), %rdi
cmpq %rbp, %rdi
je 0x16424
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/MCMC.cpp
// Function: MCMC::doMetropolisHastingsStep(double, unsigned int)
bool MCMC::doMetropolisHastingsStep(double T /*=1*/, uint maxAttempts /*=10000*/) {
  uint i=0;
  bool success = false;
  while(i < maxAttempts and !success) {
    try {
      Move proposedMove = model.proposeMove(); // Idea: if this fails (no move proposed), we could set the proposed Move to the same (identity) move.
      double before = model.getPartialLossScore(proposedMove.chr, proposedMove.start, proposedMove.stop); // score before move
      Move oldCoords = model.accept(proposedMove); //, true);
      double after = model.getPartialLossScore(proposedMove.chr, proposedMove.start, proposedMove.stop); // score after move
      if(after > before) {
	double pAccept = exp((before-after)/T);
	bool accept = util::unif_real(0,1, model.randEngine) < pAccept;
	if(not accept) {
	  Move tmp = model.accept(oldCoords); //, true); // roll back to previous coordinates.
	}
      }
      success = true;
    }
    catch(util::MoveException& e){
      i++;
    }
  }
  return success;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xc8, %rsp
movsd %xmm0, 0x18(%rsp)
xorl %r13d, %r13d
testl %esi, %esi
je 0x1b281
movl %esi, %ebx
movq %rdi, %r14
leaq 0x20(%rsp), %r15
leaq 0x58(%rsp), %r12
xorl %ebp, %ebp
movq (%r14), %rsi
movq %r15, %rdi
movl $0x1, %edx
callq 0xfc86
movq (%r14), %rdi
movq 0x20(%rsp), %rsi
movl 0x28(%rsp), %edx
movl 0x2c(%rsp), %ecx
callq 0xf82c
movsd %xmm0, 0x8(%rsp)
movq (%r14), %rsi
movq %r12, %rdi
movq %r15, %rdx
callq 0x10518
movq (%r14), %rdi
movq 0x20(%rsp), %rsi
movl 0x28(%rsp), %edx
movl 0x2c(%rsp), %ecx
callq 0xf82c
movsd 0x8(%rsp), %xmm1
ucomisd %xmm1, %xmm0
jbe 0x1b1b7
subsd %xmm0, %xmm1
divsd 0x18(%rsp), %xmm1
movapd %xmm1, %xmm0
callq 0x65c0
movsd %xmm0, 0x8(%rsp)
movq (%r14), %rdi
addq $0x20, %rdi
xorpd %xmm0, %xmm0
movsd 0xde93(%rip), %xmm1     # 0x29008
callq 0x72a4
movsd 0x8(%rsp), %xmm1
ucomisd %xmm0, %xmm1
ja 0x1b1b7
movq (%r14), %rsi
leaq 0x90(%rsp), %rdi
movq %r12, %rdx
callq 0x10518
movq 0xb8(%rsp), %rsi
testq %rsi, %rsi
je 0x1b1b7
movq 0xc0(%rsp), %rdi
shlq $0x3, %rsi
callq 0x6310
movq 0x80(%rsp), %rsi
testq %rsi, %rsi
je 0x1b1d5
movq 0x88(%rsp), %rdi
shlq $0x3, %rsi
callq 0x6310
movq 0x48(%rsp), %rsi
testq %rsi, %rsi
je 0x1b1ed
movq 0x50(%rsp), %rdi
shlq $0x3, %rsi
callq 0x6310
movb $0x1, %bpl
cmpl %ebx, %r13d
jae 0x1b283
testb $0x1, %bpl
je 0x1b0ef
jmp 0x1b283
jmp 0x1b209
jmp 0x1b209
movq %rdx, 0x10(%rsp)
movq %rax, 0x8(%rsp)
movq 0x80(%rsp), %rsi
testq %rsi, %rsi
je 0x1b23f
movq 0x88(%rsp), %rdi
shlq $0x3, %rsi
callq 0x6310
jmp 0x1b23f
jmp 0x1b235
movq %rdx, 0x10(%rsp)
movq %rax, 0x8(%rsp)
movq 0x48(%rsp), %rsi
testq %rsi, %rsi
je 0x1b263
movq 0x50(%rsp), %rdi
shlq $0x3, %rsi
callq 0x6310
jmp 0x1b263
movq %rdx, 0x10(%rsp)
movq %rax, 0x8(%rsp)
cmpl $0x1, 0x10(%rsp)
jne 0x1b29b
movq 0x8(%rsp), %rdi
callq 0x6160
incl %r13d
callq 0x64f0
jmp 0x1b1f0
xorl %ebp, %ebp
andb $0x1, %bpl
movl %ebp, %eax
addq $0xc8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x8(%rsp), %rdi
callq 0x65b0
nopl (%rax)
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/tclap-1.2.1/include/tclap/SwitchArg.h
// Function: TCLAP::SwitchArg::processArg(int*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&)
inline bool SwitchArg::processArg(int *i, std::vector<std::string>& args)
{
	if ( _ignoreable && Arg::ignoreRest() )
		return false;

	// if the whole string matches the flag or name string
	if ( argMatches( args[*i] ) )
	{
		commonProcessing();

		return true;
	}
	// if a substring matches the flag as part of a combination
	else if ( combinedSwitchesMatch( args[*i] ) )
	{
		// check again to ensure we don't misinterpret 
		// this as a MultiSwitchArg 
		if ( combinedSwitchesMatch( args[*i] ) )
			throw(CmdLineParseException("Argument already set!", 
			                            toString()));

		commonProcessing();

		// We only want to return true if we've found the last combined
		// match in the string, otherwise we return true so that other 
		// switches in the combination will have a chance to match.
		return lastCombined( args[*i] );
	}
	else
		return false;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x48, %rsp
movq %rdx, %rbx
movq %rsi, %r15
movq %rdi, %r14
cmpb $0x1, 0xa0(%rdi)
jne 0x1e40b
cmpb $0x0, 0x19f9a(%rip)     # 0x3839f
jne 0x1e4a0
movslq (%r15), %rsi
shlq $0x5, %rsi
addq (%rbx), %rsi
movq (%r14), %rax
movq %r14, %rdi
callq *0x30(%rax)
testb %al, %al
je 0x1e42e
movq %r14, %rdi
callq 0x1e570
movb $0x1, %al
jmp 0x1e4a2
movslq (%r15), %rsi
shlq $0x5, %rsi
addq (%rbx), %rsi
movq %r14, %rdi
callq 0x1e700
testb %al, %al
je 0x1e4a0
movslq (%r15), %rsi
shlq $0x5, %rsi
addq (%rbx), %rsi
movq %r14, %rdi
callq 0x1e700
testb %al, %al
jne 0x1e4ad
movq %r14, %rdi
callq 0x1e570
movslq (%r15), %rsi
movq (%rbx), %rdx
shlq $0x5, %rsi
movq 0x8(%rdx,%rsi), %rcx
cmpq $0x2, %rcx
setb %al
jb 0x1e4a2
addq %rsi, %rdx
movq (%rdx), %rdx
cmpb $0x7, 0x1(%rdx)
jne 0x1e4a0
movl $0x2, %esi
movl %esi, %edi
cmpq %rdi, %rcx
setbe %al
jbe 0x1e4a2
leal 0x1(%rdi), %esi
cmpb $0x7, (%rdx,%rdi)
je 0x1e48b
jmp 0x1e4a2
xorl %eax, %eax
addq $0x48, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movl $0x68, %edi
callq 0x61a0
movq %rax, %rbx
leaq 0x18(%rsp), %r15
movq %r15, -0x10(%r15)
leaq 0xce3e(%rip), %rsi      # 0x2b308
leaq 0xce4c(%rip), %rdx      # 0x2b31d
leaq 0x8(%rsp), %rdi
callq 0xe03a
movq (%r14), %rax
leaq 0x28(%rsp), %rdi
movq %r14, %rsi
callq *0x38(%rax)
movb $0x1, %bpl
leaq 0x8(%rsp), %rsi
leaq 0x28(%rsp), %rdx
movq %rbx, %rdi
callq 0x1e940
xorl %ebp, %ebp
leaq 0x190a1(%rip), %rsi     # 0x375a8
leaq 0x6fd2(%rip), %rdx      # 0x254e0
movq %rbx, %rdi
callq 0x6550
movq %rax, %r14
leaq 0x38(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x1e53c
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
jmp 0x1e53c
movq %rax, %r14
movb $0x1, %bpl
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x1e55b
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
jmp 0x1e55b
movq %rax, %r14
movb $0x1, %bpl
testb %bpl, %bpl
je 0x1e568
movq %rbx, %rdi
callq 0x6280
movq %r14, %rdi
callq 0x65b0
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/tclap-1.2.1/include/tclap/SwitchArg.h
// Function: TCLAP::SwitchArg::commonProcessing()
inline void SwitchArg::commonProcessing()
{
	if ( _xorSet )
		throw(CmdLineParseException(
		      "Mutually exclusive argument already set!", toString()));

	if ( _alreadySet ) 
		throw(CmdLineParseException("Argument already set!", toString()));

	_alreadySet = true;

	if ( _value == true )
		_value = false;
	else
		_value = true;

	_checkWithVisitor();
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x48, %rsp
movq %rdi, %r14
cmpb $0x1, 0xa1(%rdi)
je 0x1e5cb
cmpb $0x1, 0x91(%r14)
je 0x1e636
movb $0x1, 0x91(%r14)
xorb $0x1, 0xa3(%r14)
movq 0x98(%r14), %rdi
testq %rdi, %rdi
je 0x1e5c0
movq (%rdi), %rax
addq $0x48, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
jmpq *0x10(%rax)
addq $0x48, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movl $0x68, %edi
callq 0x61a0
movq %rax, %rbx
leaq 0x18(%rsp), %r15
movq %r15, -0x10(%r15)
leaq 0xd493(%rip), %rsi      # 0x2ba7b
leaq 0xd4b4(%rip), %rdx      # 0x2baa3
leaq 0x8(%rsp), %rdi
callq 0xe03a
movq (%r14), %rax
leaq 0x28(%rsp), %rdi
movq %r14, %rsi
callq *0x38(%rax)
movb $0x1, %bpl
leaq 0x8(%rsp), %rsi
leaq 0x28(%rsp), %rdx
movq %rbx, %rdi
callq 0x1e940
xorl %ebp, %ebp
leaq 0x18f83(%rip), %rsi     # 0x375a8
leaq 0x6eb4(%rip), %rdx      # 0x254e0
movq %rbx, %rdi
callq 0x6550
jmp 0x1e69f
movl $0x68, %edi
callq 0x61a0
movq %rax, %rbx
leaq 0x18(%rsp), %r15
movq %r15, -0x10(%r15)
leaq 0xccb5(%rip), %rsi      # 0x2b308
leaq 0xccc3(%rip), %rdx      # 0x2b31d
leaq 0x8(%rsp), %rdi
callq 0xe03a
movq (%r14), %rax
leaq 0x28(%rsp), %rdi
movq %r14, %rsi
callq *0x38(%rax)
movb $0x1, %bpl
leaq 0x8(%rsp), %rsi
leaq 0x28(%rsp), %rdx
movq %rbx, %rdi
callq 0x1e940
xorl %ebp, %ebp
leaq 0x18f18(%rip), %rsi     # 0x375a8
leaq 0x6e49(%rip), %rdx      # 0x254e0
movq %rbx, %rdi
callq 0x6550
jmp 0x1e6a3
jmp 0x1e6c3
movq %rax, %r14
leaq 0x38(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x1e6c9
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x6310
jmp 0x1e6c9
movq %rax, %r14
movb $0x1, %bpl
movq 0x8(%rsp), %rdi
cmpq %r15, %rdi
je 0x1e6ea
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
jmp 0x1e6ea
jmp 0x1e6e4
movq %rax, %r14
movb $0x1, %bpl
testb %bpl, %bpl
je 0x1e6f7
movq %rbx, %rdi
callq 0x6280
movq %r14, %rdi
callq 0x65b0
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/tclap-1.2.1/include/tclap/ValuesConstraint.h
// Function: TCLAP::ValuesConstraint<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>::ValuesConstraint(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&)
ValuesConstraint<T>::ValuesConstraint(std::vector<T>& allowed)
: _allowed(allowed),
  _typeDesc("")
{ 
    for ( unsigned int i = 0; i < _allowed.size(); i++ )
    {

#if defined(HAVE_SSTREAM)
        std::ostringstream os;
#elif defined(HAVE_STRSTREAM)
        std::ostrstream os;
#else
#error "Need a stringstream (sstream or strstream) to compile!"
#endif

        os << _allowed[i];

        std::string temp( os.str() ); 

        if ( i > 0 )
			_typeDesc += "|";
        _typeDesc += temp;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1a8, %rsp            # imm = 0x1A8
movq %rdi, %rbx
leaq 0x177c3(%rip), %rax     # 0x37c70
movq %rax, (%rdi)
leaq 0x8(%rdi), %r14
movq %r14, %rdi
callq 0x16d80
leaq 0x20(%rbx), %r15
leaq 0x30(%rbx), %rax
movq %rax, 0x28(%rsp)
movq %rax, 0x20(%rbx)
leaq 0xb9c7(%rip), %rdx      # 0x2be9b
movq %r15, %rdi
movq %rdx, %rsi
callq 0xe03a
movq 0x10(%rbx), %rax
cmpq 0x8(%rbx), %rax
je 0x205a4
movl $0x1, %r12d
xorl %r13d, %r13d
leaq 0x30(%rsp), %rbp
movq %rbp, %rdi
callq 0x63e0
movq (%r14), %rax
shlq $0x5, %r13
movq (%rax,%r13), %rsi
movq 0x8(%rax,%r13), %rdx
movq %rbp, %rdi
callq 0x6370
leaq 0x8(%rsp), %rdi
leaq 0x38(%rsp), %rsi
callq 0x64b0
cmpl $0x1, %r12d
je 0x2053f
movq %r15, %rdi
leaq 0xb5df(%rip), %rsi      # 0x2bb19
callq 0x6630
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rdx
movq %r15, %rdi
callq 0x6110
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x2056d
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbp, %rdi
movq 0x179f9(%rip), %rsi     # 0x37f70
callq 0x61c0
leaq 0xa0(%rsp), %rdi
callq 0x6120
movq 0x10(%rbx), %rax
subq 0x8(%rbx), %rax
movl %r12d, %r13d
sarq $0x5, %rax
incl %r12d
cmpq %r13, %rax
ja 0x204fb
addq $0x1a8, %rsp            # imm = 0x1A8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %r12
jmp 0x20621
movq %rax, %r12
jmp 0x20629
movq %rax, %r12
jmp 0x20609
jmp 0x205c7
movq %rax, %r12
jmp 0x205eb
movq %rax, %r12
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x205eb
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x1797e(%rip), %rsi     # 0x37f70
leaq 0x30(%rsp), %rdi
callq 0x61c0
leaq 0xa0(%rsp), %rdi
callq 0x6120
movq (%r15), %rdi
movq 0x28(%rsp), %rax
cmpq %rax, %rdi
je 0x20621
movq (%rax), %rsi
incq %rsi
callq 0x6310
movq %r14, %rdi
callq 0x889e
leaq 0x176a0(%rip), %rax     # 0x37cd0
movq %rax, (%rbx)
movq %r12, %rdi
callq 0x65b0
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/tclap-1.2.1/include/tclap/StdOutput.h
// Function: TCLAP::StdOutput::version(TCLAP::CmdLineInterface&)
inline void StdOutput::version(CmdLineInterface& _cmd) 
{
	std::string progName = _cmd.getProgramName();
	std::string xversion = _cmd.getVersion();

	std::cout << std::endl << progName << "  version: " 
			  << xversion << std::endl << std::endl;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x40, %rsp
movq %rsi, %rbx
movq (%rsi), %rax
movq %rsi, %rdi
callq *0x50(%rax)
leaq 0x30(%rsp), %r14
movq %r14, -0x10(%r14)
movq (%rax), %rsi
movq 0x8(%rax), %rdx
addq %rsi, %rdx
leaq 0x20(%rsp), %rdi
callq 0xa53a
movq (%rbx), %rax
movq %rbx, %rdi
callq *0x48(%rax)
leaq 0x10(%rsp), %r15
movq %r15, -0x10(%r15)
movq (%rax), %rsi
movq 0x8(%rax), %rdx
addq %rsi, %rdx
movq %rsp, %rdi
callq 0xa53a
movq 0x15f69(%rip), %rdi     # 0x37f80
movq (%rdi), %rax
addq -0x18(%rax), %rdi
movl $0xa, %esi
callq 0x62f0
movsbl %al, %esi
movq 0x15f4e(%rip), %rdi     # 0x37f80
callq 0x6030
movq %rax, %rdi
callq 0x6240
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdx
movq %rax, %rdi
callq 0x6370
movq %rax, %rbx
leaq 0x9e19(%rip), %rsi      # 0x2be74
movl $0xb, %edx
movq %rax, %rdi
callq 0x6370
movq (%rsp), %rsi
movq 0x8(%rsp), %rdx
movq %rbx, %rdi
callq 0x6370
movq %rax, %rbx
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x62f0
movsbl %al, %esi
movq %rbx, %rdi
callq 0x6030
movq %rax, %rdi
callq 0x6240
movq %rax, %rbx
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x62f0
movsbl %al, %esi
movq %rbx, %rdi
callq 0x6030
movq %rax, %rdi
callq 0x6240
movq (%rsp), %rdi
cmpq %r15, %rdi
je 0x220e3
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x20(%rsp), %rdi
cmpq %r14, %rdi
je 0x220fa
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x6310
addq $0x40, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %rbx
jmp 0x22122
movq %rax, %rbx
movq (%rsp), %rdi
cmpq %r15, %rdi
je 0x22122
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x6310
movq 0x20(%rsp), %rdi
cmpq %r14, %rdi
je 0x22139
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x6310
movq %rbx, %rdi
callq 0x65b0
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/../src/tclap-1.2.1/include/tclap/CmdLine.h
// Function: TCLAP::CmdLine::setOutput(TCLAP::CmdLineOutput*)
inline void CmdLine::setOutput(CmdLineOutput* co)
{
	if ( !_userSetOutput )
		delete _output;
	_userSetOutput = true;
	_output = co;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
cmpb $0x0, 0xd9(%rdi)
jne 0x226a7
movq 0xd0(%r14), %rdi
testq %rdi, %rdi
je 0x226a7
movq (%rdi), %rax
callq *0x8(%rax)
movb $0x1, 0xd9(%r14)
movq %rbx, 0xd0(%r14)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/tclap-1.2.1/include/tclap/UnlabeledValueArg.h
// Function: TCLAP::UnlabeledValueArg<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>::processArg(int*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&)
bool UnlabeledValueArg<T>::processArg(int *i, std::vector<std::string>& args) 
{
	
	if ( _alreadySet )
		return false;
	
	if ( _hasBlanks( args[*i] ) )
		return false;

	// never ignore an unlabeled arg
	
	_extractValue( args[*i] );
	_alreadySet = true;
	return true;
}

// Assembly:
cmpb $0x0, 0x91(%rdi)
je 0x27ce4
xorl %eax, %eax
retq
pushq %rbx
movq %rdi, %rbx
movslq (%rsi), %rax
movq (%rdx), %rcx
shlq $0x5, %rax
leaq (%rcx,%rax), %rsi
movq 0x8(%rcx,%rax), %rax
cmpq $0x2, %rax
setae %cl
jb 0x27d2a
movq (%rsi), %rcx
cmpb $0x7, 0x1(%rcx)
je 0x27d2e
movl $0x2, %edi
movq %rdi, %rdx
cmpq %rdi, %rax
je 0x27d24
leaq 0x1(%rdx), %rdi
cmpb $0x7, (%rcx,%rdx)
jne 0x27d12
cmpq %rdx, %rax
seta %cl
testb %cl, %cl
je 0x27d32
xorl %eax, %eax
jmp 0x27d43
movq %rbx, %rdi
callq 0x25d58
movb $0x1, 0x91(%rbx)
movb $0x1, %al
popq %rbx
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/Chrom3D[P]Chrom3D/src/tclap-1.2.1/include/tclap/UnlabeledValueArg.h
// Function: TCLAP::UnlabeledValueArg<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>::operator==(TCLAP::Arg const&) const
bool UnlabeledValueArg<T>::operator==(const Arg& a ) const
{
	if ( _name == a.getName() || _description == a.getDescription() )
		return true;
	else
		return false;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x20, %rsp
movq %rsi, %r14
movq %rdi, %rbx
movq 0x30(%rdi), %rdx
cmpq 0x30(%rsi), %rdx
jne 0x27d7c
testq %rdx, %rdx
je 0x27d81
movq 0x28(%r14), %rsi
movq 0x28(%rbx), %rdi
callq 0x6320
testl %eax, %eax
sete %r12b
jmp 0x27d84
xorl %r12d, %r12d
jmp 0x27d84
movb $0x1, %r12b
movb $0x1, %bpl
testb %r12b, %r12b
jne 0x27dc0
movq %rsp, %r15
movq %r15, %rdi
movq %r14, %rsi
callq 0x22eec
movq 0x50(%rbx), %rdx
cmpq 0x8(%r15), %rdx
jne 0x27dbe
testq %rdx, %rdx
je 0x27dc0
movq (%rsp), %rsi
movq 0x48(%rbx), %rdi
callq 0x6320
testl %eax, %eax
sete %bpl
jmp 0x27dc0
xorl %ebp, %ebp
testb %r12b, %r12b
jne 0x27de0
leaq 0x10(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x27de0
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x6310
movl %ebp, %eax
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
nop