// File: /workspace/github_c_makefile_star2_O2/fukunagatsu[P]RIblast/main.cpp
// Function: PrintUsage()
void PrintUsage() {
  cout << "RIblast - RNA-RNA interaction preriction tool. version 1.0" << endl;
  cout << "\n";
  cout << "Options\n";
  cout << "db: convert a FASTA file to RIblast database files\n";
  cout << "\n";
  cout << "RIblast db [-i InputFastaFile] [-o OutputDbName] [-r RepeatMaskingStyle]\n";
  cout << "           [-s LookupTableSize] [-w MaximalSpan] [-d MinAccessibleLength]\n";
  cout << "\n";
  cout << "  Options:\n";
  cout << " (Required)\n";
  cout << "    -i STR    RNA sequences in FASTA format\n";
  cout << "    -o STR    The database name\n";
  cout << "\n";
  cout << " (Optional)\n";
  cout << "    -r INT    Designation of repeat masking style 0:hard-masking, 1:soft-masking, 2:no-masking [default:0]\n";
  cout << "    -s INT    Lookup table size of short string search [default: 8]\n";
  cout << "    -w INT    The constraint of maximal distance between the bases that form base pairs. This parameter have to be set to 20 and over. [default: 70]\n";
  cout << "    -d INT    Minimum accessible length for accessibility approximation [defualt:5]\n";
  cout << "\n";
  cout << "\n";
  cout << "ris: search RNA-RNA interaction between a query and database sequences\n";
  cout << "\n";
  cout << "RIblast ris [-i InputFastaFile] [-o OutputFileName] [-d DatabaseFileName]\n";
  cout << "            [-l MaxSeedLength] [-e HybridizationEnergyThreshold] [-f InteractionEnergyThreshold]\n";
  cout << "            [-x DropOutLengthInGappedExtension] [-y DropOutLengthInUngappedExtension]\n";
  cout << "            [-g OutputEnergyThreshold] [-s OutputStyle]\n";
  cout << "\n";
  cout << "  Options:\n";
  cout << " (Required)\n";
  cout << "    -i STR    RNA sequences in FASTA format\n";
  cout << "    -o STR    Output file name\n";
  cout << "    -d STR    The database name\n";
  cout << "\n";
  cout << " (Optional)\n";
  cout << "    -l INT    Max size of seed length [default:20]\n";
  cout << "    -e DBL    Hybridization energy threshold for seed search [default: -6.0]\n";
  cout << "    -f DBL    Interaction energy threshold for removal of the interaction candidate before gapped extension [default: -4.0]\n";
  cout << "    -x INT    Dropout Length in gapped extension [defualt:18]\n";
  cout << "    -y INT    Dropout Length in ungapped extension [defualt:5]\n";
  cout << "    -g DBL    Energy threshold for output [defualt:-8.0]\n";
  cout << "    -s INT    Designation of output format style 0:simplified output, 1:detailed output [defualt:0]\n";
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq 0xdf862(%rip), %rbx     # 0xe2fd0
leaq 0x128cb(%rip), %rsi     # 0x16040
movq %rbx, %rdi
callq 0x31e0
movq %rax, %rdi
callq 0x3110
leaq 0x13086(%rip), %r14     # 0x16812
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
leaq 0x128dd(%rip), %rsi     # 0x1607b
movq %rbx, %rdi
callq 0x31e0
leaq 0x128d7(%rip), %rsi     # 0x16084
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
leaq 0x128f1(%rip), %rsi     # 0x160b8
movq %rbx, %rdi
callq 0x31e0
leaq 0x1292c(%rip), %rsi     # 0x16102
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
leaq 0x1295d(%rip), %r12     # 0x1614d
movq %rbx, %rdi
movq %r12, %rsi
callq 0x31e0
leaq 0x12957(%rip), %r13     # 0x16159
movq %rbx, %rdi
movq %r13, %rsi
callq 0x31e0
leaq 0x12952(%rip), %rbp     # 0x16166
movq %rbx, %rdi
movq %rbp, %rsi
callq 0x31e0
leaq 0x1296d(%rip), %rsi     # 0x16193
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
leaq 0x12974(%rip), %r15     # 0x161b4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x31e0
leaq 0x1296f(%rip), %rsi     # 0x161c1
movq %rbx, %rdi
callq 0x31e0
leaq 0x129cc(%rip), %rsi     # 0x1622d
movq %rbx, %rdi
callq 0x31e0
leaq 0x12a02(%rip), %rsi     # 0x16272
movq %rbx, %rdi
callq 0x31e0
leaq 0x12a89(%rip), %rsi     # 0x16308
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
leaq 0x12ab9(%rip), %rsi     # 0x1635d
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
leaq 0x12ae7(%rip), %rsi     # 0x163a5
movq %rbx, %rdi
callq 0x31e0
leaq 0x12b23(%rip), %rsi     # 0x163f0
movq %rbx, %rdi
callq 0x31e0
leaq 0x12b76(%rip), %rsi     # 0x16452
movq %rbx, %rdi
callq 0x31e0
leaq 0x12bbe(%rip), %rsi     # 0x164a9
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
movq %rbx, %rdi
movq %r12, %rsi
callq 0x31e0
movq %rbx, %rdi
movq %r13, %rsi
callq 0x31e0
movq %rbx, %rdi
movq %rbp, %rsi
callq 0x31e0
leaq 0x12bbc(%rip), %rsi     # 0x164e2
movq %rbx, %rdi
callq 0x31e0
leaq 0x12bcd(%rip), %rsi     # 0x16502
movq %rbx, %rdi
callq 0x31e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x31e0
movq %rbx, %rdi
movq %r15, %rsi
callq 0x31e0
leaq 0x12bc9(%rip), %rsi     # 0x16523
movq %rbx, %rdi
callq 0x31e0
leaq 0x12bee(%rip), %rsi     # 0x16557
movq %rbx, %rdi
callq 0x31e0
leaq 0x12c2d(%rip), %rsi     # 0x165a5
movq %rbx, %rdi
callq 0x31e0
leaq 0x12c9b(%rip), %rsi     # 0x16622
movq %rbx, %rdi
callq 0x31e0
leaq 0x12ccb(%rip), %rsi     # 0x16661
movq %rbx, %rdi
callq 0x31e0
leaq 0x12cfc(%rip), %rsi     # 0x166a1
movq %rbx, %rdi
callq 0x31e0
leaq 0x12d27(%rip), %rsi     # 0x166db
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x31e0