// File: 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 %rbp
movq %rsp, %rbp
subq $0x10, %rsp
movq %rdi, -0x8(%rbp)
movq 0x10aad(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xab0b(%rip), %rsi      # 0xd028
movb $0x0, %al
callq 0x2330
movq 0x10a95(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xab1c(%rip), %rsi      # 0xd051
movb $0x0, %al
callq 0x2330
movq 0x10a7d(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xab0e(%rip), %rsi      # 0xd05b
movb $0x0, %al
callq 0x2330
movq 0x10a65(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xab41(%rip), %rsi      # 0xd0a6
movb $0x0, %al
callq 0x2330
movq 0x10a4d(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xab75(%rip), %rsi      # 0xd0f2
movb $0x0, %al
callq 0x2330
movq 0x10a35(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xaba7(%rip), %rsi      # 0xd13c
movb $0x0, %al
callq 0x2330
movq 0x10a1d(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xabcb(%rip), %rsi      # 0xd178
movb $0x0, %al
callq 0x2330
movq 0x10a05(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xac24(%rip), %rsi      # 0xd1e9
movb $0x0, %al
callq 0x2330
movq 0x109ed(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xac66(%rip), %rsi      # 0xd243
movb $0x0, %al
callq 0x2330
movq 0x109d5(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xacd2(%rip), %rsi      # 0xd2c7
movb $0x0, %al
callq 0x2330
movq 0x109bd(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xad00(%rip), %rsi      # 0xd30d
movb $0x0, %al
callq 0x2330
movq 0x109a5(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xad33(%rip), %rsi      # 0xd358
movb $0x0, %al
callq 0x2330
movq 0x1098d(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
movl 0x10bcc(%rip), %edx     # 0x13208
subl $0x1, %edx
leaq 0xad4f(%rip), %rsi      # 0xd395
movb $0x0, %al
callq 0x2330
movq 0x1096c(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xad84(%rip), %rsi      # 0xd3e2
movb $0x0, %al
callq 0x2330
movq 0x10954(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xad9b(%rip), %rsi      # 0xd411
movb $0x0, %al
callq 0x2330
movq 0x1093c(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xadcd(%rip), %rsi      # 0xd45b
movb $0x0, %al
callq 0x2330
movq 0x10924(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
movsd 0x10b69(%rip), %xmm0    # 0x13210
movsd 0x10b69(%rip), %xmm1    # 0x13218
movsd 0x10b69(%rip), %xmm2    # 0x13220
leaq 0xae06(%rip), %rsi      # 0xd4c4
movb $0x3, %al
callq 0x2330
movq 0x108f4(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xae37(%rip), %rsi      # 0xd50d
movb $0x0, %al
callq 0x2330
movq 0x108dc(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xac1d(%rip), %rsi      # 0xd30b
movb $0x0, %al
callq 0x2330
movq 0x108c4(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xae42(%rip), %rsi      # 0xd548
movb $0x0, %al
callq 0x2330
movq 0x108ac(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xae63(%rip), %rsi      # 0xd581
movb $0x0, %al
callq 0x2330
movq 0x10894(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xae6f(%rip), %rsi      # 0xd5a5
movb $0x0, %al
callq 0x2330
movq 0x1087c(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xae7b(%rip), %rsi      # 0xd5c9
movb $0x0, %al
callq 0x2330
movq 0x10864(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xae83(%rip), %rsi      # 0xd5e9
movb $0x0, %al
callq 0x2330
movq 0x1084c(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
leaq 0xaeaf(%rip), %rsi      # 0xd62d
movb $0x0, %al
callq 0x2330
movq 0x10834(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movq (%rax), %rdx
leaq 0xae9c(%rip), %rsi      # 0xd639
movb $0x0, %al
callq 0x2330
movq 0x10815(%rip), %rax     # 0x12fc0
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movq (%rax), %rdx
leaq 0xaeaa(%rip), %rsi      # 0xd666
movb $0x0, %al
callq 0x2330
addq $0x10, %rsp
popq %rbp
retq
nopl (%rax)