Lines Matching refs:ostr
74 void CTabularFormatter_AllSeqIds::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
77 ostr << "query"; in PrintHeader()
79 ostr << "subject"; in PrintHeader()
86 void CTabularFormatter_AllSeqIds::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
88 ostr << "All "; in PrintHelpText()
89 PrintHeader(ostr); in PrintHelpText()
90 ostr << " Seq-id(s), separated by a ';'"; in PrintHelpText()
93 void CTabularFormatter_AllSeqIds::Print(CNcbiOstream& ostr, in Print() argument
100 ostr << *it; in Print()
104 ostr << ';'; in Print()
122 void CTabularFormatter_SeqId::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
124 PrintHeader(ostr); in PrintHelpText()
127 ostr << " accession.version"; in PrintHelpText()
131 ostr << " GI"; in PrintHelpText()
135 ostr << " id as it appears in alignment"; in PrintHelpText()
142 ostr << "; tag only for gnl seq-ids"; in PrintHelpText()
147 void CTabularFormatter_SeqId::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
150 ostr << "protein"; in PrintHeader()
152 ostr << "query"; in PrintHeader()
154 ostr << "subject"; in PrintHeader()
161 void CTabularFormatter_SeqId::Print(CNcbiOstream& ostr, in Print() argument
169 ostr << "NA"; in Print()
174 ostr << "NA"; in Print()
185 best.GetSeqId()->GetGeneral().GetTag().AsString(ostr); in Print()
189 ostr << acc; in Print()
191 ostr << best; in Print()
202 void CTabularFormatter_AlignStart::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
204 ostr << "Start of alignment in "; in PrintHelpText()
206 ostr << "query"; in PrintHelpText()
208 ostr << "subject"; in PrintHelpText()
215 void CTabularFormatter_AlignStart::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
218 ostr << "qstart"; in PrintHeader()
220 ostr << "sstart"; in PrintHeader()
227 void CTabularFormatter_AlignStart::Print(CNcbiOstream& ostr, in Print() argument
233 ostr << align.GetSeqStart(m_Row) + 1; in Print()
239 ostr << min(r.GetFrom(), r.GetTo()) + 1; in Print()
254 ostr << start + 1; in Print()
266 void CTabularFormatter_AlignEnd::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
268 ostr << "End of alignment in "; in PrintHelpText()
270 ostr << "query"; in PrintHelpText()
272 ostr << "subject"; in PrintHelpText()
279 void CTabularFormatter_AlignEnd::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
282 ostr << "qend"; in PrintHeader()
284 ostr << "send"; in PrintHeader()
291 void CTabularFormatter_AlignEnd::Print(CNcbiOstream& ostr, in Print() argument
295 ostr << align.GetSeqStop(m_Row) + 1; in Print()
301 ostr << max(r.GetFrom(), r.GetTo()) + 1; in Print()
316 ostr << stop + 1; in Print()
327 void CTabularFormatter_AlignStrand::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
329 ostr << "Strand of alignment in "; in PrintHelpText()
331 ostr << "query"; in PrintHelpText()
333 ostr << "subject"; in PrintHelpText()
340 void CTabularFormatter_AlignStrand::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
343 ostr << "qstrand"; in PrintHeader()
345 ostr << "sstrand"; in PrintHeader()
352 void CTabularFormatter_AlignStrand::Print(CNcbiOstream& ostr, in Print() argument
357 ostr << '+'; in Print()
361 ostr << '-'; in Print()
365 ostr << 'b'; in Print()
369 ostr << '?'; in Print()
381 void CTabularFormatter_SeqLength::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
383 ostr << "Length of "; in PrintHelpText()
385 ostr << "query"; in PrintHelpText()
387 ostr << "subject"; in PrintHelpText()
392 ostr << " sequence"; in PrintHelpText()
395 void CTabularFormatter_SeqLength::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
398 ostr << "qlen"; in PrintHeader()
400 ostr << "slen"; in PrintHeader()
407 void CTabularFormatter_SeqLength::Print(CNcbiOstream& ostr, in Print() argument
416 ostr << (int) score; in Print()
422 void CTabularFormatter_AlignLength::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
424 ostr << "Alignment length"; in PrintHelpText()
427 void CTabularFormatter_AlignLength::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
429 ostr << "length"; in PrintHeader()
432 void CTabularFormatter_AlignLength::Print(CNcbiOstream& ostr, in Print() argument
435 ostr << (int)m_Scores->GetScore(align, "align_length"); in Print()
440 void CTabularFormatter_AlignLengthUngap::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
442 ostr << "Alignment length not counting gaps"; in PrintHelpText()
445 void CTabularFormatter_AlignLengthUngap::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
447 ostr << "length_ungap"; in PrintHeader()
450 void CTabularFormatter_AlignLengthUngap::Print(CNcbiOstream& ostr, in Print() argument
453 ostr << (int)m_Scores->GetScore(align, "align_length_ungap"); in Print()
463 void CTabularFormatter_PercentId::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
465 ostr << "Percentage of identical matches"; in PrintHelpText()
467 ostr << " excluding gaps on either row"; in PrintHelpText()
471 void CTabularFormatter_PercentId::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
473 ostr << "pident"; in PrintHeader()
475 ostr << "(gapped)"; in PrintHeader()
477 ostr << "(ungapped)"; in PrintHeader()
481 void CTabularFormatter_PercentId::Print(CNcbiOstream& ostr, in Print() argument
490 ostr << pct_id; in Print()
495 void CTabularFormatter_PercentCoverage::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
497 ostr << (m_Row == 0 ? "Percent coverage of query in subject" in PrintHelpText()
501 void CTabularFormatter_PercentCoverage::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
503 ostr << m_Header; in PrintHeader()
506 void CTabularFormatter_PercentCoverage::Print(CNcbiOstream& ostr, in Print() argument
514 ostr << pct_cov; in Print()
519 void CTabularFormatter_GapCount::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
521 ostr << "Number of gap openings"; in PrintHelpText()
524 void CTabularFormatter_GapCount::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
526 ostr << "gapopen"; in PrintHeader()
528 void CTabularFormatter_GapCount::Print(CNcbiOstream& ostr, in Print() argument
531 ostr << align.GetNumGapOpenings(); in Print()
536 void CTabularFormatter_IdentityCount::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
538 ostr << "Number of identical matches"; in PrintHelpText()
540 void CTabularFormatter_IdentityCount::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
542 ostr << "identities"; in PrintHeader()
544 void CTabularFormatter_IdentityCount::Print(CNcbiOstream& ostr, in Print() argument
547 ostr << (int)m_Scores->GetScore(align, "num_ident"); in Print()
552 void CTabularFormatter_MismatchCount::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
554 ostr << "Number of mismatches"; in PrintHelpText()
556 void CTabularFormatter_MismatchCount::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
558 ostr << "mismatch"; in PrintHeader()
560 void CTabularFormatter_MismatchCount::Print(CNcbiOstream& ostr, in Print() argument
563 ostr << (int)m_Scores->GetScore(align, "num_mismatch"); in Print()
614 void CTabularFormatter_MismatchPositions::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
616 ostr << "Positions of aligned mismatches, comma seperated"; in PrintHelpText()
618 void CTabularFormatter_MismatchPositions::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
621 ostr << "qmismatchpos"; in PrintHeader()
623 ostr << "smismatchpos"; in PrintHeader()
629 void CTabularFormatter_MismatchPositions::Print(CNcbiOstream& ostr, in Print() argument
778 ostr << ','; in Print()
780 ostr << *it +1; in Print()
791 void CTabularFormatter_GapRanges::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
793 ostr << "Positions of gapped, unaligned, segments, comma seperated"; in PrintHelpText()
795 void CTabularFormatter_GapRanges::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
798 ostr << "qgapranges"; in PrintHeader()
800 ostr << "sgapranges"; in PrintHeader()
806 void CTabularFormatter_GapRanges::Print(CNcbiOstream& ostr, in Print() argument
818 ostr << ','; in Print()
820 ostr << it->GetFrom()+1 << "-" << it->GetTo()+1; in Print()
826 void CTabularFormatter_GapBaseCount::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
828 ostr << "Total number of gaps"; in PrintHelpText()
830 void CTabularFormatter_GapBaseCount::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
832 ostr << "gaps"; in PrintHeader()
834 void CTabularFormatter_GapBaseCount::Print(CNcbiOstream& ostr, in Print() argument
837 ostr << align.GetTotalGapCount(); in Print()
842 void CTabularFormatter_EValue::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
844 ostr << "Expect value"; in PrintHelpText()
846 void CTabularFormatter_EValue::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
848 ostr << "evalue"; in PrintHeader()
850 void CTabularFormatter_EValue::Print(CNcbiOstream& ostr, in Print() argument
866 ios_base::fmtflags cur_flags=ostr.flags(); in Print()
869 ostr << scientific << score; in Print()
872 ostr.unsetf(ios_base::scientific); in Print()
875 ostr << setiosflags(cur_flags); in Print()
881 void CTabularFormatter_EValue_Mantissa::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
883 ostr << "Expect value in mantissa format"; in PrintHelpText()
885 void CTabularFormatter_EValue_Mantissa::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
887 ostr << "evalue_mantissa"; in PrintHeader()
889 void CTabularFormatter_EValue_Mantissa::Print(CNcbiOstream& ostr, in Print() argument
930 ostr << mantissa; in Print()
936 void CTabularFormatter_EValue_Exponent::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
938 ostr << "Expect value in exponent format"; in PrintHelpText()
940 void CTabularFormatter_EValue_Exponent::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
942 ostr << "evalue_exponent"; in PrintHeader()
944 void CTabularFormatter_EValue_Exponent::Print(CNcbiOstream& ostr, in Print() argument
986 ostr << exponent; in Print()
995 void CTabularFormatter_BitScore::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
997 ostr << "Bit score"; in PrintHelpText()
999 void CTabularFormatter_BitScore::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1001 ostr << "bitscore"; in PrintHeader()
1003 void CTabularFormatter_BitScore::Print(CNcbiOstream& ostr, in Print() argument
1007 ostr << score; in Print()
1012 void CTabularFormatter_Score::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1014 ostr << "Raw score"; in PrintHelpText()
1016 void CTabularFormatter_Score::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1018 ostr << "score"; in PrintHeader()
1020 void CTabularFormatter_Score::Print(CNcbiOstream& ostr, in Print() argument
1024 ostr << score; in Print()
1038 void CTabularFormatter_AnyScore::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1040 ostr << m_Scores->HelpText(m_ScoreName); in PrintHelpText()
1043 void CTabularFormatter_AnyScore::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1045 ostr << m_ScoreName; in PrintHeader()
1049 void CTabularFormatter_AnyScore::Print(CNcbiOstream& ostr, in Print() argument
1065 ostr << score_i; in Print()
1067 ostr << score_d; in Print()
1079 void CTabularFormatter_Defline::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1081 ostr << "Defline of the "; in PrintHelpText()
1083 ostr << "query"; in PrintHelpText()
1085 ostr << "subject"; in PrintHelpText()
1090 ostr << " sequence"; in PrintHelpText()
1094 void CTabularFormatter_Defline::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1097 ostr << "qdefline"; in PrintHeader()
1099 ostr << "sdefline"; in PrintHeader()
1107 void CTabularFormatter_Defline::Print(CNcbiOstream& ostr, in Print() argument
1119 ostr << generator.GenerateDefline(bsh); in Print()
1125 void CTabularFormatter_AlignId::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1127 ostr << "Alignment ids"; in PrintHelpText()
1131 void CTabularFormatter_AlignId::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1133 ostr << "align_ids"; in PrintHeader()
1137 void CTabularFormatter_AlignId::Print(CNcbiOstream& ostr, in Print() argument
1144 ostr << ','; in Print()
1147 ostr << (*it)->GetId(); in Print()
1150 ostr << (*it)->GetStr(); in Print()
1158 void CTabularFormatter_BestPlacementGroup::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1160 ostr << "best_placement group id"; in PrintHelpText()
1163 void CTabularFormatter_BestPlacementGroup::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1165 ostr << "best_placement_group"; in PrintHeader()
1169 void CTabularFormatter_BestPlacementGroup::Print(CNcbiOstream& ostr, in Print() argument
1182 ostr << f->GetData().GetStr(); in Print()
1197 void CTabularFormatter_ProtRef::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1199 ostr << "Prot-ref of the "; in PrintHelpText()
1201 ostr << "query"; in PrintHelpText()
1203 ostr << "subject"; in PrintHelpText()
1208 ostr << " sequence"; in PrintHelpText()
1212 void CTabularFormatter_ProtRef::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1215 ostr << "qprotref"; in PrintHeader()
1217 ostr << "sprotref"; in PrintHeader()
1225 void CTabularFormatter_ProtRef::Print(CNcbiOstream& ostr, in Print() argument
1245 ostr << s; in Print()
1253 void CTabularFormatter_ExonIntrons::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1255 ostr << "Dump the "; in PrintHelpText()
1258 ostr << "exon"; in PrintHelpText()
1262 ostr << (m_Sequence == 0 ? "unaligned segment" : "intron"); in PrintHelpText()
1268 ostr << " structure"; in PrintHelpText()
1272 ostr << " lengths"; in PrintHelpText()
1277 ostr << " for the query sequence"; in PrintHelpText()
1280 ostr << " of a Spliced-seg alignment"; in PrintHelpText()
1283 void CTabularFormatter_ExonIntrons::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1286 ostr << "query_"; in PrintHeader()
1292 ostr << "exons"; in PrintHeader()
1296 ostr << "exon_len"; in PrintHeader()
1304 ostr << (m_Sequence == 0 ? "unaligned" : "introns"); in PrintHeader()
1308 ostr << (m_Sequence == 0 ? "unaligned_len" : "intron_len"); in PrintHeader()
1316 void CTabularFormatter_ExonIntrons::Print(CNcbiOstream& ostr, in Print() argument
1383 ostr << '['; in Print()
1387 ostr << ','; in Print()
1390 ostr << '(' << it->first->GetAmin()+1 in Print()
1398 ostr << ','; in Print()
1403 ostr << '(' in Print()
1411 ostr << it->GetLength(); in Print()
1416 ostr << ']'; in Print()
1428 void CTabularFormatter_TaxId::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1430 ostr << "Taxid of the "; in PrintHelpText()
1432 ostr << "query"; in PrintHelpText()
1434 ostr << "subject"; in PrintHelpText()
1439 ostr << " sequence"; in PrintHelpText()
1442 void CTabularFormatter_TaxId::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1445 ostr << "qtaxid"; in PrintHeader()
1447 ostr << "staxid"; in PrintHeader()
1454 void CTabularFormatter_TaxId::Print(CNcbiOstream& ostr, in Print() argument
1463 ostr << (int)m_Scores->GetScore(align, m_Row == 0 ? "query_taxid" in Print()
1482 void CTabularFormatter_OrgName::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1486 ostr << "Full taxname of the "; in PrintHelpText()
1490 ostr << "Species name of the "; in PrintHelpText()
1494 ostr << "Genus name of the "; in PrintHelpText()
1499 case 0: ostr << "query"; break; in PrintHelpText()
1500 case 1: ostr << "subject"; break; in PrintHelpText()
1505 ostr << " sequence"; in PrintHelpText()
1508 void CTabularFormatter_OrgName::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1511 case 0: ostr << "q"; break; in PrintHeader()
1512 case 1: ostr << "s"; break; in PrintHeader()
1519 case eFullTaxName: ostr << "taxname"; break; in PrintHeader()
1520 case eSpecies: ostr << "species"; break; in PrintHeader()
1521 case eGenus: ostr << "genus"; break; in PrintHeader()
1525 void CTabularFormatter_OrgName::Print(CNcbiOstream& ostr, in Print() argument
1565 ostr << label; in Print()
1568 ostr << "-"; in Print()
1579 void CTabularFormatter_BiggestGapBases::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1581 ostr << "size of biggest gap"; in PrintHelpText()
1583 void CTabularFormatter_BiggestGapBases::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1586 ostr << "biggestgap"; in PrintHeader()
1588 ostr << "qbiggestgap"; in PrintHeader()
1590 ostr << "sbiggestgap"; in PrintHeader()
1596 void CTabularFormatter_BiggestGapBases::Print(CNcbiOstream& ostr, in Print() argument
1599 ostr << x_CalcBiggestGap(align); in Print()
1637 void CTabularFormatter_SeqChrom::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1639 ostr << "If "; in PrintHelpText()
1641 ostr << "query"; in PrintHelpText()
1643 ostr << "subject"; in PrintHelpText()
1648 ostr << " has a chromosome, its name"; in PrintHelpText()
1651 void CTabularFormatter_SeqChrom::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1654 ostr << "qchrom"; in PrintHeader()
1656 ostr << "schrom"; in PrintHeader()
1663 void CTabularFormatter_SeqChrom::Print(CNcbiOstream& ostr, in Print() argument
1685 ostr << Chrom; in Print()
1694 void CTabularFormatter_SeqClone::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1696 ostr << "If "; in PrintHelpText()
1698 ostr << "query"; in PrintHelpText()
1700 ostr << "subject"; in PrintHelpText()
1705 ostr << " has a clone, its name"; in PrintHelpText()
1708 void CTabularFormatter_SeqClone::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1711 ostr << "qclone"; in PrintHeader()
1713 ostr << "sclone"; in PrintHeader()
1720 void CTabularFormatter_SeqClone::Print(CNcbiOstream& ostr, in Print() argument
1745 ostr << Clone; in Print()
1755 void CTabularFormatter_Tech::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1758 ostr << "Query"; in PrintHelpText()
1760 ostr << "Subject"; in PrintHelpText()
1765 ostr << " sequence tech type"; in PrintHelpText()
1768 void CTabularFormatter_Tech::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1771 ostr << "qtech"; in PrintHeader()
1773 ostr << "stech"; in PrintHeader()
1780 void CTabularFormatter_Tech::Print(CNcbiOstream& ostr, in Print() argument
1797 ostr << TechStr; in Print()
1806 void CTabularFormatter_DiscStrand::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1808 ostr << "Strand of alignment in "; in PrintHelpText()
1810 ostr << "query"; in PrintHelpText()
1812 ostr << "subject"; in PrintHelpText()
1817 ostr << ", 'b' if both in a Disc-seg alignment"; in PrintHelpText()
1820 void CTabularFormatter_DiscStrand::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1823 ostr << "qdiscstrand"; in PrintHeader()
1825 ostr << "sdiscstrand"; in PrintHeader()
1832 void CTabularFormatter_DiscStrand::Print(CNcbiOstream& ostr, in Print() argument
1838 ostr << '+'; in Print()
1840 ostr << '-'; in Print()
1842 ostr << 'b'; in Print()
1871 void CTabularFormatter_FixedText::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1873 ostr << "'" << m_Text << "' as fixed text"; in PrintHelpText()
1876 void CTabularFormatter_FixedText::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1878 ostr << m_ColName; in PrintHeader()
1881 void CTabularFormatter_FixedText::Print(CNcbiOstream& ostr, in Print() argument
1884 ostr << m_Text; in Print()
1890 void CTabularFormatter_AlignLengthRatio::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1892 ostr << "length_ungap / size of aligned query sequence range"; in PrintHelpText()
1895 void CTabularFormatter_AlignLengthRatio::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1897 ostr << "align_len_ratio"; in PrintHeader()
1900 void CTabularFormatter_AlignLengthRatio::Print(CNcbiOstream& ostr, in Print() argument
1907 ostr << double(align_length) / double(align_range); in Print()
1918 void CTabularFormatter_Cigar::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1920 ostr << "Alignment CIGAR string"; in PrintHelpText()
1924 void CTabularFormatter_Cigar::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
1926 ostr << "cigar"; in PrintHeader()
1930 void CTabularFormatter_Cigar::Print(CNcbiOstream& ostr, in Print() argument
1954 ostr << Length << Code; in Print()
1974 void CTabularFormatter_AssemblyInfo::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
1978 ostr << "Name of "; in PrintHelpText()
1981 ostr << "Accession of "; in PrintHelpText()
1984 ostr << "Chain id of "; in PrintHelpText()
1987 ostr << "Chromosome containing "; in PrintHelpText()
1991 ostr << (m_Type == eFull ? "full assembly" : "assembly unit") << " of "; in PrintHelpText()
1994 ostr << "query"; in PrintHelpText()
1996 ostr << "subject"; in PrintHelpText()
2001 ostr << " sequence"; in PrintHelpText()
2004 void CTabularFormatter_AssemblyInfo::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
2007 ostr << "q"; in PrintHeader()
2009 ostr << "s"; in PrintHeader()
2015 ostr << (m_Type == eFull ? "fullasm" : "asmunit"); in PrintHeader()
2021 ostr << "acc"; in PrintHeader()
2024 ostr << "chain"; in PrintHeader()
2027 ostr << "chromosome"; in PrintHeader()
2032 void CTabularFormatter_AssemblyInfo::Print(CNcbiOstream& ostr, in Print() argument
2048 ostr << obj.GetField(m_Type == eFull in Print()
2055 ostr << obj.GetField(m_Type == eFull in Print()
2059 ostr << "NA"; in Print()
2066 ostr << obj.GetField("GenColl Chain").GetData().GetInt(); in Print()
2068 ostr << "NA"; in Print()
2076 ostr << obj.GetField("Chromosome").GetData().GetStr(); in Print()
2078 ostr << "NA"; in Print()
2115 ostr << Assm->GetName(); in Print()
2119 ostr << Assm->GetAccession(); in Print()
2127 ostr << accession.substr(chain_start, chain_end-chain_start); in Print()
2132 ostr << Seq->GetChrName(); in Print()
2144 void CTabularFormatter_PatchType::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
2146 ostr << "Patch type, if any, of "; in PrintHelpText()
2148 ostr << "query"; in PrintHelpText()
2150 ostr << "sequence"; in PrintHelpText()
2155 ostr << " sequence"; in PrintHelpText()
2158 void CTabularFormatter_PatchType::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
2161 ostr << "qpatchtype"; in PrintHeader()
2163 ostr << "spatchtype"; in PrintHeader()
2170 void CTabularFormatter_PatchType::Print(CNcbiOstream& ostr, in Print() argument
2183 ostr << "FIX"; in Print()
2185 ostr << "NOVEL"; in Print()
2196 void CTabularFormatter_NearestGap::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
2198 ostr << "Nearest Gap, if any, or edge, of "; in PrintHelpText()
2200 ostr << "query"; in PrintHelpText()
2202 ostr << "subject"; in PrintHelpText()
2207 ostr << " sequence"; in PrintHelpText()
2210 void CTabularFormatter_NearestGap::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
2213 ostr << "qnearestgap"; in PrintHeader()
2215 ostr << "snearestgap"; in PrintHeader()
2254 void CTabularFormatter_NearestGap::Print(CNcbiOstream& ostr, in Print() argument
2258 ostr << "*"; in Print()
2267 ostr << "*"; in Print()
2282 ostr << MinGapDist; in Print()
2293 void CTabularFormatter_Traceback::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
2295 ostr << "Blast Traceback string"; in PrintHelpText()
2298 void CTabularFormatter_Traceback::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
2300 ostr << "btop"; in PrintHeader()
2304 void CTabularFormatter_Traceback::Print(CNcbiOstream& ostr, in Print() argument
2312 ostr << m_Scores->GetTraceback(m_Scores->GetScope(), align, 0); in Print()
2324 void CTabularFormatter_Indels::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
2328 ostr << "List of frameshift indels"; in PrintHelpText()
2332 ostr << "List of non-frameshifting indels"; in PrintHelpText()
2336 ostr << "List of all indels wihin CDS"; in PrintHelpText()
2341 void CTabularFormatter_Indels::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
2345 ostr << "frameshifts"; in PrintHeader()
2349 ostr << "non-frameshift indels"; in PrintHeader()
2353 ostr << "indels in cds"; in PrintHeader()
2359 void CTabularFormatter_Indels::Print(CNcbiOstream& ostr, in Print() argument
2398 ostr << ','; in Print()
2400 ostr << indel.AsString(); in Print()
2414 void CTabularFormatter_GeneSymbol::PrintHelpText(CNcbiOstream& ostr) const in PrintHelpText()
2416 ostr << "Gene symbol for " << (m_Row == 0 ? "query" : "subject"); in PrintHelpText()
2419 void CTabularFormatter_GeneSymbol::PrintHeader(CNcbiOstream& ostr) const in PrintHeader()
2421 ostr << (m_Row == 0 ? "query" : "subject") << "_gene_symbol"; in PrintHeader()
2425 void CTabularFormatter_GeneSymbol::Print(CNcbiOstream& ostr, in Print() argument
2430 ostr << "NA"; in Print()
2435 ostr << "NA"; in Print()
2439 ostr << gene_it->GetData().GetGene().GetLocus(); in Print()
2445 CTabularFormatter::CTabularFormatter(CNcbiOstream& ostr, CScoreLookup &scores, in CTabularFormatter() argument
2447 : m_Scores(&scores), m_Ostr(ostr), m_UnavailableString(unavailable_string) in CTabularFormatter()