| ! | Bio.Sequence.SeqData, Bio.Sequence |
| ? | Bio.Sequence.SeqData |
| Ala | Bio.Sequence.SeqData, Bio.Sequence |
| Align |
| 1 (Type/Class) | Bio.Alignment.Bowtie |
| 2 (Data Constructor) | Bio.Alignment.Bowtie |
| Alignment | Bio.Alignment.AlignData |
| Amino | Bio.Sequence.SeqData, Bio.Sequence |
| andSameSeq | Bio.Location.OnSeq |
| Ann | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Annotation | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| appendHeader | Bio.Sequence.SeqData, Bio.Sequence |
| Arg | Bio.Sequence.SeqData, Bio.Sequence |
| asksGFF | Bio.GFF3.FeatureHierSequences |
| Asm | Bio.Alignment.ACE |
| Asn | Bio.Sequence.SeqData, Bio.Sequence |
| Asp | Bio.Sequence.SeqData, Bio.Sequence |
| Assembly | Bio.Alignment.ACE |
| Asx | Bio.Sequence.SeqData, Bio.Sequence |
| attrByTag | Bio.GFF3.Feature |
| attributes | Bio.GFF3.Feature |
| attrTag | Bio.GFF3.Feature |
| attrValues | Bio.GFF3.Feature |
| Aux | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| aux |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| b36 | Bio.Sequence.SFF_name |
| bases | Bio.Sequence.SFF |
| bits |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| blastdate | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| BlastFlat |
| 1 (Type/Class) | Bio.Alignment.BlastFlat |
| 2 (Data Constructor) | Bio.Alignment.BlastFlat |
| BlastHit |
| 1 (Type/Class) | Bio.Alignment.BlastData |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| BlastMatch |
| 1 (Type/Class) | Bio.Alignment.BlastData |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| blastn_default | Bio.Alignment.Matrices |
| blastprogram | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| BlastRecord |
| 1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| blastreferences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| BlastResult |
| 1 (Type/Class) | Bio.Alignment.BlastData |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| blastversion | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| blosum45 | Bio.Alignment.Matrices |
| blosum62 | Bio.Alignment.Matrices |
| blosum80 | Bio.Alignment.Matrices |
| bounds |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| Branch | Bio.Clustering |
| castToAmino | Bio.Sequence.SeqData, Bio.Sequence |
| castToNuc | Bio.Sequence.SeqData, Bio.Sequence |
| checkInvariants |
| 1 (Function) | Bio.Location.LocMap |
| 2 (Function) | Bio.GFF3.FeatureHier |
| children |
| 1 (Function) | Bio.GFF3.FeatureHier |
| 2 (Function) | Bio.GFF3.FeatureHierSequences |
| childrenM | Bio.GFF3.FeatureHier |
| Chr | Bio.Alignment.AlignData |
| chromosomes | Bio.GFF3.SGD |
| clip_adapter_left | Bio.Sequence.SFF |
| clip_adapter_right | Bio.Sequence.SFF |
| clip_qual_left | Bio.Sequence.SFF |
| clip_qual_right | Bio.Sequence.SFF |
| Clustered | Bio.Clustering |
| cluster_sl | Bio.Clustering |
| columns | Bio.Alignment.AlignData |
| CommonHeader |
| 1 (Type/Class) | Bio.Sequence.SFF |
| 2 (Data Constructor) | Bio.Sequence.SFF |
| Comp | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| compact | Bio.Sequence.HashWord |
| compl | Bio.Sequence.SeqData, Bio.Sequence |
| complement | Bio.Sequence.HashWord |
| contig | Bio.Alignment.ACE |
| ContigLoc |
| 1 (Type/Class) | Bio.Location.ContigLocation |
| 2 (Data Constructor) | Bio.Location.ContigLocation |
| contigLoc | Bio.GFF3.Feature |
| contigous | Bio.Sequence.HashWord, Bio.Sequence |
| ContigSeqLoc | Bio.Location.SeqLocation |
| convert | Bio.Sequence.SFF |
| countIO | Bio.Util |
| countSeqs | Bio.Sequence.Fasta |
| Cys | Bio.Sequence.SeqData, Bio.Sequence |
| database | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| date | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| dbchars | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| dbsequences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| decCh | Bio.Sequence.SFF_name |
| decode2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
| decode36 | Bio.Sequence.SFF_name |
| decodeDate | Bio.Sequence.SFF_name |
| decodeKO | Bio.Sequence.KEGG |
| decodeLocation | Bio.Sequence.SFF_name |
| decodeReadName | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| decodeUP | Bio.Sequence.KEGG |
| decomment | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| defragSeq | Bio.Sequence.SeqData |
| Del | Bio.Alignment.AlignData |
| delete |
| 1 (Function) | Bio.Location.LocMap |
| 2 (Function) | Bio.GFF3.FeatureHier |
| deleteBy | Bio.Location.LocMap |
| Dir | Bio.Alignment.AlignData |
| display |
| 1 (Function) | Bio.Location.Position |
| 2 (Function) | Bio.Location.ContigLocation |
| 3 (Function) | Bio.Location.Location |
| 4 (Function) | Bio.Location.SeqLocation |
| displayContigSeqLoc | Bio.Location.SeqLocation |
| displaySeqPos | Bio.Location.SeqLocation |
| divMods | Bio.Sequence.SFF_name |
| E | Bio.Util.TestBase |
| Edit | Bio.Alignment.AlignData |
| EditList | Bio.Alignment.AlignData |
| EL | Bio.Util.TestBase |
| empty | Bio.Location.SeqLocMap |
| encode2Bit | Bio.Sequence.TwoBit |
| encode36 | Bio.Sequence.SFF_name |
| encodeDate | Bio.Sequence.SFF_name |
| encodeLocation | Bio.Sequence.SFF_name |
| encodeReadName | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| encodeRegion | Bio.Sequence.SFF_name |
| end | Bio.GFF3.Feature |
| endPos |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| entropy | Bio.Sequence.Entropy, Bio.Sequence |
| Eq | Bio.Util.TestBase |
| ES | Bio.Util.TestBase |
| escapeAllBut | Bio.GFF3.Escape |
| escapeAllOf | Bio.GFF3.Escape |
| escapeByteString | Bio.GFF3.Escape |
| ESet | Bio.Util.TestBase |
| EST | Bio.Util.TestBase |
| ESTq | Bio.Util.TestBase |
| EST_long | Bio.Util.TestBase |
| EST_set | Bio.Util.TestBase |
| EST_short | Bio.Util.TestBase |
| eval | Bio.Alignment.AlignData |
| EvidenceCode | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| extend |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| extractGaps | Bio.Alignment.AlignData |
| e_val |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| Feature |
| 1 (Type/Class) | Bio.GFF3.Feature |
| 2 (Data Constructor) | Bio.GFF3.Feature |
| FeatureHier | Bio.GFF3.FeatureHier |
| FeatureHierSequences | Bio.GFF3.FeatureHierSequences |
| features |
| 1 (Function) | Bio.GFF3.FeatureHier |
| 2 (Function) | Bio.GFF3.FeatureHierSequences |
| featureSequence | Bio.GFF3.FeatureHierSequences |
| flatten | Bio.Alignment.BlastFlat |
| Flow | Bio.Sequence.SFF |
| flow | Bio.Sequence.SFF |
| flowgram | Bio.Sequence.SFF |
| flowgram_fmt | Bio.Sequence.SFF |
| flow_index | Bio.Sequence.SFF |
| flow_length | Bio.Sequence.SFF |
| fragments | Bio.Alignment.ACE |
| Frame | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| fromIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
| fromList |
| 1 (Function) | Bio.Location.LocMap |
| 2 (Function) | Bio.Location.SeqLocMap |
| 3 (Function) | Bio.GFF3.FeatureHier |
| fromLists | Bio.GFF3.FeatureHierSequences |
| fromN | Bio.Util.TestBase |
| fromPosLen | Bio.Location.ContigLocation |
| fromQ | Bio.Util.TestBase |
| fromStartEnd | Bio.Location.ContigLocation |
| fromStr | Bio.Sequence.SeqData, Bio.Sequence |
| ftype | Bio.GFF3.Feature |
| Func | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Fwd |
| 1 (Data Constructor) | Bio.Alignment.AlignData |
| 2 (Data Constructor) | Bio.Location.Strand |
| gapped | Bio.Sequence.HashWord |
| Gaps | Bio.Alignment.AlignData |
| geneCDSes | Bio.GFF3.SGD |
| geneCDS_SLM | Bio.GFF3.SGD |
| genes | Bio.GFF3.SGD |
| geneSeqLoc | Bio.GFF3.SGD |
| geneSequence | Bio.GFF3.SGD |
| genkeys | Bio.Sequence.HashWord |
| genNonNegOffset | Bio.Util.TestBase |
| genOffset | Bio.Util.TestBase |
| genPositiveOffset | Bio.Util.TestBase |
| genReadKegg | Bio.Sequence.KEGG |
| getSequence | Bio.GFF3.FeatureHierSequences |
| GFFAttr |
| 1 (Type/Class) | Bio.GFF3.Feature |
| 2 (Data Constructor) | Bio.GFF3.Feature |
| Gln | Bio.Sequence.SeqData, Bio.Sequence |
| global_align |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| global_score |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| Glu | Bio.Sequence.SeqData, Bio.Sequence |
| Glx | Bio.Sequence.SeqData, Bio.Sequence |
| Gly | Bio.Sequence.SeqData, Bio.Sequence |
| GO | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoClass | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoDef |
| 1 (Type/Class) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| 2 (Data Constructor) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoHierarchy | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoTerm | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| group | Bio.Alignment.Soap |
| hash | Bio.Sequence.HashWord, Bio.Sequence |
| hashes | Bio.Sequence.HashWord, Bio.Sequence |
| HashF | Bio.Sequence.HashWord, Bio.Sequence |
| hasqual | Bio.Sequence.SeqData |
| HF | Bio.Sequence.HashWord, Bio.Sequence |
| His | Bio.Sequence.SeqData, Bio.Sequence |
| hits | Bio.Alignment.BlastData |
| hRead2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
| hReadFasta | Bio.Sequence.Fasta, Bio.Sequence |
| hReadFastQ | Bio.Sequence.FastQ, Bio.Sequence |
| hReadPhd | Bio.Sequence.Phd, Bio.Sequence |
| hWrite2Bit | Bio.Sequence.TwoBit |
| hWriteFasta | Bio.Sequence.Fasta, Bio.Sequence |
| hWriteFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
| hWriteFastQ | Bio.Sequence.FastQ, Bio.Sequence |
| hWriteQual | Bio.Sequence.Fasta, Bio.Sequence |
| h_from |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| h_to |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| IC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IDA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| identity |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| ids | Bio.GFF3.Feature |
| IEA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IEP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IGC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IGI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Ile | Bio.Sequence.SeqData, Bio.Sequence |
| IMP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Index | Bio.Sequence.SFF |
| index_length | Bio.Sequence.SFF |
| index_offset | Bio.Sequence.SFF |
| indirect | Bio.Alignment.Multiple |
| Ins | Bio.Alignment.AlignData |
| insert |
| 1 (Function) | Bio.Location.LocMap |
| 2 (Function) | Bio.Location.SeqLocMap |
| 3 (Function) | Bio.GFF3.FeatureHier |
| insertGaps | Bio.Alignment.AlignData |
| integralRandomR | Bio.Util.TestBase |
| IPI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| isCurated | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| isN | Bio.Sequence.HashWord |
| isRepl | Bio.Alignment.AlignData |
| ISS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| isWithin |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| 3 (Function) | Bio.Location.SeqLocation |
| k2n | Bio.Sequence.HashWord |
| k2n' | Bio.Sequence.HashWord |
| key | Bio.Sequence.SFF |
| key_length | Bio.Sequence.SFF |
| KO |
| 1 (Type/Class) | Bio.Sequence.KEGG |
| 2 (Data Constructor) | Bio.Sequence.KEGG |
| ksort | Bio.Sequence.HashWord, Bio.Sequence |
| KWords | Bio.Sequence.Entropy, Bio.Sequence |
| kwords | Bio.Sequence.Entropy, Bio.Sequence |
| lazyMany | Bio.Util.Parsex |
| Leaf | Bio.Clustering |
| leftoffset | Bio.Alignment.Bowtie |
| length |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| 3 (Function) | Bio.Alignment.Bowtie |
| 4 (Function) | Bio.Alignment.Soap |
| 5 (Function) | Bio.GFF3.Feature |
| Leu | Bio.Sequence.SeqData, Bio.Sequence |
| lines | Bio.Util |
| Loc |
| 1 (Type/Class) | Bio.Location.Location |
| 2 (Data Constructor) | Bio.Location.Location |
| loc | Bio.GFF3.Feature |
| local_align |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| local_score |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| LocMap | Bio.Location.LocMap |
| lookupId |
| 1 (Function) | Bio.GFF3.FeatureHier |
| 2 (Function) | Bio.GFF3.FeatureHierSequences |
| lookupIdChildren | Bio.GFF3.FeatureHier |
| lookupOverlaps |
| 1 (Function) | Bio.Location.LocMap |
| 2 (Function) | Bio.Location.SeqLocMap |
| lookupWithin |
| 1 (Function) | Bio.Location.LocMap |
| 2 (Function) | Bio.Location.SeqLocMap |
| Lys | Bio.Sequence.SeqData, Bio.Sequence |
| matches | Bio.Alignment.BlastData |
| Met | Bio.Sequence.SeqData, Bio.Sequence |
| Minus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| Mismatch |
| 1 (Type/Class) | Bio.Alignment.Bowtie |
| 2 (Data Constructor) | Bio.Alignment.Bowtie |
| mismatches |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| mismatchSeqPos |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| mkSeqs | Bio.Sequence.Fasta |
| mmoffset | Bio.Alignment.Bowtie |
| mylines | Bio.Util |
| N | Bio.Util.TestBase |
| n2i' | Bio.Sequence.HashWord |
| n2k | Bio.Sequence.HashWord |
| name |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| 3 (Function) | Bio.GFF3.Feature |
| namedSLM | Bio.GFF3.SGD |
| name_length | Bio.Sequence.SFF |
| NAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| ND | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| nhit | Bio.Alignment.Soap |
| nmismatch |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| noncodingExons | Bio.GFF3.SGD |
| noncodingSeqLoc | Bio.GFF3.SGD |
| noncodingSequence | Bio.GFF3.SGD |
| NR | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Nuc | Bio.Sequence.SeqData, Bio.Sequence |
| Nucleotide | Bio.Util.TestBase |
| num_bases | Bio.Sequence.SFF |
| num_reads | Bio.Sequence.SFF |
| Offset | Bio.Sequence.SeqData, Bio.Sequence |
| offset |
| 1 (Function) | Bio.Location.Position |
| 2 (Function) | Bio.Alignment.Soap |
| offset5 | Bio.Location.ContigLocation |
| on | Bio.Alignment.AlignData |
| onSameSeq | Bio.Location.OnSeq |
| OnSeq |
| 1 (Type/Class) | Bio.Location.OnSeq |
| 2 (Data Constructor) | Bio.Location.OnSeq |
| onSeqName | Bio.Location.OnSeq |
| onSeqObj | Bio.Location.OnSeq |
| OnSeqs | Bio.Location.OnSeq |
| overlaps |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| 3 (Function) | Bio.Location.SeqLocation |
| overlap_align | Bio.Alignment.QAlign |
| overlap_score | Bio.Alignment.QAlign |
| P | Bio.Util.TestBase |
| pairend | Bio.Alignment.Soap |
| pam30 | Bio.Alignment.Matrices |
| pam70 | Bio.Alignment.Matrices |
| parentIds | Bio.GFF3.Feature |
| parents |
| 1 (Function) | Bio.GFF3.FeatureHier |
| 2 (Function) | Bio.GFF3.FeatureHierSequences |
| parentsM | Bio.GFF3.FeatureHier |
| parse |
| 1 (Function) | Bio.Alignment.Blast |
| 2 (Function) | Bio.Sequence.FastQ |
| 3 (Function) | Bio.Alignment.Bowtie |
| 4 (Function) | Bio.Alignment.Soap |
| 5 (Function) | Bio.GFF3.Feature |
| 6 (Function) | Bio.GFF3.FeatureHierSequences |
| parseMismatch | Bio.Alignment.Soap |
| parseWithFasta | Bio.GFF3.Feature |
| perSeq | Bio.Location.OnSeq |
| perSeqUpdate | Bio.Location.OnSeq |
| phase | Bio.GFF3.Feature |
| Phe | Bio.Sequence.SeqData, Bio.Sequence |
| Plus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| Pos |
| 1 (Type/Class) | Bio.Location.Position |
| 2 (Data Constructor) | Bio.Location.Position |
| posInto |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| posOutof |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| Pro | Bio.Sequence.SeqData, Bio.Sequence |
| Proc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| progressive | Bio.Alignment.Multiple |
| Protein | Bio.Util.TestBase |
| ptest | Bio.Alignment.ACE |
| putSeqLn | Bio.Sequence.SeqData |
| Q | Bio.Util.TestBase |
| qlength |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| Qual | Bio.Sequence.SeqData, Bio.Sequence.Fasta, Bio.Sequence.SFF, Bio.Sequence |
| qual |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| QualData | Bio.Sequence.SeqData, Bio.Sequence.SFF, Bio.Sequence |
| Quality | Bio.Util.TestBase |
| quality | Bio.Sequence.SFF |
| qualMx | Bio.Alignment.QAlign |
| qualnt | Bio.Alignment.Soap |
| query |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| queryQual | Bio.Alignment.Bowtie |
| querySequ | Bio.Alignment.Bowtie |
| q_from |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| q_to |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| RCA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| rcontig | Bio.Sequence.HashWord, Bio.Sequence |
| rcpacked | Bio.Sequence.HashWord, Bio.Sequence |
| read2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
| readACE | Bio.Alignment.ACE |
| readbase | Bio.Alignment.Bowtie |
| ReadBlock |
| 1 (Type/Class) | Bio.Sequence.SFF |
| 2 (Data Constructor) | Bio.Sequence.SFF |
| readFasta | Bio.Sequence.Fasta, Bio.Sequence |
| readFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
| readFastQ | Bio.Sequence.FastQ, Bio.Sequence |
| readGO | Bio.Sequence.GOA |
| readGOA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| ReadHeader |
| 1 (Type/Class) | Bio.Sequence.SFF |
| 2 (Data Constructor) | Bio.Sequence.SFF |
| ReadName |
| 1 (Type/Class) | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| 2 (Data Constructor) | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| readnt | Bio.Alignment.Soap |
| readObo | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| readPhd | Bio.Sequence.Phd, Bio.Sequence |
| readQual | Bio.Sequence.Fasta, Bio.Sequence |
| reads | Bio.Alignment.ACE |
| readSFF | Bio.Sequence.SFF |
| readTerms | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| readXML |
| 1 (Function) | Bio.Alignment.BlastXML |
| 2 (Function) | Bio.Alignment.BlastFlat |
| read_header | Bio.Sequence.SFF |
| read_name | Bio.Sequence.SFF |
| refbase | Bio.Alignment.Bowtie |
| refCLoc | Bio.Alignment.Bowtie |
| refCSeqLoc |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| refname |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| refnt | Bio.Alignment.Soap |
| refSeqLoc |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| refSeqPos |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| refstart | Bio.Alignment.Soap |
| region | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| removePrefix | Bio.Sequence.KEGG |
| Repl | Bio.Alignment.AlignData |
| results | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| Rev | Bio.Alignment.AlignData |
| RevCompl | Bio.Location.Strand |
| revCompl | Bio.Location.Strand |
| revcompl | Bio.Sequence.SeqData, Bio.Sequence |
| revcompl' | Bio.Sequence.SeqData, Bio.Sequence |
| rRNAs | Bio.GFF3.SGD |
| runGFF | Bio.GFF3.FeatureHierSequences |
| runGFFIO | Bio.GFF3.FeatureHierSequences |
| SA | Bio.Alignment.Soap |
| SAM | Bio.Alignment.Soap |
| sameRead | Bio.Alignment.Bowtie |
| score | Bio.GFF3.Feature |
| Selector | Bio.Alignment.AlignData |
| Seq | Bio.Sequence.SeqData, Bio.Sequence |
| SeqData | Bio.Sequence.SeqData, Bio.Sequence.SFF, Bio.Sequence |
| seqData |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| 3 (Function) | Bio.Location.SeqLocation |
| 4 (Function) | Bio.GFF3.FeatureHierSequences |
| seqdata | Bio.Sequence.SeqData, Bio.Sequence |
| seqDataPadded |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| seqheader | Bio.Sequence.SeqData, Bio.Sequence |
| SeqId | Bio.Alignment.BlastData |
| seqid | Bio.GFF3.Feature |
| seqlabel | Bio.Sequence.SeqData, Bio.Sequence |
| seqlength | Bio.Sequence.SeqData, Bio.Sequence |
| SeqLoc | Bio.Location.SeqLocation |
| seqLoc | Bio.GFF3.Feature |
| SeqLocMap | Bio.Location.SeqLocMap |
| SeqName | Bio.Location.OnSeq |
| seqNt | Bio.Location.Position |
| seqNtPadded | Bio.Location.Position |
| SeqPos | Bio.Location.SeqLocation |
| seqqual | Bio.Sequence.SeqData, Bio.Sequence |
| seqToStr | Bio.Sequence.SeqData |
| sequ |
| 1 (Function) | Bio.Alignment.Bowtie |
| 2 (Function) | Bio.Alignment.Soap |
| Sequence | Bio.Sequence.SeqData, Bio.Sequence |
| sequence' | Bio.Util |
| sequences | Bio.GFF3.FeatureHierSequences |
| Ser | Bio.Sequence.SeqData, Bio.Sequence |
| setHeader | Bio.Sequence.SeqData, Bio.Sequence |
| SFF |
| 1 (Type/Class) | Bio.Sequence.SFF |
| 2 (Data Constructor) | Bio.Sequence.SFF |
| sffToSequence | Bio.Sequence.SFF |
| Shape | Bio.Sequence.HashWord |
| showalign | Bio.Alignment.AlignData |
| showT | Bio.Util.TestBase |
| simpleMx | Bio.Alignment.Matrices |
| slength |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| slide |
| 1 (Function) | Bio.Location.Position |
| 2 (Function) | Bio.Location.ContigLocation |
| SoapAlign | Bio.Alignment.Soap |
| SoapAlignMismatch | Bio.Alignment.Soap |
| sortExons | Bio.GFF3.SGD |
| source | Bio.GFF3.Feature |
| splitWhen | Bio.Util |
| start | Bio.GFF3.Feature |
| startPos |
| 1 (Function) | Bio.Location.ContigLocation |
| 2 (Function) | Bio.Location.Location |
| STP | Bio.Sequence.SeqData, Bio.Sequence |
| Strand |
| 1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| 2 (Type/Class) | Bio.Location.Strand |
| strand |
| 1 (Function) | Bio.Location.Position |
| 2 (Function) | Bio.Location.ContigLocation |
| 3 (Function) | Bio.Alignment.Bowtie |
| 4 (Function) | Bio.Alignment.Soap |
| 5 (Function) | Bio.GFF3.Feature |
| Stranded | Bio.Location.Strand |
| stranded | Bio.Location.Strand |
| Strands | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| subject |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| SubstMx | Bio.Alignment.AlignData |
| T | Bio.Util.TestBase |
| TAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Test | Bio.Util.TestBase |
| test |
| 1 (Function) | Bio.Sequence.SFF |
| 2 (Function) | Bio.Alignment.QAlign |
| Thr | Bio.Sequence.SeqData, Bio.Sequence |
| time |
| 1 (Function) | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| 2 (Function) | Bio.Util.TestBase |
| toIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
| toStr | Bio.Sequence.SeqData, Bio.Sequence |
| toStrings | Bio.Alignment.AlignData |
| translate | Bio.Sequence.SeqData, Bio.Sequence |
| Trp | Bio.Sequence.SeqData, Bio.Sequence |
| Tyr | Bio.Sequence.SeqData, Bio.Sequence |
| unEscapeByteString | Bio.GFF3.Escape |
| UniProtAcc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Unknown | Bio.Sequence.SeqData, Bio.Sequence |
| unparse |
| 1 (Function) | Bio.Sequence.FastQ |
| 2 (Function) | Bio.Alignment.Soap |
| 3 (Function) | Bio.GFF3.Feature |
| unparseMismatch | Bio.Alignment.Soap |
| unval | Bio.Sequence.HashWord |
| Val | Bio.Sequence.SeqData, Bio.Sequence |
| val | Bio.Sequence.HashWord |
| withinContigSeqLoc | Bio.Location.SeqLocation |
| withNameAndSeq | Bio.Location.OnSeq |
| withSeqData | Bio.Location.OnSeq |
| write2Bit | Bio.Sequence.TwoBit |
| writeACE | Bio.Alignment.ACE |
| writeFasta | Bio.Sequence.Fasta, Bio.Sequence |
| writeFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
| writeFastQ | Bio.Sequence.FastQ, Bio.Sequence |
| writeQual | Bio.Sequence.Fasta, Bio.Sequence |
| writeSFF | Bio.Sequence.SFF |
| writeSFF' | Bio.Sequence.SFF |
| Xaa | Bio.Sequence.SeqData, Bio.Sequence |
| Xle | Bio.Sequence.SeqData, Bio.Sequence |
| x_loc | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
| y_loc | Bio.Sequence.SFF_name, Bio.Sequence.SFF |
