ARB
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Classes | |
struct | formatTable |
Macros | |
#define | __NO_CTYPE |
#define | kFormCount 30 |
#define | kMaxFormName 15 |
#define | kDupmatch -2 |
#define | kMaxwhichlist 50 |
#define | kOptOkay 1 |
#define | kOptNone 0 |
#define | Exit(a) exit(a) |
#define | exit_main(err) |
#define | indexout() |
Functions | |
char * | formatstr (short format) |
int | rs_isdigit (int c) |
int | parseformat (char *name2) |
static void | dumpSeqList (char *list, short format) |
void | usage () |
void | erralert (short err) |
int | chooseFormat (boolean quietly) |
boolean | checkopt (boolean casesense, char *sopt, const char *smatch, short minword) |
void | resetGlobals () |
int | readopt (char *sopt) |
main (int argc, char *argv[]) | |
Variables | |
const char * | title = "readSeq (1Feb93), multi-format molbio sequence reader.\n" |
static char | inputfilestore [256] |
static char * | inputfile = inputfilestore |
const char * | formats [kMaxFormat+1] |
const struct formatTable | formname [] |
const char * | kASN1headline = "Bioseq-set ::= {\nseq-set {\n" |
const char | compl [] = " !\"#$%&'()*+,-./0123456789:;<=>?@TVGHNNCDNNMNKNNYRYSAABWNRN[\\]^_`tvghnncdnnmnknnyrysaabwnrn{|}~" |
boolean | chooseall = false |
boolean | quietly = false |
boolean | gotinputfile = false |
boolean | listonly = false |
boolean | closeout = false |
boolean | verbose = false |
boolean | manyout = false |
boolean | dolower = false |
boolean | doupper = false |
boolean | doreverse = false |
boolean | askout = true |
boolean | dopipe = false |
boolean | interleaved = false |
short | nfile = 0 |
short | iwhichlist =0 |
short | nwhichlist = 0 |
short | whichlist [kMaxwhichlist+1] |
long | whichSeq = 0 |
long | outform = kNoformat |
char | onamestore [128] |
char * | oname = onamestore |
FILE * | foo = NULL |
#define kFormCount 30 |
Definition at line 205 of file readseq.c.
Referenced by parseformat().
#define kMaxFormName 15 |
Definition at line 206 of file readseq.c.
Referenced by parseformat().
#define kDupmatch -2 |
Referenced by parseformat().
#define exit_main | ( | err | ) |
#define indexout | ( | ) |
Referenced by main().
Definition at line 252 of file readseq.c.
References kASN1, kASNseqentry, kASNseqset, kMaxFormat, kPhylip, kPhylipInterleave, and kPhylipSequential.
Referenced by dumpSeqList(), and main().
Definition at line 266 of file readseq.c.
Referenced by main(), parseformat(), and readopt().
Definition at line 270 of file readseq.c.
References formname, kDupmatch, kFormCount, kMaxFormat, kMaxFormName, kNoformat, min, formatTable::num, rs_isdigit(), skipwhitespace, and to_lower.
Referenced by chooseFormat(), and readopt().
void usage | ( | ) |
Definition at line 328 of file readseq.c.
References kMaxFormat, kMinFormat, and title.
Referenced by main(), readopt(), and string2enum_or_die().
void erralert | ( | short | err | ) |
Definition at line 379 of file readseq.c.
References eASNerr, eFileCreate, eFileNotFound, eItemNotFound, eMemFull, eNoData, eOneFormat, eUnequalSize, and eUnknownFormat.
Definition at line 408 of file readseq.c.
References kMaxFormat, kMinFormat, kNoformat, kPearson, outform, and parseformat().
Referenced by main().
void resetGlobals | ( | ) |
Definition at line 466 of file readseq.c.
References askout, closeout, dolower, dopipe, doreverse, doupper, foo, gotinputfile, gPretty, gPrettyInit, interleaved, iwhichlist, kNoformat, listonly, manyout, nfile, nwhichlist, onamestore, outform, quietly, verbose, and whichSeq.
Referenced by main().
Definition at line 486 of file readseq.c.
References askout, prettyopts::baseonlynum, checkopt(), closeout, prettyopts::degap, dolower, prettyopts::domatch, dopipe, doreverse, doupper, eFileCreate, eOptionBad, erralert(), foo, prettyopts::gapchar, gotinputfile, gPretty, prettyopts::interline, iwhichlist, kMaxwhichlist, kOptNone, kOptOkay, listonly, prettyopts::matchchar, max, prettyopts::nameleft, prettyopts::nameright, prettyopts::nametop, prettyopts::namewidth, nfile, prettyopts::noleaves, prettyopts::numbot, prettyopts::numleft, prettyopts::numright, prettyopts::numtop, prettyopts::numwidth, nwhichlist, outform, parseformat(), rs_isdigit(), prettyopts::seqwidth, prettyopts::spacer, prettyopts::tab, usage(), verbose, whichlist, and whichSeq.
Referenced by main().
Definition at line 714 of file readseq.c.
References askout, chooseFormat(), closeout, compressSeq(), prettyopts::degap, dolower, prettyopts::domatch, dopipe, doreverse, doupper, dumpSeqList(), eFileCreate, eItemNotFound, eMemFull, eOneFormat, erralert(), eUnequalSize, exit_main, foo, format(), formatstr(), fputc(), fputs(), prettyopts::gapchar, GCGchecksum(), getseqtype(), gotinputfile, gPretty, indexout, inputfile, inputfilestore, interleaved, prettyopts::interline, prettyopts::isactive, iwhichlist, kAmino, kASN1, kASNseqentry, kASNseqset, kDNA, kGCG, kMSF, kNoformat, kNucleic, kOtherSeq, kPAUP, kPhylip, kPhylip2, kPhylip4, kPIR, kPlain, kPretty, kRNA, listonly, listSeqs(), manyout, prettyopts::matchchar, nfile, prettyopts::noleaves, prettyopts::numbot, prettyopts::numline, prettyopts::numtop, nwhichlist, oname, outform, quietly, readopt(), readSeq(), readSeqFp(), resetGlobals(), rs_isdigit(), s, seq, seqchecksum, seqFileFormat(), skipwhitespace, title, to_lower, to_upper, usage(), verbose, whichlist, whichSeq, and writeSeq().
const char* title = "readSeq (1Feb93), multi-format molbio sequence reader.\n" |
Definition at line 22 of file readseq.c.
Referenced by askCopyMoveRuleset_cb(), aw_help_helpfile_changed_cb(), aw_help_history(), aw_status_timer_event(), awt_create_input_mask(), awt_create_load_box(), FINAL_TYPE< SEQTYPE >::create_child_progress(), initial_progress::create_child_progress(), create_config_manager_window(), RegFieldSelection::create_window(), EXP_create_experiments_submenu(), GDE_popup_filename_browser(), GEN_create_gene_species_submenu(), GEN_create_organism_submenu(), FINAL_TYPE< SEQTYPE >::get_title(), Helpfile::get_title(), main(), makeTitle(), PS_GNUPlot(), quick_scan_input_mask(), Helpfile::readHelp(), timed_window_title_cb(), usage(), and Helpfile::writeXML().
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static |
Definition at line 182 of file readseq.c.
Referenced by main(), Helpfile::readHelp(), and Helpfile::writeXML().
const char* formats[kMaxFormat+1] |
const struct formatTable formname[] |
Referenced by export_go_cb(), parseformat(), and update_exportTest_result_cb().
const char* kASN1headline = "Bioseq-set ::= {\nseq-set {\n" |
const char compl[] = " !\"#$%&'()*+,-./0123456789:;<=>?@TVGHNNCDNNMNKNNYRYSAABWNRN[\\]^_`tvghnncdnnmnknnyrysaabwnrn{|}~" |
Definition at line 456 of file readseq.c.
Referenced by main(), and resetGlobals().
Definition at line 456 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 457 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 457 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 457 of file readseq.c.
Referenced by main(), readopt(), resetGlobals(), and start_remote_command_for_application().
Definition at line 458 of file readseq.c.
Referenced by main(), and resetGlobals().
Definition at line 458 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 458 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 458 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 459 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 459 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 459 of file readseq.c.
Referenced by main(), readSeqMain(), and resetGlobals().
short nfile = 0 |
Definition at line 460 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
short iwhichlist =0 |
Definition at line 460 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
short nwhichlist = 0 |
Definition at line 460 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
short whichlist[kMaxwhichlist+1] |
long whichSeq = 0 |
Definition at line 462 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().
Definition at line 462 of file readseq.c.
Referenced by chooseFormat(), main(), readopt(), and resetGlobals().
char onamestore[128] |
Definition at line 463 of file readseq.c.
Referenced by resetGlobals().
char * oname = onamestore |
Definition at line 463 of file readseq.c.
Referenced by export_format_multiple(), gb_overwriteName(), FunInfo::has_name(), main(), and parse_names_into_gene_struct().
FILE* foo = NULL |
Definition at line 464 of file readseq.c.
Referenced by main(), readopt(), and resetGlobals().