!=,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 |