sequence fr_nextseq(fastareader fr,sequence seq) {
char *cline;
if (feof(fr->file)) {
return NULL;
}
seq_clear(seq);
while (strlen(fr->linebuffer) == 0) {
cline = fgets(fr->linebuffer,LINEBUFFERSIZE,fr->file);
if (cline == NULL) {
/* let's hope that's EOF, not error */
return NULL;
}
stripWhiteSpace(fr->linebuffer);
fr->lineno++;
}
if (fr->linebuffer[0] != '>') {
/* syntax error, apparently... */
fprintf(stderr,"syntax error reading '%s', line %d\n",
fr->filename,fr->lineno);
return NULL;
}
seq_setName(seq,fr->linebuffer+1);
fgets(fr->linebuffer,LINEBUFFERSIZE,fr->file);
stripWhiteSpace(fr->linebuffer);
while (!feof(fr->file) && fr->linebuffer[0] != '>') {
seq_append(seq,fr->linebuffer,strlen(fr->linebuffer));
fgets(fr->linebuffer,LINEBUFFERSIZE,fr->file);
stripWhiteSpace(fr->linebuffer);
}
return seq;
}
int isFastaFile(char *fn) {
FILE *fd;
int rv = 1;
fd = fopen(fn,"r");
if (fd == NULL) {
return 0;
}
fgets(scrap,MAXLINELEN,fd);
stripWhiteSpace(scrap);
if (scrap[0] != '>') {
rv = 0; /* doesn't appear to be Fasta */
}
/* check a second header line, just to be sure... */
fgets(scrap,MAXLINELEN,fd);
fgets(scrap,MAXLINELEN,fd);
stripWhiteSpace(scrap);
if (scrap[0] != '>') {
rv = 0; /* doesn't appear to be Fasta */
}
fclose(fd);
return rv;
}
int isFastqFile(char *fn) {
FILE *fd;
int rv = 1;
fd = fopen(fn,"r");
if (fd == NULL) {
return 0;
}
fgets(scrap,MAXLINELEN,fd);
stripWhiteSpace(scrap);
if (scrap[0] != '@') {
rv = 0; /* doesn't appear to be Fastq */
}
/* check sub-header */
fgets(scrap,MAXLINELEN,fd);
fgets(scrap,MAXLINELEN,fd);
stripWhiteSpace(scrap);
if (scrap[0] != '+') {
rv = 0; /* doesn't appear to be Fastq */
}
fgets(scrap,MAXLINELEN,fd);
/* and check a second time to be sure... */
fgets(scrap,MAXLINELEN,fd);
stripWhiteSpace(scrap);
if (scrap[0] != '@') {
rv = 0; /* doesn't appear to be Fastq */
}
/* check sub-header */
fgets(scrap,MAXLINELEN,fd);
fgets(scrap,MAXLINELEN,fd);
stripWhiteSpace(scrap);
if (scrap[0] != '+') {
rv = 0; /* doesn't appear to be Fastq */
}
fclose(fd);
return rv;
}
std::string Toker::getTok()
{
std::string tok = "";
stripWhiteSpace();
if(isSingleCharTok(nextChar))
{
getChar();
tok.append(1,currChar);
return tok;
}
do
{
if(isFileEnd())
return tok;
getChar();
if(isBeginComment())
{
if(tok.length() > 0)
{
this->putback(currChar);
return tok;
}
tok = eatComment();
if(doReturnComments)
return tok;
else
{
tok = "";
continue;
}
}
if(isBeginQuote())
{
if(tok.length() > 0)
{
this->putback(currChar);
return tok;
}
tok = eatQuote();
return tok;
}
std::locale loc;
if(!isspace(currChar, loc))
tok.append(1,currChar);
} while(!isTokEnd() || tok.length() == 0);
return tok;
}
int main(int argc, char **argv)
{
atexit(cleanup);
options = calloc(sizeof(struct opts_t), 1);
tableList = calloc(sizeof(*tableList), 1);
options->mode = -1;
options->rating = RATING_UNDEFINED;
if (argc < 2)
exitmsg(1, "Try -help for usage information\n");
parseArgs(argv + 1, options);
if (!options->backlog_path[0])
snprintf(options->backlog_path, 256, "%s/.backlog", getenv("HOME"));
if (!modified && readTables(tableList, options->backlog_path))
printf("Couldn't open '%s': %s\nYou can force the creation of this file by passing -force\n\n", options->backlog_path, strerror(errno));
struct entry_t *entry = 0;
struct table_t *table = 0;
if (options->mode == RATING_UNDEFINED && !options->searchMode && !modified)
exitmsg(1, "Must specify a mode\n");
if (options->rating != RATING_UNDEFINED && (options->rating < -1 || options->rating > 10))
exitmsg(1, "Rating must be in the range of -1 to 10\n");
char *entrystr = "Entry not found\n";
char *tablestr = "Table not found\n";
char *err_dupe = "An entry with that name already exists in that table\n";
char *err_dupe_table = "A table with that name already exists\n";
char help_msg[] =
"Available options:\n"
" -t\n"
"\tSwitch to table mode\n"
" -help\n"
"\tPrint this message\n"
" -insert\n"
"\tAdd entry/table\n"
" -rm\n"
"\tRemove entry/table\n"
" -mv\n"
"\tMove entry between tables\n"
" -ls\n"
"\tList tables, can be used with -name to print specific table\n"
" -find\n"
"\tSearch for entry, can be used with -name to search within table\n"
" -rate <INT>\n"
"\tSet rating on entry\n"
" -rename\n"
"\tRename entry/table\n"
" -name <STRING>\n"
"\tSet name\n"
" -new <STRING>\n"
"\tSet new name\n"
" -src <STRING>\n"
"\tSet source name\n"
" -dest <STRING>\n"
"\tSet destination name\n"
" -roll\n"
"\tReturn random entry\n"
" -mal\n"
"\tSearch MAL for entry\n"
" -nyaa\n"
"\tSearch Nyaa for entry\n"
" -baka\n"
"\tSearch BakaBT for entry (through Google)\n"
" -anidb\n"
"\tSearch AniDB for entry\n"
" -force\n"
"\tForce write-out to backlog file\n"
" -path\n"
"\tOverride the default backlog path (~/.backlog)\n"
" -nobak\n"
"\tDon't backup backlog file";
if (options->mode == MODE_LIST) { //List tables.
if (options->sourceName) {
table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
}
if (table) {
bklgPrintTable(table, stdout);
} else {
char buffer[32];
struct tm *tm;
time_t utime = time(0);
tm = localtime(&utime);
strftime(buffer, 32, "%d/%m/%Y\n", tm);
puts(buffer);
bklgPrintAllTables(tableList, stdout);
}
}
else if (options->mode == MODE_ENTRY_ADD && options->tableMode) { //Add table.
if (!options->entryName)
exitmsg(1, "Name required\n");
if (bklgGetTableExact(tableList, options->entryName))
exitmsg(1, err_dupe_table);
puts("Added table");
bklgTableAdd(tableList, options->entryName);
modified = 1;
}
else if (options->mode == MODE_ENTRY_REMOVE && options->tableMode) { //Remove table.
if (!options->entryName)
exitmsg(1, "Name required\n");
struct table_t *table = bklgGetTable(tableList, options->entryName);
if (!table)
exitmsg(1, tablestr);
printf("Remove \"%s\"? [Y,n]: ", table->name);
if (confirm()) {
puts("Table removed");
bklgLnodeDestroy(tableList, table->parent);
bklgTableDestroy(table);
modified = 1;
}
}
else if (options->mode == MODE_ENTRY_ADD) { //Add entry.
if (!options->entryName || !options->destinationName)
exitmsg(1, "Name and destination required, rating optional\n");
table = bklgGetTable(tableList, options->destinationName);
if (!table)
exitmsg(1, tablestr);
if (bklgGetEntryExact(table->entries, options->entryName))
exitmsg(1, err_dupe);
printf("Add entry to \"%s\"? [Y,n]: ", table->name);
if (confirm()) {
puts("Entry added");
entry = bklgEntryAdd(table->entries, options->entryName, options->rating == -2 ? -1 : options->rating);
modified = 1;
}
}
else if (options->mode == MODE_ENTRY_REMOVE) { //Remove entry.
if (!options->entryName)
exitmsg(1, "Name required, source optional\n");
struct entry_t *entry = 0;
if (!options->sourceName) {
entry = bklgGetEntryAllTables(tableList, options->entryName, &table);
} else {
table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
entry = bklgGetEntry(table->entries, options->entryName);
}
if (!entry)
exitmsg(1, entrystr);
printf("Remove \"%s\" from \"%s\"? [Y,n]: ", entry->name, table->name);
if (confirm()) {
puts("Entry removed");
bklgLnodeDestroy(table->entries, entry->parent);
free(entry);
modified = 1;
}
}
else if (options->mode == MODE_ENTRY_MOVE) { //Move entry to another table.
if (!options->entryName || !options->destinationName)
exitmsg(1, "Name and destination required, source optional\n");
struct entry_t *oldEntry = 0;
struct table_t *sourceTable = 0;
if (!options->sourceName) {
oldEntry = bklgGetEntryAllTables(tableList, options->entryName, &sourceTable);
} else {
sourceTable = bklgGetTable(tableList, options->sourceName);
if (!sourceTable)
exitmsg(1, "Source table not found\n");
oldEntry = bklgGetEntry(sourceTable->entries, options->entryName);
}
if (!oldEntry)
exitmsg(1, entrystr);
struct table_t *destTable = bklgGetTable(tableList, options->destinationName);
if (!destTable)
exitmsg(1, "Destination table not found\n");
if (bklgGetEntryExact(destTable->entries, oldEntry->name))
exitmsg(1, err_dupe);
printf("Move \"%s\" from \"%s\" to \"%s\"? [Y,n]: ", oldEntry->name, sourceTable->name, destTable->name);
if (confirm()) {
puts("Entry moved");
entry = bklgEntryAdd(destTable->entries, oldEntry->name, (options->rating < -1 ? oldEntry->rating : options->rating));
bklgLnodeDestroy(sourceTable->entries, oldEntry->parent);
free(oldEntry);
modified = 1;
}
}
else if (options->mode == MODE_FIND) { //Find entry.
if (!options->entryName)
exitmsg(1, "Name required, source optional\n");
if (!options->sourceName) {
entry = bklgGetEntryAllTables(tableList, options->entryName, &table);
} else {
table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
entry = bklgGetEntry(table->entries, options->entryName);
}
if (entry) {
char rating[8];
snprintf(rating, 8, "%i/10", entry->rating);
printf("Best match:\n\tName: %s\n\tRating: %s\n\tParent table: %s\n", entry->name, entry->rating == -1 ? "none" : rating, table->name);
} else {
exitmsg(1, entrystr);
}
}
else if (options->rating != RATING_UNDEFINED) { //Set a rating.
if (!options->entryName)
exitmsg(1, "Name required, rating and source optional\n");
if (!options->sourceName) {
entry = bklgGetEntryAllTables(tableList, options->entryName, &table);
} else {
table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
entry = bklgGetEntry(table->entries, options->entryName);
}
if (!entry)
exitmsg(1, entrystr);
printf("Change rating of \"%s\"? [Y,n]: ", entry->name);
if (confirm()) {
puts("Changed rating");
entry->rating = options->rating;
modified = 1;
}
}
else if (options->mode == MODE_ENTRY_RENAME && options->tableMode) { //Rename table.
if (!options->entryName || !options->entryNewName)
exitmsg(1, "Name and new name required\n");
table = bklgGetTable(tableList, options->entryName);
if (!table)
exitmsg(1, tablestr);
if (bklgGetTableExact(tableList, options->entryNewName))
exitmsg(1, err_dupe_table);
printf("Rename \"%s\"? [Y,n]: ", table->name);
if (confirm()) {
puts("Renamed table");
char tmp[64];
char *tmpp = 0;
strncpy(tmp, options->entryNewName, 64);
tmpp = stripWhiteSpace(tmp);
strncpy(table->name, tmpp, 64);
modified = 1;
}
}
else if (options->mode == MODE_ENTRY_RENAME) { //Rename entry.
if (!options->entryName || !options->entryNewName)
exitmsg(1, "Name and new name required, source optional\n");
if (!options->sourceName) {
entry = bklgGetEntryAllTables(tableList, options->entryName, &table);
} else {
table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
entry = bklgGetEntry(table->entries, options->entryName);
}
if (!entry)
exitmsg(1, entrystr);
if (bklgGetEntryExact(table->entries, options->entryNewName))
exitmsg(1, err_dupe);
printf("Rename \"%s\"? [Y,n]: ", entry->name);
if (confirm()) {
puts("Renamed entry");
char tmp[128];
char *tmpp = 0;
strncpy(tmp, options->entryNewName, 128);
tmpp = stripWhiteSpace(tmp);
strncpy(entry->name, tmpp, 128);
modified = 1;
}
}
else if (options->mode == MODE_RANDOM) { //Choose random entry.
if (!options->sourceName)
exitmsg(1, "Source required\n");
struct table_t *table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
srand(time(0) * getpid());
size_t len = listlen(table->entries);
int randomindex = rand() % len;
struct lnode_t *current = table->entries->tail;
for (int i = 0; i < randomindex; i++) {
current = current->next;
}
entry = current->data;
char rating[8];
snprintf(rating, 8, "%i/10", entry->rating);
printf("Random entry at index %i out of %zu:\n\tName: %s\n\tRating: %s\n\tParent table: %s\n", randomindex + 1, len, entry->name, entry->rating == -1 ? "none" : rating, table->name);
}
if (options->searchMode) { //Search various sites for entry.
if (!entry && !options->entryName) {
exitmsg(1, "Name required, source optional\n");
} else if (!entry) {
struct table_t *table = 0;
if (!options->sourceName) {
entry = bklgGetEntryAllTables(tableList, options->entryName, &table);
} else {
if (!table) {
table = bklgGetTable(tableList, options->sourceName);
if (!table)
exitmsg(1, tablestr);
}
entry = bklgGetEntry(table->entries, options->entryName);
}
if (!entry)
exitmsg(1, entrystr);
}
printf("Searching web for \"%s\"\n", entry->name);
webSearch(entry, options->searchMode);
}
else if (options->mode == MODE_HELP) { //Print usage stuff.
puts(help_msg);
}
if (modified) {
if (backup) {
char bakpath[256];
snprintf(bakpath, 256, "%s.bak", options->backlog_path);
if (rename(options->backlog_path, bakpath) == -1)
exitmsg(1, "Failed to rename to '%s': %s\n", bakpath, strerror(errno));
}
if (writeTables(tableList, options->backlog_path))
exitmsg(1, "Failed to open '%s' for writing: %s\n", options->backlog_path, strerror(errno));
}
exit(0);
}