int
editor_type::command (command_type& ct)
{
static const std::wstring onemore (L"cdijkmnpstw");
std::wstring doc;
if (1 == ct.naddr)
line2 = line1;
if (line1 > line2 || buffer.dollar () < line1 || buffer.dollar () < line2)
return '?';
if (line1 == 0 && onemore.find (ct.command) != std::wstring::npos)
return '?';
switch (ct.command) {
default: return '?';
case 'a': ct.command = cmd_a (ct); break;
case 'c': ct.command = cmd_c (ct); break;
case 'd': ct.command = cmd_d (ct); break;
case 'e': ct.command = cmd_e (ct); break;
case 'f': ct.command = cmd_f (ct); break;
case 'i': ct.command = cmd_i (ct); break;
case 'j': ct.command = cmd_j (ct); break;
case 'k': ct.command = cmd_k (ct); break;
case 'm': ct.command = cmd_m (ct); break;
case 'n': ct.command = cmd_n (ct); break;
case 'p': ct.command = cmd_p (ct); break;
case 'r': ct.command = cmd_r (ct); break;
case 's': ct.command = cmd_s (ct); break;
case 't': ct.command = cmd_t (ct); break;
case 'w': ct.command = cmd_w (ct); break;
case '=': ct.command = cmd_equal (ct); break;
case '\n': ct.command = cmd_p (ct); break;
}
print_dot (ct);
return ct.command;
}
int freq_display(void)
{
extern float freq;
extern int trxmode;
int x_position = 40;
int y_position = 17;
int location = 0;
char fbuffer[8];
print_space(y_position, x_position);
print_space(y_position + 1, x_position);
print_space(y_position + 2, x_position);
print_space(y_position + 3, x_position);
print_space(y_position + 4, x_position);
nicebox(16, 39, 5, 35, "TRX");
print_dot(y_position + 4, 28 + x_position + 1);
sprintf(fbuffer, "%7.1f", freq);
location = 32;
if (fbuffer[0] != ' ')
print_big_number(fbuffer[0] - 48, y_position, x_position, 4);
if (fbuffer[1] != ' ')
print_big_number(fbuffer[1] - 48, y_position, x_position, 9);
if (fbuffer[2] != ' ')
print_big_number(fbuffer[2] - 48, y_position, x_position, 14);
if (fbuffer[3] != ' ')
print_big_number(fbuffer[3] - 48, y_position, x_position, 19);
if (fbuffer[4] != ' ')
print_big_number(fbuffer[4] - 48, y_position, x_position, 24);
if (fbuffer[6] != ' ')
print_big_number(fbuffer[6] - 48, y_position, x_position, 31);
attron(COLOR_PAIR(C_HEADER) | A_STANDOUT);
if (trxmode == CWMODE)
mvprintw(18, 41, "CW");
else if (trxmode == SSBMODE)
mvprintw(19, 41, "SSB");
else
mvprintw(19, 41, "DIG");
refreshp();
return (0);
}
int main(int argc, char *argv[])
{
int verbose = 0;
bool printBLIF = false;
bool printDot = false;
bool printStatistics = false;
int cycles = 0;
int outputstyle = 0;
bool testv = false;
bool printVerilog = false;
std::ifstream testvectors;
--argc; ++argv;
try {
while (argc > 0 && argv[0][0] == '-') {
switch (argv[0][1]) {
case 'b': printBLIF = true; break;
case 'd': printDot = true; break;
case 's': printStatistics = true; break;
case 'V':
--argc; ++argv;
if (argc == 0) throw UsageError();
verbose = atoi(argv[0]);
break;
case 'c':
--argc; ++argv;
if (argc == 0) throw UsageError();
cycles = atoi(argv[0]);
break;
case 'o':
--argc; ++argv;
if (argc == 0) throw UsageError();
outputstyle = atoi(argv[0]);
break;
case 't':
--argc; ++argv;
if (argc == 0) throw UsageError();
testv = true;
testvectors.open(argv[0]);
break;
case 'v': printVerilog = true; break;
default:
throw UsageError();
}
--argc; ++argv;
}
if (argc > 1) throw UsageError();
{
BLIF::Netlist *n;
if (argc == 1) {
std::ifstream i(argv[0]);
if (!i.is_open()) {
std::cerr << "could not open " << argv[0] << std::endl;
return 1;
}
n = BLIF::read_blif(i);
i.close();
} else {
n = BLIF::read_blif(std::cin);
}
if (printBLIF) print_blif(std::cout, *n);
if (printDot) print_dot(std::cout, *n);
if (printVerilog) print_verilog(std::cout, *n);
if (printStatistics) {
unsigned int gates = 0;
unsigned int inputs = 0;
unsigned int outputs = 0;
unsigned int latches = 0;
for ( std::vector<BLIF::Gate*>::const_iterator i = n->gates.begin() ;
i != n->gates.end() ; i++ ) {
if ( (*i)->is_input ) inputs++;
if ( (*i)->is_output ) outputs++;
if ( (*i)->is_latch ) latches++;
if ( !( (*i)->is_input || (*i)->is_latch) ) gates++;
}
std::cerr
<< "gates: " << gates << " latches: " << latches
<< " inputs: " << inputs << " outputs: " << outputs << std::endl;
}
if (cycles > 0 || testv) {
// Run simulation
BLIF::Simulator sim(*n);
sim.debug = verbose & 1;
if (outputstyle == 1) {
for ( std::vector<BLIF::Gate*>::const_iterator j =
sim.outputs.begin() ;
j != sim.outputs.end() ; j++ )
std::cout << (*j)->name << ' ';
for ( std::vector<BLIF::Gate*>::const_iterator j =
sim.latches.begin() ;
j != sim.latches.end() ; j++ )
std::cout << (*j)->name << ' ';
std::cout << '\n';
}
for ( int i = 0 ; cycles > 0 ? i < cycles : true ; i++ ) {
if ( testv ) {
std::string line;
getline(testvectors, line);
if (testvectors.fail()) break;
if ( line.size() < sim.inputs.size() ) {
std::cerr << "Not enough inputs (" << line.size() << '<'
<< sim.inputs.size() << ") in test vector file\n";
break;
}
std::string::const_iterator j = line.begin();
for ( std::vector<BLIF::Gate*>::const_iterator i =
sim.inputs.begin() ; i != sim.inputs.end() ; j++ ) {
if ((*j) != ' ') {
sim.setInput(*i, (*j) == '1');
i++;
}
}
}
sim.simulate();
switch (outputstyle) {
case 1:
for ( std::vector<BLIF::Gate*>::const_iterator j =
sim.outputs.begin() ;
j != sim.outputs.end() ; j++ )
std::cout << (sim.getOutput(*j) ? '1' : '0');
std::cout << ' ';
for ( std::vector<BLIF::Gate*>::const_iterator j =
sim.latches.begin() ;
j != sim.latches.end() ; j++ )
std::cout << (sim.getLatch(*j) ? '1' : '0');
std::cout << '\n';
break;
default:
{
char buf[5];
sprintf(buf, "%4d", i);
std::cout << buf;
for ( std::vector<BLIF::Gate*>::const_iterator j =
sim.outputs.begin() ;
j != sim.outputs.end() ; j++ )
std::cout << ' ' << (*j)->name << '='
<< (sim.getOutput(*j) ? '1' : '0');
std::cout << '\n';
}
break;
}
}
}
}
} catch (UsageError &) {
std::cerr <<
"Usage: cec-blifutil [-b] [-d] [-s] [-V <level>] [-c <cycles>] [-o <style>] [-v] [<file.blif>]\n"
"-v Print Verilog version of input netlist\n"
"-b Print BLIF version of input netlist\n"
"-d Print dot version of input\n"
"-s Print statistics on the netlist\n"
"-c <cycles> Simulate for the given number of cycles\n"
"-t <vectorfile> Use this file of test vectors as input stimuli\n"
"-o <style> Set the simulation output style to 0, 1, 2, etc.\n"
"-V <level> Set verbosity to <level>\n"
;
return 1;
}
return 0;
}
int main(int argc, char** argv) {
std::int8_t m = 5;
std::int8_t n = -4;
std::int8_t g = -8;
std::int8_t e = -6;
std::int8_t q = -10;
std::int8_t c = -4;
std::uint8_t algorithm = 0;
std::uint8_t result = 0;
std::string dot_path = "";
char opt;
while ((opt = getopt_long(argc, argv, "m:n:g:e:q:c:l:r:d:h", options, nullptr)) != -1) {
switch (opt) {
case 'm': m = atoi(optarg); break;
case 'n': n = atoi(optarg); break;
case 'g': g = atoi(optarg); break;
case 'e': e = atoi(optarg); break;
case 'q': q = atoi(optarg); break;
case 'c': c = atoi(optarg); break;
case 'l': algorithm = atoi(optarg); break;
case 'r': result = atoi(optarg); break;
case 'd': dot_path = optarg; break;
case 'v': std::cout << version << std::endl; return 0;
case 'h': help(); return 0;
default: return 1;
}
}
if (optind >= argc) {
std::cerr << "[spoa::] error: missing input file!" << std::endl;
help();
return 1;
}
std::string sequences_path = argv[optind];
auto is_suffix = [](const std::string& src, const std::string& suffix) -> bool {
if (src.size() < suffix.size()) {
return false;
}
return src.compare(src.size() - suffix.size(), suffix.size(), suffix) == 0;
};
std::unique_ptr<bioparser::Parser<spoa::Sequence>> sparser = nullptr;
if (is_suffix(sequences_path, ".fasta") || is_suffix(sequences_path, ".fa") ||
is_suffix(sequences_path, ".fasta.gz") || is_suffix(sequences_path, ".fa.gz")) {
sparser = bioparser::createParser<bioparser::FastaParser, spoa::Sequence>(
sequences_path);
} else if (is_suffix(sequences_path, ".fastq") || is_suffix(sequences_path, ".fq") ||
is_suffix(sequences_path, ".fastq.gz") || is_suffix(sequences_path, ".fq.gz")) {
sparser = bioparser::createParser<bioparser::FastqParser, spoa::Sequence>(
sequences_path);
} else {
std::cerr << "[spoa::] error: file " << sequences_path <<
" has unsupported format extension (valid extensions: .fasta, "
".fasta.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz)!" <<
std::endl;
return 1;
}
std::unique_ptr<spoa::AlignmentEngine> alignment_engine;
try {
alignment_engine = spoa::createAlignmentEngine(
static_cast<spoa::AlignmentType>(algorithm), m, n, g, e, q, c);
} catch(std::invalid_argument& exception) {
std::cerr << exception.what() << std::endl;
return 1;
}
auto graph = spoa::createGraph();
std::vector<std::unique_ptr<spoa::Sequence>> sequences;
sparser->parse(sequences, -1);
std::size_t max_sequence_size = 0;
for (const auto& it: sequences) {
max_sequence_size = std::max(max_sequence_size, it->data().size());
}
alignment_engine->prealloc(max_sequence_size, 4);
for (const auto& it: sequences) {
auto alignment = alignment_engine->align(it->data(), graph);
try {
graph->add_alignment(alignment, it->data(), it->quality());
} catch(std::invalid_argument& exception) {
std::cerr << exception.what() << std::endl;
return 1;
}
}
if (result == 0 || result == 2) {
std::string consensus = graph->generate_consensus();
std::cout << "Consensus (" << consensus.size() << ")" << std::endl;
std::cout << consensus << std::endl;
}
if (result == 1 || result == 2) {
std::vector<std::string> msa;
graph->generate_multiple_sequence_alignment(msa);
std::cout << "Multiple sequence alignment" << std::endl;
for (const auto& it: msa) {
std::cout << it << std::endl;
}
}
graph->print_dot(dot_path);
return 0;
}
int print_big_number(int number, int y_position, int x_position,
int location)
{
switch (number) {
case 1:{
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 2:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position);
print_dot(y_position + 4, location + x_position);
print_dot(y_position + 4, location + x_position + 1);
print_dot(y_position + 4, location + x_position + 2);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 3:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position);
print_dot(y_position + 4, location + x_position + 1);
print_dot(y_position + 4, location + x_position + 2);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 4:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 5:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position);
print_dot(y_position + 4, location + x_position + 1);
print_dot(y_position + 4, location + x_position + 2);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 6:{
print_dot(y_position, location + x_position);
print_dot(y_position + 1, location + x_position);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position);
print_dot(y_position + 4, location + x_position + 1);
print_dot(y_position + 4, location + x_position + 2);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 7:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 8:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position);
print_dot(y_position + 4, location + x_position + 1);
print_dot(y_position + 4, location + x_position + 2);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 9:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 1);
print_dot(y_position + 2, location + x_position + 2);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position + 3);
break;
}
case 0:{
print_dot(y_position, location + x_position);
print_dot(y_position, location + x_position + 1);
print_dot(y_position, location + x_position + 2);
print_dot(y_position, location + x_position + 3);
print_dot(y_position + 1, location + x_position);
print_dot(y_position + 1, location + x_position + 3);
print_dot(y_position + 2, location + x_position);
print_dot(y_position + 2, location + x_position + 3);
print_dot(y_position + 3, location + x_position);
print_dot(y_position + 3, location + x_position + 3);
print_dot(y_position + 4, location + x_position);
print_dot(y_position + 4, location + x_position + 1);
print_dot(y_position + 4, location + x_position + 2);
print_dot(y_position + 4, location + x_position + 3);
break;
}
}
refreshp();
return (0);
}