// File: gcollet[P]MstatX/src/msa.cpp
// Function: Msa::fitToAlphabet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
void
Msa :: fitToAlphabet(string alph1){
	int alph_size = (int) alph1.size();
	for (int i(0); i < nseq; i++){
		for (int j(0); j < ncol; j++){
			if (mali_seq[i][j] != '-' && mali_seq[i][j] != ' ' && (int) alph1.find(mali_seq[i][j]) >= alph_size){
				int k = (int) alphabet.find(mali_seq[i][j]);
				if (k < (int) alphabet.size()){
					alphabet.erase(alphabet.begin() + k);
				}
				int pos = (int) aa_type_list[j].find(mali_seq[i][j]);
				if (pos < (int) aa_type_list[j].size()){
					aa_type_list[j].erase(aa_type_list[j].begin() + pos);
					nb_type[j]--;
				}
				mali_seq[i][j] = '-';
			}
		}
	}
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0xa0, %rsp
movq %rsi, -0x80(%rbp)
movq %rdi, %rax
movq -0x80(%rbp), %rdi
movq %rdi, -0x78(%rbp)
movq %rax, -0x8(%rbp)
movq %rdi, -0x10(%rbp)
movq -0x8(%rbp), %rax
movq %rax, -0x70(%rbp)
callq 0x4260
movl %eax, -0x14(%rbp)
movl $0x0, -0x18(%rbp)
movq -0x70(%rbp), %rcx
movl -0x18(%rbp), %eax
cmpl 0xc8(%rcx), %eax
jge 0x130a9
movl $0x0, -0x1c(%rbp)
movq -0x70(%rbp), %rcx
movl -0x1c(%rbp), %eax
cmpl 0xcc(%rcx), %eax
jge 0x13099
movq -0x70(%rbp), %rdi
addq $0x38, %rdi
movslq -0x18(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x46c0
movsbl (%rax), %eax
cmpl $0x2d, %eax
je 0x13089
movq -0x70(%rbp), %rdi
addq $0x38, %rdi
movslq -0x18(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x46c0
movsbl (%rax), %eax
cmpl $0x20, %eax
je 0x13089
movq -0x70(%rbp), %rdi
addq $0x38, %rdi
movslq -0x18(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x46c0
movq -0x78(%rbp), %rdi
xorl %ecx, %ecx
movl %ecx, %edx
movsbl (%rax), %esi
callq 0x4480
cmpl -0x14(%rbp), %eax
jl 0x13089
movq -0x70(%rbp), %rdi
addq $0x38, %rdi
movslq -0x18(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x46c0
movq -0x70(%rbp), %rdi
xorl %ecx, %ecx
movl %ecx, %edx
movsbl (%rax), %esi
callq 0x4480
movq -0x70(%rbp), %rdi
movl %eax, -0x20(%rbp)
movl -0x20(%rbp), %eax
movl %eax, -0x84(%rbp)
callq 0x4260
movq %rax, %rcx
movl -0x84(%rbp), %eax
cmpl %ecx, %eax
jge 0x12f69
movq -0x70(%rbp), %rdi
callq 0x4300
movq %rax, -0x38(%rbp)
movslq -0x20(%rbp), %rsi
leaq -0x38(%rbp), %rdi
callq 0x13960
movq %rax, -0x30(%rbp)
leaq -0x28(%rbp), %rdi
leaq -0x30(%rbp), %rsi
callq 0x139a0
movq -0x70(%rbp), %rdi
movq -0x28(%rbp), %rsi
callq 0x4430
movq %rax, -0x40(%rbp)
movq -0x70(%rbp), %rdi
addq $0x50, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x74a0
movq -0x70(%rbp), %rdi
movq %rax, -0x90(%rbp)
addq $0x38, %rdi
movslq -0x18(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x46c0
movq -0x90(%rbp), %rdi
xorl %ecx, %ecx
movl %ecx, %edx
movsbl (%rax), %esi
callq 0x4480
movq -0x70(%rbp), %rdi
movl %eax, -0x44(%rbp)
movl -0x44(%rbp), %eax
movl %eax, -0x88(%rbp)
addq $0x50, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
callq 0x4260
movq %rax, %rcx
movl -0x88(%rbp), %eax
cmpl %ecx, %eax
jge 0x13069
movq -0x70(%rbp), %rdi
addq $0x50, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x74a0
movq -0x70(%rbp), %rdi
movq %rax, -0x98(%rbp)
addq $0x50, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
callq 0x4300
movq %rax, -0x60(%rbp)
movslq -0x44(%rbp), %rsi
leaq -0x60(%rbp), %rdi
callq 0x13960
movq %rax, -0x58(%rbp)
leaq -0x50(%rbp), %rdi
leaq -0x58(%rbp), %rsi
callq 0x139a0
movq -0x98(%rbp), %rdi
movq -0x50(%rbp), %rsi
callq 0x4430
movq -0x70(%rbp), %rdi
movq %rax, -0x68(%rbp)
addq $0xb0, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x7480
movl (%rax), %ecx
addl $-0x1, %ecx
movl %ecx, (%rax)
movq -0x70(%rbp), %rdi
addq $0x38, %rdi
movslq -0x18(%rbp), %rsi
callq 0x74a0
movq %rax, %rdi
movslq -0x1c(%rbp), %rsi
callq 0x46c0
movb $0x2d, (%rax)
jmp 0x1308b
movl -0x1c(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x1c(%rbp)
jmp 0x12e43
jmp 0x1309b
movl -0x18(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x18(%rbp)
jmp 0x12e29
addq $0xa0, %rsp
popq %rbp
retq
nopw %cs:(%rax,%rax)