, including all inherited members.
| acronymWithAllDigits(const string &str, const int n=1) | feature | [private, static] |
| addGene(const string &gene, string &allele) | feature | [private, static] |
| addSubseq(const string &seq) | feature | [inline, static] |
| begin | feature | [private] |
| cleanGene(const string &gene, const string wd) | feature | [private, static] |
| clear() | feature | |
| clear() | feature | |
| complement | feature | [private] |
| complement() const | feature | |
| composeTitle() | feature | [private] |
| copy(const feature &lo) | feature | [private] |
| curFeat | feature | [private] |
| dbxref | feature | [private] |
| dumpFeat(ostream &bd) const | feature | |
| dumpGeneName(const string &file) | feature | [static] |
| dumpSubseq(const string &file) | feature | [static] |
| end | feature | [private] |
| endInfo(ostream &ous, const bool emark=true) const | feature | |
| endInfo(ostream &ous) const | feature | |
| existSubseq(const string &seq) | feature | [inline, static] |
| feat | feature | [private] |
| feat() const | feature | [inline] |
| feature() | feature | |
| feature(const feature &fe) | feature | |
| feature() | feature | [inline] |
| feature(const feature &feat) | feature | |
| findex() const | feature | |
| findQualif(const char *qk, string &vv) const | feature | |
| ft | feature | [private, static] |
| geneallele() const | feature | [private] |
| genecnt | feature | [private, static] |
| genen2s | feature | [private, static] |
| geneOfSymbol(const string &sym) | feature | [private, static] |
| genesbl | feature | [private, static] |
| getAllQualifiers() const | feature | |
| getBegin() const | feature | [inline] |
| getBeginEndinfo() const | feature | |
| getDbxrefString() const | feature | |
| getEnd() const | feature | [inline] |
| getEndEndinfo() const | feature | |
| getGeneSymbol(const string &gene, string &allele) | feature | [static] |
| getGeneSymbol(const string &gene) | feature | [static] |
| getLocationString() const | feature | [inline] |
| getName() const | feature | [inline] |
| getNumSeg() const | feature | [inline] |
| getOperation() const | feature | [inline] |
| getQualifierValue(const string &qkey) const | feature | |
| getSegop() const | feature | [inline] |
| getTaxid() const | feature | |
| goodGeneSymbol(const string &gene, string &symbol) | feature | [private, static] |
| hasDbxref() const | feature | [inline] |
| hasQualifier(const string &key) const | feature | [inline] |
| insertGeneAsSymbol(const string &gene) | feature | [private, static] |
| insertGeneSymbol(const string &gene, const string &symbol) | feature | [private, static] |
| insertQualifier(const string &key, string &value) | feature | [private] |
| is(const char *ff) const | feature | [inline] |
| isAbnormal() const | feature | |
| isComplement() const | feature | [inline] |
| isGoodGeneSymbol(const string &gene, const string &symbol) | feature | [private, static] |
| isGreek(const string &str) | feature | [private, static] |
| isjoinseg() const | feature | |
| isRomanNumber(const string &str) | feature | [private, static] |
| join enum value | feature | |
| l | feature | [private] |
| loadGeneName(const string &file) | feature | [static] |
| loadSubseq(const string &file) | feature | [static] |
| loc | feature | [private] |
| loc | feature | [private] |
| locIsJoin() const | feature | [inline] |
| locop | feature | [private] |
| locs | feature | [private] |
| locstr | feature | [private] |
| locstr | feature | [private] |
| makeGeneSymbol(const string &gene) | feature | [private, static] |
| maxl | feature | [private] |
| mktitle(string &tt) const | feature | [private] |
| n | feature | [private] |
| name | feature | [private] |
| newfeat() const | feature | [inline] |
| next(string &ln, istream &ins) | feature | |
| nextGeneSymbol() | feature | [private, static] |
| nextQualifier(istream &ins, string &ln) | feature | [private] |
| noend() const | feature | |
| nojunkGene(const string &gene) | feature | [private, static] |
| noLeft | feature | [private] |
| none enum value | feature | |
| noRight | feature | [private] |
| nostart() const | feature | |
| nq | feature | [private] |
| onone | feature | [private] |
| operator<<(ostream &ous, const feature &feat) | feature | [friend] |
| operator=(const feature &fe) | feature | |
| operator=(const feature &feat) | feature | |
| order enum value | feature | |
| orgtag(const seqinfo &sinf) | feature | [friend] |
| outgeneline(ostream &ous, const gbdnaseq &seq, const string &tag) const | feature | [private] |
| output(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| outRange(ostream &ous) const | feature | |
| outRange(ostream &ous, const char ed) const | feature | [inline] |
| outRange(ostream &ous) const | feature | |
| outSeg(ostream &ous) const | feature | |
| outSeg(ostream &ous) const | feature | |
| outSegMultiple(ostream &ous, const gbdnaseq &seq) const | feature | |
| parseLoc() | feature | [private] |
| PRTOUT | feature | [static] |
| qfind(const char *kq) const | feature | |
| qindex(const char qual[]) const | feature | [private] |
| qnv | feature | [private] |
| qt | feature | [private, static] |
| QUAL | feature | [static] |
| QUAL_SPACE | feature | [static] |
| QUAL_VAL | feature | [static] |
| qualifiers | feature | [private] |
| qv | feature | [private] |
| qvmap(const char *k) const | feature | |
| read(ifstream &ins, char ln[]) | feature | |
| read(istream &ins, char nxt[]) | feature | |
| readloc(istream &ins, char ln[]) | feature | [private] |
| readValidQualifier(const string &file) | feature | [static] |
| replseq | feature | [private] |
| RNAdump(ostream &ous, const seqinfo &sinf) const | feature | [private] |
| RNAdump(ostream &ous, const gbdnaseq &seq) const | feature | [private] |
| rptdump(ostream &ous, const seqinfo &sinf) const | feature | [private] |
| segop | feature | [private] |
| Segrelation enum name | feature | |
| separateAllele(const string &gene) | feature | [private, static] |
| shortIsGeneSymbol(const string &str, string::size_type idx, const int seplen) | feature | [private, static] |
| subCDS(ostream &seq, ostream &sub, const string &cdsKey, const string &title, int tlnIdx, const seqinfo &sqinf) const | feature | [private] |
| subCDS(ostream &ous, ostream &sub, const gbdnaseq &seq, const string &cdsKey, const string &prtKey, const string &title) const | feature | [private] |
| subkey(string &sk) const | feature | [private] |
| subseq | feature | [private, static] |
| tokey(string &tk) const | feature | [private] |
| validqual | feature | [private, static] |
| vb | feature | [private] |
| ve | feature | [private] |
| wFeature(ostream &ous, const seqinfo &sinf) const | feature | |
| wjoinseg(ostream &sub, seqinfo &sinf) const | feature | |
| write(ostream &ous) const | feature | |
| writeAceDNA(ostream &ous, ostream &sub, ostream &snp, gbdnaseq &seq) | feature | |
| writeAceProtein(ostream &ous, gbprtseq &prt) | feature | |
| writeAllele(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| writeCDS(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| writeCDS(ostream &ous, ostream &sub, const gbdnaseq &seq) | feature | [private] |
| writeExon(ostream &ous) const | feature | |
| writeFeature(ostream &ous, const gbdnaseq &seq) const | feature | [private] |
| writeFeatureOfWholeSeq(ostream &ous, const gbdnaseq &seq) const | feature | [private] |
| writeGene(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| writeGene(ostream &ous, ostream &sub, gbdnaseq &seq) const | feature | [private] |
| writeImmuno(ostream &ous, ostream &sub, const gbdnaseq &seq) const | feature | [private] |
| writemRNA(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| writemRNA(ostream &ous, ostream &sub, const gbdnaseq &seq) | feature | [private] |
| writeProtein(ostream &sub, const gbdnaseq &seq, const string &key, const string &title) const | feature | [private] |
| writePrtRegion(ostream &ous, gbprtseq &prt) const | feature | [private] |
| writePrtSite(ostream &ous, gbprtseq &prt) const | feature | [private] |
| writeRange(ostream &ous) const | feature | [inline] |
| writeRNA(ostream &sout, ostream &subout, seqinfo &sinf) const | feature | |
| writeRNA(ostream &sout, ostream &subout, gbdnaseq &seq) | feature | [private] |
| writerpt(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| writeSegCDS(ostream &sub, const gbdnaseq &seq) | feature | [private] |
| writeSegmRNA(ostream &sub, const gbdnaseq &seq) | feature | [private] |
| writeSNP(ostream &snp, gbdnaseq &seq) const | feature | [private] |
| writeSource(ostream &seqout, ostream &subsout, seqinfo &sinf) const | feature | |
| writeSource(ostream &ous, ostream &sub, gbdnaseq &seq) | feature | [private] |
| writeToken(ostream &seq, ostream &sub, seqinfo &sinf, const dseq &nt) const | feature | |
| writeUTR(ostream &seq, ostream &sub, seqinfo &sinf) const | feature | |
| xHiddenGeneSymbol(const string &str, const string &sep) | feature | [private, static] |
| ~feature() | feature | |
| ~feature() | feature | [inline] |
