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"GENETIC_CODE_TABLE", "getGeneticCode", "RNA_GENETIC_CODE" ] }, { "page": "getSeq", "title": "getSeq", "topics": [ "getSeq" ] }, { "page": "gregexpr2", "title": "A replacement for R standard gregexpr function", "topics": [ "gregexpr2" ] }, { "page": "HNF4alpha", "title": "Known HNF4alpha binding sequences", "topics": [ "HNF4alpha" ] }, { "page": "injectHardMask", "title": "Injecting a hard mask in a sequence", "topics": [ "injectHardMask", "injectHardMask,MaskedXString-method", "injectHardMask,XStringViews-method" ] }, { "page": "IUPAC_CODE_MAP", "title": "The IUPAC Extended Genetic Alphabet", "topics": [ "IUPAC_CODE_MAP", "mergeIUPACLetters" ] }, { "page": "lcsuffix", "title": "Find Longest Common Prefix/Suffix", "topics": [ "lcprefix", "lcprefix,character,character-method", "lcprefix,character,XString-method", "lcprefix,XString,character-method", "lcprefix,XString,XString-method", "lcsuffix", "lcsuffix,character,character-method", "lcsuffix,character,XString-method", "lcsuffix,XString,character-method", "lcsuffix,XString,XString-method" ] }, { "page": "letter", "title": "Subsetting a string", "topics": [ "letter", "letter,character-method", "letter,MaskedXString-method", "letter,XString-method", "letter,XStringViews-method" ] }, { "page": "letterFrequency", "title": "Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences", "topics": [ "alphabetFrequency", "alphabetFrequency,AAString-method", "alphabetFrequency,AAStringSet-method", "alphabetFrequency,DNAString-method", "alphabetFrequency,DNAStringSet-method", "alphabetFrequency,MaskedXString-method", "alphabetFrequency,RNAString-method", "alphabetFrequency,RNAStringSet-method", "alphabetFrequency,XString-method", "alphabetFrequency,XStringSet-method", "alphabetFrequency,XStringViews-method", "consensusMatrix", "consensusMatrix,character-method", "consensusMatrix,matrix-method", "consensusMatrix,XStringSet-method", "consensusMatrix,XStringViews-method", "consensusString", "consensusString,ANY-method", "consensusString,BStringSet-method", "consensusString,DNAStringSet-method", "consensusString,matrix-method", "consensusString,RNAStringSet-method", "consensusString,XStringViews-method", "hasOnlyBaseLetters", "hasOnlyBaseLetters,DNAString-method", "hasOnlyBaseLetters,DNAStringSet-method", "hasOnlyBaseLetters,MaskedXString-method", "hasOnlyBaseLetters,RNAString-method", "hasOnlyBaseLetters,RNAStringSet-method", "hasOnlyBaseLetters,XStringViews-method", "letterFrequency", "letterFrequency,MaskedXString-method", "letterFrequency,XString-method", "letterFrequency,XStringSet-method", "letterFrequency,XStringViews-method", "letterFrequencyInSlidingView", "letterFrequencyInSlidingView,XString-method", "uniqueLetters", "uniqueLetters,MaskedXString-method", "uniqueLetters,XString-method", "uniqueLetters,XStringSet-method", "uniqueLetters,XStringViews-method" ] }, { "page": "longestConsecutive", "title": "Obtain the length of the longest substring containing only 'letter'", "topics": [ "longestConsecutive" ] }, { "page": "lowlevel-matching", "title": "Low-level matching functions", "topics": [ "hasLetterAt", "isMatchingAt", "isMatchingEndingAt", "isMatchingEndingAt,character-method", "isMatchingEndingAt,XString-method", "isMatchingEndingAt,XStringSet-method", "isMatchingStartingAt", "isMatchingStartingAt,character-method", "isMatchingStartingAt,XString-method", "isMatchingStartingAt,XStringSet-method", "lowlevel-matching", "neditAt", "neditEndingAt", "neditEndingAt,character-method", "neditEndingAt,XString-method", "neditEndingAt,XStringSet-method", "neditStartingAt", "neditStartingAt,character-method", "neditStartingAt,XString-method", "neditStartingAt,XStringSet-method", "which.isMatchingAt", "which.isMatchingEndingAt", "which.isMatchingEndingAt,character-method", "which.isMatchingEndingAt,XString-method", "which.isMatchingEndingAt,XStringSet-method", "which.isMatchingStartingAt", "which.isMatchingStartingAt,character-method", "which.isMatchingStartingAt,XString-method", "which.isMatchingStartingAt,XStringSet-method" ] }, { "page": "MaskedXString-class", "title": "MaskedXString objects", "topics": [ "as.character,MaskedXString-method", "class:MaskedAAString", "class:MaskedBString", "class:MaskedDNAString", "class:MaskedRNAString", "class:MaskedXString", "coerce,AAString,MaskedAAString-method", "coerce,BString,MaskedBString-method", "coerce,DNAString,MaskedDNAString-method", "coerce,MaskedAAString,AAString-method", "coerce,MaskedBString,BString-method", "coerce,MaskedDNAString,DNAString-method", "coerce,MaskedRNAString,RNAString-method", "coerce,MaskedXString,MaskCollection-method", "coerce,MaskedXString,MaskedAAString-method", "coerce,MaskedXString,MaskedBString-method", "coerce,MaskedXString,MaskedDNAString-method", "coerce,MaskedXString,MaskedRNAString-method", "coerce,MaskedXString,NormalIRanges-method", "coerce,MaskedXString,Views-method", "coerce,MaskedXString,XStringViews-method", "coerce,RNAString,MaskedRNAString-method", "collapse,MaskedXString-method", "gaps,MaskedXString-method", "length,MaskedXString-method", "MaskedAAString", "MaskedAAString-class", "MaskedBString", "MaskedBString-class", "MaskedDNAString", "MaskedDNAString-class", "maskedratio,MaskedXString-method", "MaskedRNAString", "MaskedRNAString-class", "maskedwidth,MaskedXString-method", "MaskedXString", "MaskedXString-class", "masks", "masks,MaskedXString-method", "masks,XString-method", "masks<-", "masks<-,MaskedXString,MaskCollection-method", "masks<-,MaskedXString,NULL-method", "masks<-,XString,ANY-method", "masks<-,XString,NULL-method", "nchar,MaskedXString-method", "seqtype,MaskedXString-method", "seqtype<-,MaskedXString-method", "show,MaskedXString-method", "subseq,MaskedXString-method", "toString,MaskedXString-method", "unmasked", "unmasked,MaskedXString-method", "unmasked,XString-method", "Views,MaskedXString-method" ] }, { "page": "maskMotif", "title": "Masking by content (or by position)", "topics": [ "mask", "maskMotif", "maskMotif,MaskedXString,character-method", "maskMotif,MaskedXString,XString-method", "maskMotif,XString,ANY-method" ] }, { "page": "match-utils", "title": "Utility functions operating on the matches returned by a high-level matching function", "topics": [ "coverage,MaskedXString-method", "coverage,MIndex-method", "match-utils", "mismatch", "mismatch,ANY,XStringViews-method", "nmatch", "nmatch,ANY,XStringViews-method", "nmismatch", "nmismatch,ANY,XStringViews-method" ] }, { "page": "matchLRPatterns", "title": "Find paired matches in a sequence", "topics": [ "matchLRPatterns", "matchLRPatterns,MaskedXString-method", "matchLRPatterns,XString-method", "matchLRPatterns,XStringViews-method" ] }, { "page": "matchPattern", "title": "String searching functions", "topics": [ "countPattern", "countPattern,character-method", "countPattern,MaskedXString-method", "countPattern,XString-method", "countPattern,XStringSet-method", "countPattern,XStringViews-method", "matchPattern", "matchPattern,character-method", "matchPattern,MaskedXString-method", "matchPattern,XString-method", "matchPattern,XStringSet-method", "matchPattern,XStringViews-method", "vcountPattern", "vcountPattern,character-method", "vcountPattern,MaskedXString-method", "vcountPattern,XString-method", "vcountPattern,XStringSet-method", "vcountPattern,XStringViews-method", "vmatchPattern", "vmatchPattern,character-method", "vmatchPattern,MaskedXString-method", "vmatchPattern,XString-method", "vmatchPattern,XStringSet-method", "vmatchPattern,XStringViews-method" ] }, { "page": "matchPDict-exact", "title": "Matching a dictionary of patterns against a reference", "topics": [ "countPDict", "countPDict,MaskedXString-method", "countPDict,XString-method", "countPDict,XStringSet-method", "countPDict,XStringViews-method", "extractAllMatches", "matchPDict", "matchPDict,MaskedXString-method", "matchPDict,XString-method", "matchPDict,XStringSet-method", "matchPDict,XStringViews-method", "matchPDict-exact", "vcountPDict", "vcountPDict,MaskedXString-method", "vcountPDict,XString-method", "vcountPDict,XStringSet-method", "vcountPDict,XStringViews-method", "vmatchPDict", "vmatchPDict,ANY-method", "vmatchPDict,MaskedXString-method", "vmatchPDict,XString-method", "vwhichPDict", "vwhichPDict,MaskedXString-method", "vwhichPDict,XString-method", "vwhichPDict,XStringSet-method", "vwhichPDict,XStringViews-method", "whichPDict", "whichPDict,MaskedXString-method", "whichPDict,XString-method", "whichPDict,XStringSet-method", "whichPDict,XStringViews-method" ] }, { "page": "matchPDict-inexact", "title": "Inexact matching with matchPDict()/countPDict()/whichPDict()", "topics": [ "matchPDict-inexact" ] }, { "page": "matchProbePair", "title": "Find \"theoretical amplicons\" mapped to a probe pair", "topics": [ "matchProbePair", "matchProbePair,DNAString-method", "matchProbePair,MaskedDNAString-method", "matchProbePair,XStringViews-method" ] }, { "page": "matchPWM", "title": "PWM creating, matching, and related utilities", "topics": [ "countPWM", "countPWM,character-method", "countPWM,DNAString-method", "countPWM,MaskedDNAString-method", "countPWM,XStringViews-method", "matchPWM", "matchPWM,character-method", "matchPWM,DNAString-method", "matchPWM,MaskedDNAString-method", "matchPWM,XStringViews-method", "maxScore", "maxScore,ANY-method", "maxWeights", "maxWeights,matrix-method", "minScore", "minScore,ANY-method", "minWeights", "minWeights,matrix-method", "PWM", "PWM,character-method", "PWM,DNAStringSet-method", "PWM,matrix-method", "PWMscoreStartingAt", "reverseComplement,matrix-method", "unitScale" ] }, { "page": "MIndex-class", "title": "MIndex objects", "topics": [ "ByPos_MIndex-class", "class:ByPos_MIndex", "class:MIndex", "coerce,MIndex,CompressedIRangesList-method", "elementNROWS,MIndex-method", "endIndex", "endIndex,ByPos_MIndex-method", "length,MIndex-method", "MIndex", "MIndex-class", "names,MIndex-method", "names<-,MIndex-method", "show,MIndex-method", "startIndex", "startIndex,ByPos_MIndex-method", "unlist,MIndex-method", "width0", "width0,MIndex-method", "[[,ByPos_MIndex-method" ] }, { "page": "misc", "title": "Some miscellaneous stuff", "topics": [ "misc", "N50" ] }, { "page": "MultipleAlignment-class", "title": "MultipleAlignment objects", "topics": [ "AAMultipleAlignment", "AAMultipleAlignment-class", "alphabetFrequency,MultipleAlignment-method", "as.character,MultipleAlignment-method", "as.matrix,MultipleAlignment-method", "class:AAMultipleAlignment", "class:DNAMultipleAlignment", "class:MultipleAlignment", "class:RNAMultipleAlignment", "coerce,character,AAMultipleAlignment-method", "coerce,character,DNAMultipleAlignment-method", "coerce,character,RNAMultipleAlignment-method", "coerce,MultipleAlignment,AAStringSet-method", "coerce,MultipleAlignment,BStringSet-method", "coerce,MultipleAlignment,DNAStringSet-method", "coerce,MultipleAlignment,RNAStringSet-method", "colmask", "colmask,MultipleAlignment-method", "colmask<-", "colmask<-,MultipleAlignment,ANY-method", "colmask<-,MultipleAlignment,NULL-method", "consensusMatrix,MultipleAlignment-method", "consensusString,AAMultipleAlignment-method", "consensusString,DNAMultipleAlignment-method", "consensusString,MultipleAlignment-method", "consensusString,RNAMultipleAlignment-method", "consensusViews", "consensusViews,AAMultipleAlignment-method", "consensusViews,DNAMultipleAlignment-method", "consensusViews,MultipleAlignment-method", "consensusViews,RNAMultipleAlignment-method", "detail", "detail,MultipleAlignment-method", "dim,MultipleAlignment-method", "DNAMultipleAlignment", "DNAMultipleAlignment-class", "maskeddim", "maskeddim,MultipleAlignment-method", "maskedncol", "maskedncol,MultipleAlignment-method", "maskednrow", "maskednrow,MultipleAlignment-method", "maskedratio,MultipleAlignment-method", "maskGaps", "maskGaps,MultipleAlignment-method", "maskMotif,MultipleAlignment,ANY-method", "MultipleAlignment", "MultipleAlignment-class", "nchar,MultipleAlignment-method", "ncol,MultipleAlignment-method", "nrow,MultipleAlignment-method", "readAAMultipleAlignment", "readDNAMultipleAlignment", "readRNAMultipleAlignment", "RNAMultipleAlignment", "RNAMultipleAlignment-class", "rowmask", "rowmask,MultipleAlignment-method", "rowmask<-", "rowmask<-,MultipleAlignment,ANY-method", "rowmask<-,MultipleAlignment,NULL-method", "rownames,MultipleAlignment-method", "rownames<-,MultipleAlignment-method", "seqtype,MultipleAlignment-method", "show,MultipleAlignment-method", "unmasked,MultipleAlignment-method", "write.phylip" ] }, { "page": "nucleotideFrequency", "title": "Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)", "topics": [ "dinucleotideFrequency", "mkAllStrings", "nucleotideFrequencyAt", "nucleotideFrequencyAt,XStringSet-method", "nucleotideFrequencyAt,XStringViews-method", "oligonucleotideFrequency", "oligonucleotideFrequency,MaskedXString-method", "oligonucleotideFrequency,XString-method", "oligonucleotideFrequency,XStringSet-method", "oligonucleotideFrequency,XStringViews-method", "oligonucleotideTransitions", "trinucleotideFrequency" ] }, { "page": "padAndClip", "title": "Pad and clip strings", "topics": [ "padAndClip", "stackStrings" ] }, { "page": "PDict-class", "title": "PDict objects", "topics": [ "ACtree2", "ACtree2-class", "as.list,MTB_PDict-method", "class:ACtree2", "class:Expanded_TB_PDict", "class:MTB_PDict", "class:PDict", "class:PDict3Parts", "class:PreprocessedTB", "class:TB_PDict", "class:Twobit", "computeAllFlinks", "computeAllFlinks,ACtree2-method", "duplicated,PDict-method", "duplicated,PreprocessedTB-method", "Expanded_TB_PDict", "Expanded_TB_PDict-class", "hasAllFlinks", "hasAllFlinks,ACtree2-method", "head,PDict3Parts-method", "head,TB_PDict-method", "initialize,ACtree2-method", "initialize,PreprocessedTB-method", "initialize,Twobit-method", "length,PDict-method", "length,PDict3Parts-method", "length,PreprocessedTB-method", "MTB_PDict", "MTB_PDict-class", "names,PDict-method", "names<-,PDict-method", "nnodes", "nnodes,ACtree2-method", "patternFrequency", "patternFrequency,PDict-method", "PDict", "PDict,AsIs-method", "PDict,character-method", "PDict,DNAStringSet-method", "PDict,probetable-method", "PDict,XStringViews-method", "PDict-class", "PDict3Parts", "PDict3Parts-class", "PreprocessedTB", "PreprocessedTB-class", "show,ACtree2-method", "show,MTB_PDict-method", "show,TB_PDict-method", "show,Twobit-method", "tail,PDict3Parts-method", "tail,TB_PDict-method", "tb", "tb,PDict3Parts-method", "tb,PreprocessedTB-method", "tb,TB_PDict-method", "tb.width", "tb.width,PDict3Parts-method", "tb.width,PreprocessedTB-method", "tb.width,TB_PDict-method", "TB_PDict", "TB_PDict-class", "Twobit", "Twobit-class", "width,PDict-method", "width,PDict3Parts-method", "width,PreprocessedTB-method", "[[,PDict-method" ] }, { "page": "predefined_scoring_matrices", "title": "Predefined scoring matrices", "topics": [ "BLOSUM100", "BLOSUM45", "BLOSUM50", "BLOSUM62", "BLOSUM80", "PAM120", "PAM250", "PAM30", "PAM40", "PAM70", "predefined_scoring_matrices", "print.moved_to_pwalign_pkg" ] }, { "page": "QualityScaledXStringSet-class", "title": "QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects", "topics": [ "class:QualityScaledAAStringSet", "class:QualityScaledBStringSet", "class:QualityScaledDNAStringSet", "class:QualityScaledRNAStringSet", "class:QualityScaledXStringSet", "narrow,QualityScaledXStringSet-method", "parallel_slot_names,QualityScaledXStringSet-method", "quality", "quality,QualityScaledXStringSet-method", "QualityScaledAAStringSet", "QualityScaledAAStringSet-class", "QualityScaledBStringSet", "QualityScaledBStringSet-class", "QualityScaledDNAStringSet", "QualityScaledDNAStringSet-class", "QualityScaledRNAStringSet", "QualityScaledRNAStringSet-class", "QualityScaledXStringSet", "QualityScaledXStringSet-class", "readQualityScaledDNAStringSet", "reverse,QualityScaledXStringSet-method", "reverseComplement,QualityScaledDNAStringSet-method", "reverseComplement,QualityScaledRNAStringSet-method", "show,QualityScaledXStringSet-method", "windows,QualityScaledXStringSet-method", "writeQualityScaledXStringSet" ] }, { "page": "replaceAt", "title": "Extract/replace arbitrary substrings from/in a string or set of strings.", "topics": [ "extractAt", "extractAt,XString-method", "extractAt,XStringSet-method", "replaceAt", "replaceAt,XString-method", "replaceAt,XStringSet-method" ] }, { "page": "replaceLetterAt", "title": "Replacing letters in a sequence (or set of sequences) at some specified locations", "topics": [ ".inplaceReplaceLetterAt", "replaceLetterAt", "replaceLetterAt,DNAString-method", "replaceLetterAt,DNAStringSet-method" ] }, { "page": "reverseComplement", "title": "Sequence reversing and complementing", "topics": [ "complement", "complement,DNAString-method", "complement,DNAStringSet-method", "complement,MaskedDNAString-method", "complement,MaskedRNAString-method", "complement,RNAString-method", "complement,RNAStringSet-method", "complement,XStringViews-method", "reverse,MaskedXString-method", "reverseComplement", "reverseComplement,DNAString-method", "reverseComplement,DNAStringSet-method", "reverseComplement,MaskedDNAString-method", "reverseComplement,MaskedRNAString-method", "reverseComplement,RNAString-method", "reverseComplement,RNAStringSet-method", "reverseComplement,XStringViews-method" ] }, { "page": "RNAString-class", "title": "RNAString objects", "topics": [ "class:RNAString", "RNAString", "RNAString-class", "RNA_ALPHABET", "RNA_BASES" ] }, { "page": "seqinfo-methods", "title": "seqinfo() method for DNAStringSet objects", "topics": [ "seqinfo", "seqinfo,DNAStringSet-method", "seqinfo<-,DNAStringSet-method" ] }, { "page": "toComplex", "title": "Turning a DNA sequence into a vector of complex numbers", "topics": [ "toComplex", "toComplex,DNAString-method" ] }, { "page": "translate", "title": "Translating DNA/RNA sequences", "topics": [ "codons", "codons,DNAString-method", "codons,MaskedDNAString-method", "codons,MaskedRNAString-method", "codons,RNAString-method", "translate", "translate,DNAString-method", "translate,DNAStringSet-method", "translate,MaskedDNAString-method", "translate,MaskedRNAString-method", "translate,RNAString-method", "translate,RNAStringSet-method" ] }, { "page": "trimLRPatterns", "title": "Trim Flanking Patterns from Sequences", "topics": [ "trimLRPatterns", "trimLRPatterns,character-method", "trimLRPatterns,XString-method", "trimLRPatterns,XStringSet-method" ] }, { "page": "xscat", "title": "Concatenate sequences contained in XString, XStringSet and/or XStringViews objects", "topics": [ "xscat" ] }, { "page": "XString-class", "title": "BString objects", "topics": [ "alphabet", "alphabet,ANY-method", "as.character,XString-method", "as.vector,XString-method", "BString", "BString-class", "class:BString", "class:XString", "coerce,character,AAString-method", "coerce,character,BString-method", "coerce,character,DNAString-method", "coerce,character,RNAString-method", "coerce,character,XString-method", "coerce,XString,AAString-method", "coerce,XString,BString-method", "coerce,XString,DNAString-method", "coerce,XString,RNAString-method", "Compare,character,XString-method", "Compare,XString,character-method", "Compare,XString,XString-method", "nchar,XString-method", "seqtype,AAString-method", "seqtype,BString-method", "seqtype,DNAString-method", "seqtype,RNAString-method", "seqtype<-,XString-method", "show,XString-method", "showAsCell,XString-method", "substr,XString-method", "substring,XString-method", "toString,XString-method", "updateObject,AAString-method", "updateObject,XString-method", "XString", "XString-class" ] }, { "page": "XStringQuality-class", "title": "PhredQuality, SolexaQuality and IlluminaQuality objects", "topics": [ "alphabet,XStringQuality-method", "as.matrix,XStringQuality-method", "as.vector,XStringQuality-method", "class:IlluminaQuality", "class:PhredQuality", "class:SolexaQuality", "class:XStringQuality", "coerce,BString,IlluminaQuality-method", "coerce,BString,PhredQuality-method", "coerce,BString,SolexaQuality-method", "coerce,BStringSet,IlluminaQuality-method", "coerce,BStringSet,PhredQuality-method", "coerce,BStringSet,SolexaQuality-method", "coerce,character,IlluminaQuality-method", "coerce,character,PhredQuality-method", "coerce,character,SolexaQuality-method", "coerce,integer,IlluminaQuality-method", "coerce,integer,PhredQuality-method", "coerce,integer,SolexaQuality-method", "coerce,IntegerList,IlluminaQuality-method", "coerce,IntegerList,PhredQuality-method", "coerce,IntegerList,SolexaQuality-method", "coerce,numeric,IlluminaQuality-method", "coerce,numeric,PhredQuality-method", "coerce,numeric,SolexaQuality-method", "coerce,NumericList,IlluminaQuality-method", "coerce,NumericList,PhredQuality-method", "coerce,NumericList,SolexaQuality-method", "coerce,XStringQuality,CompressedIntegerList-method", "coerce,XStringQuality,CompressedNumericList-method", "coerce,XStringQuality,IntegerList-method", "coerce,XStringQuality,matrix-method", "coerce,XStringQuality,NumericList-method", "encoding", "encoding,XStringQuality-method", "IlluminaQuality", "IlluminaQuality-class", "PhredQuality", "PhredQuality-class", "SolexaQuality", "SolexaQuality-class", "XStringQuality", "XStringQuality-class" ] }, { "page": "XStringSet-class", "title": "XStringSet objects", "topics": [ "AAStringSet", "AAStringSet-class", "anyNA,XStringSet-method", "as.character,XStringSet-method", "as.data.frame,XStringSet-method", "as.factor,XStringSet-method", "as.matrix,XStringSet-method", "as.vector,XStringSet-method", "BStringSet", "BStringSet-class", "class:AAStringSet", "class:BStringSet", "class:DNAStringSet", "class:RNAStringSet", "class:XStringSet", "coerce,ANY,AAStringSet-method", "coerce,ANY,BStringSet-method", "coerce,ANY,DNAStringSet-method", "coerce,ANY,RNAStringSet-method", "coerce,ANY,XStringSet-method", "DNAStringSet", "DNAStringSet-class", "is.na,XStringSet-method", "narrow,character-method", "nchar,XStringSet-method", "RNAStringSet", "RNAStringSet-class", "seqtype,XStringSet-method", "seqtype<-,XStringSet-method", "show,XStringSet-method", "showAsCell,XStringSet-method", "subseq,character-method", "subseq<-,character-method", "subseq<-,XStringSet-method", "threebands,character-method", "toString,XStringSet-method", "unlist,XStringSet-method", "updateObject,AAStringSet-method", "updateObject,XStringSet-method", "width,character-method", "windows,character-method", "XStringSet", "XStringSet-class" ] }, { "page": "XStringSet-comparison", "title": "Element-wise comparison of XStringSet objects", "topics": [ "match,Vector,XStringSet-method", "match,vector,XStringSet-method", "match,XStringSet,Vector-method", "match,XStringSet,vector-method", "match,XStringSet,XStringSet-method", "pcompare,Vector,XStringSet-method", "pcompare,vector,XStringSet-method", "pcompare,XStringSet,Vector-method", "pcompare,XStringSet,vector-method", "pcompare,XStringSet,XStringSet-method", "XStringSet-comparison" ] }, { "page": "XStringSet-io", "title": "Read/write an XStringSet object from/to a file", "topics": [ "fasta.index", "fasta.seqlengths", "fastq.geometry", "fastq.seqlengths", "readAAStringSet", "readBStringSet", "readDNAStringSet", "readRNAStringSet", "saveXStringSet", "writeXStringSet", "XStringSet-io" ] }, { "page": "XStringSetList-class", "title": "XStringSetList objects", "topics": [ "AAStringSetList", "AAStringSetList-class", "BStringSetList", "BStringSetList-class", "class:AAStringSetList", "class:BStringSetList", "class:DNAStringSetList", "class:RNAStringSetList", "class:XStringSetList", "coerce,List,AAStringSetList-method", "coerce,list,AAStringSetList-method", "coerce,List,BStringSetList-method", "coerce,list,BStringSetList-method", "coerce,List,DNAStringSetList-method", "coerce,list,DNAStringSetList-method", "coerce,List,RNAStringSetList-method", "coerce,list,RNAStringSetList-method", "coerce,List,XStringSetList-method", "coerce,list,XStringSetList-method", "DNAStringSetList", "DNAStringSetList-class", "nchar,XStringSetList-method", "relistToClass,XStringSet-method", "RNAStringSetList", "RNAStringSetList-class", "seqtype,XStringSetList-method", "seqtype<-,XStringSetList-method", "show,XStringSetList-method", "showAsCell,XStringSetList-method", "XStringSetList", "XStringSetList-class" ] }, { "page": "XStringViews-class", "title": "The XStringViews class", "topics": [ "!=,character,XStringViews-method", "!=,XString,XStringViews-method", "!=,XStringViews,character-method", "!=,XStringViews,XString-method", "!=,XStringViews,XStringViews-method", "==,character,XStringViews-method", "==,XString,XStringViews-method", 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