// File: /workspace/github_cpp_makefile_star2_O3/myudelson[P]hmm-scalable/HMMProblem.cpp
// Function: HMMProblem::readModelBody(_IO_FILE*, param*, int*, bool)
void HMMProblem::readModelBody(FILE *fid, struct param* param, NDAT *line_no,  bool overwrite) {
	NPAR i,j,m;
	NCAT k = 0, idxk = 0;
    std::map<std::string,NCAT>::iterator it;
	string s;
    char col[2048];
    //
    readNullObsRatio(fid, param, line_no);
    //
    // init param
    //
    if(overwrite) {
        this->p->map_group_fwd = new map<string,NCAT>();
        this->p->map_group_bwd = new map<NCAT,string>();
        this->p->map_skill_fwd = new map<string,NCAT>();
        this->p->map_skill_bwd = new map<NCAT,string>();
    }
	//
	// read skills
	//
	for(k=0; k<param->nK; k++) {
		// read skill label
        fscanf(fid,"%*s\t%[^\n]\n",col);
        s = string( col );
        (*line_no)++;
        if(overwrite) {
            this->p->map_skill_fwd->insert(pair<string,NCAT>(s, (NCAT)this->p->map_skill_fwd->size()));
            this->p->map_skill_bwd->insert(pair<NCAT,string>((NCAT)this->p->map_skill_bwd->size(), s));
            idxk = k;
        } else {
            it = this->p->map_skill_fwd->find(s);
            if( it==this->p->map_skill_fwd->end() ) { // not found, skip 3 lines and continue
                fscanf(fid, "%*[^\n]\n");
                fscanf(fid, "%*[^\n]\n");
                fscanf(fid, "%*[^\n]\n");
                (*line_no)+=3;
                continue; // skip this iteration
            }
            else
                idxk =it->second;
        }
        // read PI
        fscanf(fid,"PI\t");
        for(i=0; i<(this->p->nS-1); i++) { // read 1 less then necessary
            fscanf(fid,"%[^\t]\t",col);
            this->pi[idxk][i] = atof(col);
        }
        fscanf(fid,"%[^\n]\n",col);// read last one
        this->pi[idxk][i] = atof(col);
        (*line_no)++;
		// read A
        fscanf(fid,"A\t");
		for(i=0; i<this->p->nS; i++)
			for(j=0; j<this->p->nS; j++) {
                if(i==(this->p->nS-1) && j==(this->p->nS-1)) {
                    fscanf(fid,"%[^\n]\n", col); // last one;
                    this->A[idxk][i][j] = atof(col);
                }
                else {
                    fscanf(fid,"%[^\t]\t", col); // not las one
                    this->A[idxk][i][j] = atof(col);
                }
			}
        (*line_no)++;
		// read B
        fscanf(fid,"B\t");
		for(i=0; i<this->p->nS; i++)
			for(m=0; m<this->p->nO; m++) {
                if(i==(this->p->nS-1) && m==(this->p->nO-1)) {
                    fscanf(fid,"%[^\n]\n", col); // last one;
                    this->B[idxk][i][m] = atof(col);
                }
                else {
                    fscanf(fid,"%[^\t]\t", col); // not last one
                    this->B[idxk][i][m] = atof(col);
                }
			}
        (*line_no)++;
	} // for all k
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x868, %rsp            # imm = 0x868
movl %r8d, 0x4(%rsp)
movq %rcx, %r15
movq %rsi, %r12
movq %rdi, %r13
leaq 0x48(%rsp), %rax
movq %rax, -0x10(%rax)
movq $0x0, -0x8(%rax)
movb $0x0, (%rax)
movq %rdx, 0x58(%rsp)
callq 0x190c2
cmpb $0x0, 0x4(%rsp)
je 0x192c1
movl $0x30, %edi
callq 0x4210
movq %rax, %rcx
addq $0x8, %rcx
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rax)
movaps %xmm0, (%rax)
movq %rcx, 0x18(%rax)
movq %rcx, 0x20(%rax)
movq $0x0, 0x28(%rax)
movq 0x88(%r13), %rbx
movq %rax, 0x920(%rbx)
movl $0x30, %edi
callq 0x4210
movq %rax, %rcx
addq $0x8, %rcx
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rax)
movaps %xmm0, (%rax)
movq %rcx, 0x18(%rax)
movq %rcx, 0x20(%rax)
movq $0x0, 0x28(%rax)
movq %rax, 0x928(%rbx)
movl $0x30, %edi
callq 0x4210
movq %rax, %rcx
addq $0x8, %rcx
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rax)
movaps %xmm0, (%rax)
movq %rcx, 0x18(%rax)
movq %rcx, 0x20(%rax)
movq $0x0, 0x28(%rax)
movq %rax, 0x940(%rbx)
movl $0x30, %edi
callq 0x4210
movq %rax, %rcx
addq $0x8, %rcx
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rax)
movaps %xmm0, (%rax)
movq %rcx, 0x18(%rax)
movq %rcx, 0x20(%rax)
movq $0x0, 0x28(%rax)
movq %rax, 0x948(%rbx)
movq 0x58(%rsp), %rax
cmpl $0x0, 0x8c0(%rax)
jle 0x19693
leaq 0x60(%rsp), %rbp
movl $0x0, (%rsp)
movq %r15, 0x30(%rsp)
movq %r12, %rdi
leaq 0x1b579(%rip), %rsi     # 0x34867
movq %rbp, %rdx
xorl %eax, %eax
callq 0x4460
leaq 0x18(%rsp), %rbx
movq %rbx, 0x8(%rsp)
movq %rbp, %rdi
callq 0x4100
leaq (%rsp,%rax), %rdx
addq $0x60, %rdx
leaq 0x8(%rsp), %r14
movq %r14, %rdi
movq %rbp, %rsi
callq 0xa7c0
leaq 0x38(%rsp), %rdi
movq %r14, %rsi
callq 0x42c0
movq 0x8(%rsp), %rdi
cmpq %rbx, %rdi
je 0x19346
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4220
incl (%r15)
movq 0x88(%r13), %rax
movq 0x940(%rax), %r14
cmpb $0x0, 0x4(%rsp)
je 0x1941f
movq 0x28(%r14), %rbx
leaq 0x18(%rsp), %rax
movq %rax, 0x8(%rsp)
movq 0x38(%rsp), %rsi
movq 0x40(%rsp), %rdx
addq %rsi, %rdx
leaq 0x8(%rsp), %r15
movq %r15, %rdi
callq 0xa6be
movl %ebx, 0x28(%rsp)
movq %r14, %rdi
movq %r15, %rsi
callq 0x100c0
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
movq 0x30(%rsp), %r15
je 0x193ba
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4220
movq 0x88(%r13), %rax
movq 0x948(%rax), %r14
movl 0x28(%r14), %eax
movl %eax, 0x8(%rsp)
leaq 0x20(%rsp), %rax
movq %rax, 0x10(%rsp)
movq 0x38(%rsp), %rsi
movq 0x40(%rsp), %rdx
addq %rsi, %rdx
leaq 0x10(%rsp), %rdi
callq 0xa6be
movq %r14, %rdi
leaq 0x8(%rsp), %rsi
callq 0x1028a
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0x1941a
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x4220
movl (%rsp), %ebx
jmp 0x1944a
movq %r14, %rdi
leaq 0x38(%rsp), %rsi
callq 0xffc8
movq 0x88(%r13), %rcx
movq 0x940(%rcx), %rcx
addq $0x8, %rcx
cmpq %rcx, %rax
je 0x1963f
movl 0x40(%rax), %ebx
movq %r12, %rdi
leaq 0x1b13a(%rip), %rsi     # 0x3458e
xorl %eax, %eax
callq 0x4460
movq 0x88(%r13), %rax
cmpb $0x2, 0x8b8(%rax)
movslq %ebx, %r14
jl 0x194bc
xorl %ebx, %ebx
movq %r12, %rdi
leaq 0x1b400(%rip), %rsi     # 0x3487a
movq %rbp, %rdx
xorl %eax, %eax
callq 0x4460
movq %rbp, %rdi
callq 0x42d0
movq 0x38(%r13), %rax
movq (%rax,%r14,8), %rax
movsbq %bl, %rbx
movsd %xmm0, (%rax,%rbx,8)
incb %bl
movsbl %bl, %eax
movq 0x88(%r13), %rcx
movsbl 0x8b8(%rcx), %ecx
decl %ecx
cmpl %eax, %ecx
jg 0x19470
movsbq %bl, %rbx
jmp 0x194be
xorl %ebx, %ebx
movq %r12, %rdi
leaq 0x1b3a3(%rip), %rsi     # 0x3486b
movq %rbp, %rdx
xorl %eax, %eax
callq 0x4460
movq %rbp, %rdi
callq 0x42d0
movq 0x38(%r13), %rax
movq (%rax,%r14,8), %rax
movsd %xmm0, (%rax,%rbx,8)
incl (%r15)
movq %r12, %rdi
leaq 0x1b09e(%rip), %rsi     # 0x34592
xorl %eax, %eax
callq 0x4460
movq 0x88(%r13), %rax
movb 0x8b8(%rax), %al
testb %al, %al
jle 0x19580
xorl %r15d, %r15d
testb %al, %al
jle 0x19574
xorl %ebx, %ebx
movsbl %al, %eax
decl %eax
movl %ebx, %ecx
xorl %eax, %ecx
xorl %r15d, %eax
orl %ecx, %eax
leaq 0x1b341(%rip), %rsi     # 0x3486b
je 0x19533
leaq 0x1b347(%rip), %rsi     # 0x3487a
movq %r12, %rdi
movq %rbp, %rdx
xorl %eax, %eax
callq 0x4460
movq %rbp, %rdi
callq 0x42d0
movq 0x40(%r13), %rax
movq (%rax,%r14,8), %rax
movq (%rax,%r15,8), %rax
movsd %xmm0, (%rax,%rbx,8)
incq %rbx
movq 0x88(%r13), %rax
movb 0x8b8(%rax), %al
movsbq %al, %rcx
cmpq %rcx, %rbx
jl 0x19515
jmp 0x19578
movsbq %al, %rcx
incq %r15
cmpq %rcx, %r15
jl 0x1950f
movq 0x30(%rsp), %r15
incl (%r15)
movq %r12, %rdi
leaq 0x1b003(%rip), %rsi     # 0x34595
xorl %eax, %eax
callq 0x4460
movq 0x88(%r13), %rax
movl $0x1, %ebx
cmpb $0x0, 0x8b8(%rax)
jle 0x19677
xorl %r15d, %r15d
movb 0x8b9(%rax), %cl
testb %cl, %cl
jle 0x19623
xorl %ebx, %ebx
movsbl %cl, %ecx
movsbl 0x8b8(%rax), %eax
decl %eax
xorl %r15d, %eax
decl %ecx
xorl %ebx, %ecx
orl %eax, %ecx
leaq 0x1b28e(%rip), %rsi     # 0x3486b
je 0x195e6
leaq 0x1b294(%rip), %rsi     # 0x3487a
movq %r12, %rdi
movq %rbp, %rdx
xorl %eax, %eax
callq 0x4460
movq %rbp, %rdi
callq 0x42d0
movq 0x48(%r13), %rax
movq (%rax,%r14,8), %rax
movq (%rax,%r15,8), %rax
movsd %xmm0, (%rax,%rbx,8)
incq %rbx
movq 0x88(%r13), %rax
movsbq 0x8b9(%rax), %rcx
cmpq %rcx, %rbx
jl 0x195c1
incq %r15
movsbq 0x8b8(%rax), %rcx
cmpq %rcx, %r15
jl 0x195b5
movq 0x30(%rsp), %r15
movl $0x1, %ebx
jmp 0x19677
movq %r12, %rdi
leaq 0x1b229(%rip), %rsi     # 0x34872
xorl %eax, %eax
callq 0x4460
movq %r12, %rdi
leaq 0x1b218(%rip), %rsi     # 0x34872
xorl %eax, %eax
callq 0x4460
movl $0x3, %ebx
movq %r12, %rdi
leaq 0x1b202(%rip), %rsi     # 0x34872
xorl %eax, %eax
callq 0x4460
addl %ebx, (%r15)
movl (%rsp), %ecx
incl %ecx
movq 0x58(%rsp), %rax
movl %ecx, (%rsp)
cmpl 0x8c0(%rax), %ecx
jl 0x192e4
movq 0x38(%rsp), %rdi
leaq 0x48(%rsp), %rax
cmpq %rax, %rdi
je 0x196af
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x4220
addq $0x868, %rsp            # imm = 0x868
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x1970b
jmp 0x1970b
jmp 0x1970b
jmp 0x1970b
movq %rax, %rbx
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x1970e
movq 0x18(%rsp), %rsi
jmp 0x196f9
movq %rax, %rbx
movq 0x10(%rsp), %rdi
leaq 0x20(%rsp), %rax
cmpq %rax, %rdi
je 0x1970e
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x4220
jmp 0x1970e
jmp 0x1970b
jmp 0x1970b
jmp 0x1970b
jmp 0x1970b
movq %rax, %rbx
movq 0x38(%rsp), %rdi
leaq 0x48(%rsp), %rax
cmpq %rax, %rdi
je 0x1972a
movq 0x48(%rsp), %rsi
incq %rsi
callq 0x4220
movq %rbx, %rdi
callq 0x4430