// File: /workspace/github_cpp_makefile_star2_O3/nanjiangshu[P]calSOV/calSOV.cpp
// Function: PrintHelp(char**)
void PrintHelp(char** argv)
{
    fprintf(stdout,"Usage: calSOV [options] file1 file2 ...\n");
    fprintf(stdout,"OPTIONS:\n");
    fprintf(stdout,"  -o, --out <outfile>  : output the result to outfile, (default = stdout)\n");
    fprintf(stdout,"  -l, --list listfile  : set the file containing a list of predicted files\n");
    fprintf(stdout,"  -f, --format 0|1|2|3 : set the format of the input file, (default = 1)\n");
    fprintf(stdout,"  -q3, --isOutQ3 yes|no: wheter output q3, (default = yes)\n");
    fprintf(stdout,"  -m, --method  0|1|2|3: set the method to get predicted secondary structure state from Res file, (default = 1)\n");
    fprintf(stdout,"  -statq3              : anylyze the Q3 for residues predicted at different confidences \n");
    fprintf(stdout,"  -chkfstdir           : folder to which Res from checkfirst program are stored, this need to be supplied when -statq3 is enabled \n");
    fprintf(stdout,"  -selconf     0|1     : selection of the confidence, (default = 0) \n");
    fprintf(stdout,"                       : 0 -- raw confidence, 1 -- normalized confidence \n");
    fprintf(stdout,"  -binwidth <real>     : set halfbinwidth, (default = 1.0) \n");
    fprintf(stdout,"  -max, --max-length   : set the max length of the sequence, (default = %d)\n", maxSeqLength-1);
    fprintf(stdout,"  -proof, --proof      : enable proof reading\n");
    fprintf(stdout,"  -proofmethod int     : set the method for proof reading, (default = 0)\n");
    fprintf(stdout,"  -polypara a1 a2 a3   : input three parameters for polynormail function which normalize the confidence\n");
    fprintf(stdout,"                       : default a1=%8.6lf , a2 = %8.6lf , a3 = %8.6lf \n", poly_a1, poly_a2 ,poly_a3);
    fprintf(stdout,"  -h, --help           : print this help message and exit\n");
    fprintf(stdout,"\n");
    fprintf(stdout,"Created on 2009-07-23, updated 2016-11-03, Nanjiang Shu\n");
    fprintf(stdout,"\nFormat description of input file:\n");
    fprintf(stdout,"    Format 0: prediction Res* file\n");
    fprintf(stdout,"    Format 1: AA OSEC PSEC NUM\n");
    fprintf(stdout,"    Format 2: Fasta format, >AA, >OSEC, >PSEC, order not important\n");
    fprintf(stdout,"\nExamples:\n");
    fprintf(stdout,"    %s -f 1 test/16VPA.psipred.format_1.txt\n", argv[0]);
    fprintf(stdout,"    %s -f 2 test/16VPA.psipred.format_2.txt\n", argv[0]);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x89b6(%rip), %r14      # 0xafc0
movq (%r14), %rcx
leaq 0x4a6c(%rip), %rdi      # 0x7080
movl $0x28, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4a7c(%rip), %rdi      # 0x70a9
movl $0x9, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4a6d(%rip), %rdi      # 0x70b3
movl $0x4a, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4a9f(%rip), %rdi      # 0x70fe
movl $0x4b, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4ad2(%rip), %rdi      # 0x714a
movl $0x49, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4b03(%rip), %rdi      # 0x7194
movl $0x3b, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4b26(%rip), %rdi      # 0x71d0
movl $0x70, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4b7e(%rip), %rdi      # 0x7241
movl $0x59, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4bbf(%rip), %rdi      # 0x729b
movl $0x83, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4c2a(%rip), %rdi      # 0x731f
movl $0x45, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4c57(%rip), %rdi      # 0x7365
movl $0x4a, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4c89(%rip), %rdi      # 0x73b0
movl $0x3c, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rdi
movl 0x8a39(%rip), %edx      # 0xb178
decl %edx
leaq 0x4ca5(%rip), %rsi      # 0x73ed
xorl %eax, %eax
callq 0x2240
movq (%r14), %rcx
leaq 0x4ce1(%rip), %rdi      # 0x743a
movl $0x2e, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4cf7(%rip), %rdi      # 0x7469
movl $0x49, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4d28(%rip), %rdi      # 0x74b3
movl $0x68, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rdi
movsd 0x89db(%rip), %xmm0     # 0xb180
movsd 0x89db(%rip), %xmm1     # 0xb188
movsd 0x89db(%rip), %xmm2     # 0xb190
leaq 0x4d60(%rip), %rsi      # 0x751c
movb $0x3, %al
callq 0x2240
movq (%r14), %rcx
leaq 0x4d98(%rip), %rdi      # 0x7565
movl $0x3a, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rsi
movl $0xa, %edi
callq 0x2200
movq (%r14), %rcx
leaq 0x4dad(%rip), %rdi      # 0x75a0
movl $0x38, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4dcd(%rip), %rdi      # 0x75d9
movl $0x23, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4dd8(%rip), %rdi      # 0x75fd
movl $0x23, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4de3(%rip), %rdi      # 0x7621
movl $0x1f, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4dea(%rip), %rdi      # 0x7641
movl $0x43, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rcx
leaq 0x4e15(%rip), %rdi      # 0x7685
movl $0xb, %esi
movl $0x1, %edx
callq 0x2290
movq (%r14), %rdi
movq (%rbx), %rdx
leaq 0x4e05(%rip), %rsi      # 0x7691
xorl %eax, %eax
callq 0x2240
movq (%r14), %rdi
movq (%rbx), %rdx
leaq 0x4e1e(%rip), %rsi      # 0x76be
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x2240