// File: /workspace/github_cpp_makefile_star2_O2/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 %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdi, %rbx
movq 0x8b91(%rip), %r13      # 0xafc0
movq (%r13), %rcx
leaq 0x4bee(%rip), %rdi      # 0x7028
pushq $0x28
popq %rsi
pushq $0x1
popq %r14
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4bfd(%rip), %rdi      # 0x7051
pushq $0x9
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4bf1(%rip), %rdi      # 0x705b
pushq $0x4a
popq %r12
movq %r12, %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4c22(%rip), %rdi      # 0x70a6
pushq $0x4b
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4c58(%rip), %rdi      # 0x70f2
pushq $0x49
popq %r15
movq %r15, %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4c88(%rip), %rdi      # 0x713c
pushq $0x3b
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4cae(%rip), %rdi      # 0x7178
pushq $0x70
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4d09(%rip), %rdi      # 0x71e9
pushq $0x59
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4d4d(%rip), %rdi      # 0x7243
movl $0x83, %esi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4db9(%rip), %rdi      # 0x72c7
pushq $0x45
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4de9(%rip), %rdi      # 0x730d
movq %r12, %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4e1e(%rip), %rdi      # 0x7358
pushq $0x3c
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rdi
movl 0x8c51(%rip), %edx      # 0xb1a0
decl %edx
leaq 0x4e3d(%rip), %rsi      # 0x7395
xorl %eax, %eax
callq 0x2290
movq (%r13), %rcx
leaq 0x4e78(%rip), %rdi      # 0x73e2
pushq $0x2e
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4e91(%rip), %rdi      # 0x7411
movq %r15, %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4ec5(%rip), %rdi      # 0x745b
pushq $0x68
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rdi
movsd 0x8bfb(%rip), %xmm0     # 0xb1a8
movsd 0x8bfb(%rip), %xmm1     # 0xb1b0
movsd 0x8bfb(%rip), %xmm2     # 0xb1b8
leaq 0x4f00(%rip), %rsi      # 0x74c4
movb $0x3, %al
callq 0x2290
movq (%r13), %rcx
leaq 0x4f37(%rip), %rdi      # 0x750d
pushq $0x3a
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rsi
pushq $0xa
popq %rdi
callq 0x2240
movq (%r13), %rcx
leaq 0x4f50(%rip), %rdi      # 0x7548
pushq $0x38
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4f73(%rip), %rdi      # 0x7581
pushq $0x23
popq %r15
movq %r15, %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4f7d(%rip), %rdi      # 0x75a5
movq %r15, %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4f8b(%rip), %rdi      # 0x75c9
pushq $0x1f
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4f95(%rip), %rdi      # 0x75e9
pushq $0x43
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rcx
leaq 0x4fc3(%rip), %rdi      # 0x762d
pushq $0xb
popq %rsi
movq %r14, %rdx
callq 0x22e0
movq (%r13), %rdi
movq (%rbx), %rdx
leaq 0x4fb6(%rip), %rsi      # 0x7639
xorl %eax, %eax
callq 0x2290
movq (%r13), %rdi
movq (%rbx), %rdx
leaq 0x4fce(%rip), %rsi      # 0x7666
xorl %eax, %eax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
jmp 0x2290