// File: /workspace/github_cpp_makefile_star2_O3/gcollet[P]MstatX/src/msa.cpp
// Function: Msa::printBasic()
void
Msa :: printBasic(){
	string dictionary = "ARNDCQEGHILKMFPSTWYV-";
	vector<int> counts(dictionary.size(), 0);
	string out_name = Options::Get().output_fname;
	out_name = out_name.substr(0,out_name.find('.')) + ".aa_count";
	ofstream file(out_name.c_str());
	if (!file.is_open()){
	  cerr << "Cannot open file " << out_name << "\n";
		exit(0);
	}
	for (int a(0); a < (int) dictionary.size(); a++) {
		file << dictionary[a] << " ";
	}
	file << "\n";
	for (int col(0); col < ncol; col++){
		for (int seq(0); seq < nseq; seq++){
			int pos = (int) dictionary.find(mali_seq[seq][col]);
			if (pos < (int) dictionary.size()){
				counts[pos]++;
			} else {
				cerr << mali_seq[seq][col] << " is not in the dictionary\n";
			}
		}
		for (int a(0); a < (int) dictionary.size(); a++) {
			file << counts[a] << " ";
			counts[a] = 0;
		}
		file << "\n";
	}
	file.close();
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x278, %rsp            # imm = 0x278
movq %rdi, %rbx
leaq 0x10(%rsp), %r15
movq %r15, -0x10(%r15)
leaq 0x446b(%rip), %rsi      # 0x10747
leaq 0x4479(%rip), %rdx      # 0x1075c
movq %rsp, %r14
movq %r14, %rdi
callq 0xa6ea
movq 0x8(%r14), %rsi
leaq 0x78(%rsp), %rdx
movl $0x0, (%rdx)
leaq 0x40(%rsp), %rdi
leaq 0x20(%rsp), %rcx
callq 0x6244
callq 0x4f1c
leaq 0x30(%rsp), %r12
movq %r12, -0x10(%r12)
movq 0xa8(%rax), %rsi
movq 0xb0(%rax), %rdx
addq %rsi, %rdx
leaq 0x20(%rsp), %rdi
callq 0x5cca
leaq 0x20(%rsp), %r14
movq %r14, %rdi
movl $0x2e, %esi
xorl %edx, %edx
callq 0x4330
leaq 0x58(%rsp), %rdi
movq %r14, %rsi
xorl %edx, %edx
movq %rax, %rcx
callq 0x4270
leaq 0x43fa(%rip), %rsi      # 0x1075d
leaq 0x58(%rsp), %rdi
callq 0x44c0
leaq 0x88(%rsp), %r15
movq %r15, -0x10(%r15)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
je 0xc39a
movq %rdx, 0x78(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x88(%rsp)
jmp 0xc3a1
movups (%rcx), %xmm0
movups %xmm0, (%r15)
movq 0x8(%rax), %rdx
leaq 0x78(%rsp), %r14
movq %rdx, 0x8(%r14)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
leaq 0x20(%rsp), %rdi
movq %r14, %rsi
callq 0x4300
movq (%r14), %rdi
cmpq %r15, %rdi
je 0xc3e2
movq 0x88(%rsp), %rsi
incq %rsi
callq 0x4250
leaq 0x68(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0xc3fd
movq 0x68(%rsp), %rsi
incq %rsi
callq 0x4250
movq 0x20(%rsp), %rsi
leaq 0x78(%rsp), %rdi
movl $0x10, %edx
callq 0x4290
leaq 0xe8(%rsp), %rdi
callq 0x4070
testb %al, %al
je 0xc63c
cmpl $0x0, 0x8(%rsp)
jle 0xc47a
xorl %r13d, %r13d
leaq 0x78(%rsp), %r14
leaq 0x58(%rsp), %r15
leaq 0x417e(%rip), %r12      # 0x105bf
movq (%rsp), %rax
movb (%rax,%r13), %al
movb %al, 0x58(%rsp)
movl $0x1, %edx
movq %r14, %rdi
movq %r15, %rsi
callq 0x42a0
movl $0x1, %edx
movq %rax, %rdi
movq %r12, %rsi
callq 0x42a0
incq %r13
movslq 0x8(%rsp), %rax
cmpq %rax, %r13
jl 0xc441
leaq 0x40a3(%rip), %rsi      # 0x10524
leaq 0x78(%rsp), %rdi
movl $0x1, %edx
callq 0x42a0
cmpl $0x0, 0xcc(%rbx)
jle 0xc59d
xorl %r12d, %r12d
leaq 0x78(%rsp), %rbp
leaq 0x4113(%rip), %r15      # 0x105bf
cmpl $0x0, 0xc8(%rbx)
jle 0xc531
xorl %r13d, %r13d
xorl %r14d, %r14d
movq 0x38(%rbx), %rax
movq (%rax,%r13), %rax
movsbl (%rax,%r12), %esi
movq %rsp, %rdi
xorl %edx, %edx
callq 0x4330
cmpl 0x8(%rsp), %eax
jge 0xc4e4
movq 0x40(%rsp), %rcx
cltq
incl (%rcx,%rax,4)
jmp 0xc51e
movq 0x38(%rbx), %rax
movq (%rax,%r13), %rax
movb (%rax,%r12), %al
movb %al, 0x58(%rsp)
movl $0x1, %edx
movq 0x9ae8(%rip), %rdi      # 0x15fe8
leaq 0x58(%rsp), %rsi
callq 0x42a0
movl $0x1a, %edx
movq %rax, %rdi
leaq 0x424e(%rip), %rsi      # 0x10767
callq 0x42a0
incq %r14
movslq 0xc8(%rbx), %rax
addq $0x20, %r13
cmpq %rax, %r14
jl 0xc4bb
cmpl $0x0, 0x8(%rsp)
jle 0xc576
movq 0x40(%rsp), %rax
xorl %r14d, %r14d
movl (%rax,%r14,4), %esi
movq %rbp, %rdi
callq 0x4420
movl $0x1, %edx
movq %rax, %rdi
movq %r15, %rsi
callq 0x42a0
movq 0x40(%rsp), %rax
movl $0x0, (%rax,%r14,4)
incq %r14
movslq 0x8(%rsp), %rcx
cmpq %rcx, %r14
jl 0xc540
movl $0x1, %edx
movq %rbp, %rdi
leaq 0x3f9f(%rip), %rsi      # 0x10524
callq 0x42a0
incq %r12
movslq 0xcc(%rbx), %rax
cmpq %rax, %r12
jl 0xc4ac
leaq 0x78(%rsp), %rdi
callq 0x4340
movq 0x99fa(%rip), %rax      # 0x15fa8
movq (%rax), %rcx
movq 0x18(%rax), %rax
leaq 0x80(%rsp), %rdi
movq %rcx, -0x8(%rdi)
movq -0x18(%rcx), %rcx
movq %rax, 0x78(%rsp,%rcx)
callq 0x41f0
leaq 0x170(%rsp), %rdi
callq 0x40c0
movq 0x20(%rsp), %rdi
leaq 0x30(%rsp), %rax
cmpq %rax, %rdi
je 0xc5f8
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x4250
movq 0x40(%rsp), %rdi
testq %rdi, %rdi
leaq 0x10(%rsp), %rbx
je 0xc614
movq 0x50(%rsp), %rsi
subq %rdi, %rsi
callq 0x4250
movq (%rsp), %rdi
cmpq %rbx, %rdi
je 0xc62a
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x4250
addq $0x278, %rsp            # imm = 0x278
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x99a5(%rip), %rdi      # 0x15fe8
leaq 0x39d6(%rip), %rsi      # 0x10020
movl $0x11, %edx
callq 0x42a0
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdx
movq 0x9983(%rip), %rdi      # 0x15fe8
callq 0x42a0
leaq 0x3eb3(%rip), %rsi      # 0x10524
movq %rax, %rdi
callq 0x4230
xorl %edi, %edi
callq 0x42e0
movq %rax, %rbx
leaq 0x10(%rsp), %r15
jmp 0xc6d8
movq %rax, %rbx
leaq 0x68(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0xc6d8
movq 0x68(%rsp), %rsi
incq %rsi
callq 0x4250
jmp 0xc6d8
movq %rax, %rbx
jmp 0xc6d8
movq %rax, %rbx
jmp 0xc706
movq %rax, %rbx
jmp 0xc6ef
jmp 0xc6c1
jmp 0xc6c1
jmp 0xc6c1
jmp 0xc6c1
movq %rax, %rbx
leaq 0x78(%rsp), %rdi
callq 0x4370
leaq 0x10(%rsp), %r15
leaq 0x30(%rsp), %r12
movq 0x20(%rsp), %rdi
cmpq %r12, %rdi
je 0xc6ef
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x4250
movq 0x40(%rsp), %rdi
testq %rdi, %rdi
je 0xc706
movq 0x50(%rsp), %rsi
subq %rdi, %rsi
callq 0x4250
movq (%rsp), %rdi
cmpq %r15, %rdi
je 0xc71c
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x4250
movq %rbx, %rdi
callq 0x4440