| !=,BString,BString-method |
The BString class |
| !=,BString,BStringViews-method |
The BStringViews class |
| !=,BString,character-method |
The BString class |
| !=,BStringViews,BString-method |
The BStringViews class |
| !=,BStringViews,BStringViews-method |
The BStringViews class |
| !=,BStringViews,character-method |
The BStringViews class |
| !=,character,BString-method |
The BString class |
| !=,character,BStringViews-method |
The BStringViews class |
| ==,BString,BString-method |
The BString class |
| ==,BString,BStringViews-method |
The BStringViews class |
| ==,BString,character-method |
The BString class |
| ==,BStringViews,BString-method |
The BStringViews class |
| ==,BStringViews,BStringViews-method |
The BStringViews class |
| ==,BStringViews,character-method |
The BStringViews class |
| ==,character,BString-method |
The BString class |
| ==,character,BStringViews-method |
The BStringViews class |
| AAString |
The AAString class |
| AAString-class |
The AAString class |
| AA_ALPHABET |
The AAString class |
| adjacentViews |
Basic functions for creating BStringViews objects |
| align1 |
The BStringAlign class |
| align1,BStringAlign-method |
The BStringAlign class |
| align2 |
The BStringAlign class |
| align2,BStringAlign-method |
The BStringAlign class |
| alignScore |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| alphabet |
The BString class |
| alphabet,AAString-method |
The AAString class |
| alphabet,BString-method |
The BString class |
| alphabet,BStringAlign-method |
The BStringAlign class |
| alphabet,DNAString-method |
The DNAString class |
| alphabet,RNAString-method |
The RNAString class |
| alphabetFrequency |
Function to calculate the frequency of letters in a biological sequence |
| alphabetFrequency,BString-method |
Function to calculate the frequency of letters in a biological sequence |
| alphabetFrequency,BStringViews-method |
Function to calculate the frequency of letters in a biological sequence |
| alphabetFrequency,DNAString-method |
Function to calculate the frequency of letters in a biological sequence |
| alphabetFrequency,RNAString-method |
Function to calculate the frequency of letters in a biological sequence |
| AMINO_ACID_CODE |
The Single-Letter Amino Acid Code |
| as.character,BString-method |
The BString class |
| as.character,BStringViews-method |
The BStringViews class |
| as.complex,DNAString-method |
Converting a DNAString to a vector of complexes |
| as.list,BStringViews-method |
The BStringViews class |
| as.matrix,BStringViews-method |
The BStringViews class |
| last |
The BStringViews class |
| last,BStringViews-method |
The BStringViews class |
| lcprefix |
Longest Common Prefix/Suffix/Substring searching functions |
| lcprefix,BString,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcprefix,BString,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcprefix,character,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcprefix,character,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr,BString,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr,BString,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr,character,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsubstr,character,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix,BString,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix,BString,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix,character,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| lcsuffix,character,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| length,BString-method |
The BString class |
| length,BStringAlign-method |
The BStringAlign class |
| length,BStringViews-method |
The BStringViews class |
| letter |
Subsetting a string |
| letter,BString-method |
Subsetting a string |
| letter,BStringViews-method |
Subsetting a string |
| letter,character-method |
Subsetting a string |
| nchar,BString-method |
The BString class |
| nchar,BStringAlign-method |
The BStringAlign class |
| nchar,BStringViews-method |
The BStringViews class |
| needwunsQS |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| needwunsQS,BString,BString-method |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| needwunsQS,BString,character-method |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| needwunsQS,character,BString-method |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| needwunsQS,character,character-method |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| palindromeArmLength |
Searching a sequence for palindromes |
| palindromeArmLength,BString-method |
Searching a sequence for palindromes |
| palindromeArmLength,BStringViews-method |
Searching a sequence for palindromes |
| palindromeLeftArm |
Searching a sequence for palindromes |
| palindromeLeftArm,BString-method |
Searching a sequence for palindromes |
| palindromeLeftArm,BStringViews-method |
Searching a sequence for palindromes |
| palindromeRightArm |
Searching a sequence for palindromes |
| palindromeRightArm,BString-method |
Searching a sequence for palindromes |
| palindromeRightArm,BStringViews-method |
Searching a sequence for palindromes |
| PAM120 |
Scoring matrices |
| PAM250 |
Scoring matrices |
| PAM30 |
Scoring matrices |
| PAM40 |
Scoring matrices |
| PAM70 |
Scoring matrices |
| pattern |
The BStringPartialMatches class |
| pattern,BStringPartialMatches-method |
The BStringPartialMatches class |
| pmatchPattern |
Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern,BString-method |
Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern,BStringViews-method |
Longest Common Prefix/Suffix/Substring searching functions |
| pmatchPattern,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
| print.needwunsQS |
quadratic-space, simple gap implementation of Needleman-Wunsch global alignment algorithm |
| score |
The BStringAlign class |
| score,BStringAlign-method |
The BStringAlign class |
| scoring.matrices |
Scoring matrices |
| show,BString-method |
The BString class |
| show,BStringAlign-method |
The BStringAlign class |
| show,BStringPartialMatches-method |
The BStringPartialMatches class |
| show,BStringViews-method |
The BStringViews class |
| start |
The BStringViews class |
| start,BStringViews-method |
The BStringViews class |
| subBString |
Fast substring extraction |
| subject |
The BStringViews class |
| subject,BStringViews-method |
The BStringViews class |
| subpatterns |
The BStringPartialMatches class |
| subpatterns,BStringPartialMatches-method |
The BStringPartialMatches class |
| substr |
Fast substring extraction |
| substr,BString-method |
Fast substring extraction |
| substr,BStringViews-method |
Fast substring extraction |
| substring |
Fast substring extraction |
| substring,BString-method |
Fast substring extraction |
| substring,BStringViews-method |
Fast substring extraction |
| subviews |
Fast substring extraction |