List of all items
Structs
- Align
- AlignScores
- AlignSums
- AlignfoldProbMats
- AlignfoldProbMatsAvg
- AlignfoldScores
- AlignfoldSums
- ArrayBase
- Axis
- BufReader
- BufWriter
- Dim
- FastaRecord
- File
- FoldScoreSets
- FoldScores
- FoldSums
- HAIRPIN_SCORES_SPECIAL
- HashMap
- HashSet
- LoopSums
- MatchProbMats
- NewAxis
- Options
- Path
- Pool
- Reader
- env::Args
- env::ArgsOs
- env::JoinPathsError
- env::SplitPaths
- env::Vars
- env::VarsOs
Enums
Traits
- AsArray
- Bounded
- BufRead
- Dimension
- Display
- FromPrimitive
- Hash
- HashIndex
- Integer
- NdFloat
- One
- Ord
- PrimInt
- Read
- Seek
- Send
- ShapeBuilder
- Sync
- ToPrimitive
- Unsigned
- Write
- Zero
Macros
Functions
- Dim
- Ix0
- Ix1
- Ix2
- Ix3
- Ix4
- Ix5
- Ix6
- IxDyn
- align_char2base
- arr0
- arr1
- arr2
- aview0
- aview1
- aview2
- aview_mut1
- bytes2seq
- char2base
- consprob
- consprob_core
- create_dir
- durbin_algo
- env::args
- env::args_os
- env::current_dir
- env::current_exe
- env::home_dir
- env::join_paths
- env::remove_var
- env::set_current_dir
- env::set_var
- env::split_paths
- env::temp_dir
- env::var
- env::var_os
- env::vars
- env::vars_os
- expf
- filter_basepair_probs
- filter_fold_scores
- filter_match_probs
- from_utf8_unchecked
- get_2loop_score
- get_2loop_score_contra
- get_2loop_sums
- get_abs_diff
- get_accessible_score
- get_align_sums
- get_alignfold_probs
- get_alignfold_sums
- get_basepair_probs
- get_basepair_probs_contra
- get_bulge_score_contra
- get_fold_sums
- get_fold_sums_contra
- get_hairpin_score
- get_hairpin_score_contra
- get_helix_close_score
- get_interior_score_contra
- get_junction_score
- get_junction_score_single
- get_loop_sums
- get_max_basepair_span
- get_multibranch_close_score
- get_sparse_poss
- get_special_hairpin_score
- get_stack_score_contra
- get_terminal_mismatch_score
- has_canonical_basepair
- has_valid_sums
- invert_basepair
- ln_exp_1p
- logsumexp
- matches_augu
- max
- mccaskill_algo
- min
- multizip
- pair_probs2avg_probs
- print_program_usage
- range
- range_inclusive
- read_align_clustal
- read_align_fasta
- read_align_stockholm
- scale
- write_alignfold_prob_mats
- write_readme
Type Definitions
- AlignfoldProbsHashedIds
- ArcArray
- Arg
- Args
- Array
- Array0
- Array1
- Array2
- Array3
- Array4
- Array5
- Array6
- ArrayD
- ArrayView
- ArrayView0
- ArrayView1
- ArrayView2
- ArrayView3
- ArrayView4
- ArrayView5
- ArrayView6
- ArrayViewD
- ArrayViewMut
- ArrayViewMut0
- ArrayViewMut1
- ArrayViewMut2
- ArrayViewMut3
- ArrayViewMut4
- ArrayViewMut5
- ArrayViewMut6
- ArrayViewMutD
- Base
- Basepair
- BasepairScores
- BoolsHashedPoss
- BulgeScores0x1
- BulgeScoresInit
- BulgeScoresLen
- Char
- Col
- Cols
- ContextProf
- ContextProfSetPair
- ContextProfs
- CowArray
- DanglingScores
- FastaId
- FastaRecords
- FoldChar
- FoldScoreSetPair
- FoldStr
- HairpinScoresInit
- HairpinScoresLen
- HairpinScoresSpecial
- HelixCloseScores
- Inputs2loopSumsGetter
- InputsAlignfoldProbsGetter
- InputsConsprobCore
- InputsInsideSumsGetter
- InputsLoopSumsGetter
- InsertScores
- Interior1x2
- Interior2x2
- InteriorScores1x1
- InteriorScores1x1Contra
- InteriorScores1x2
- InteriorScores2x2
- InteriorScoresAsymmetric
- InteriorScoresBonus
- InteriorScoresExplicit
- InteriorScoresInit
- InteriorScoresLen
- InteriorScoresSymmetric
- Ix0
- Ix1
- Ix2
- Ix3
- Ix4
- Ix5
- Ix6
- IxDyn
- LoopSumsHashedPoss
- LoopSumsMat
- MatchProbsHashedIds
- MatchScores
- NumThreads
- OutputsSparsePossGetter
- ParamSetsHashedIds
- Pos
- PosMapSets
- PosMaps
- PosPair
- PosPairMat
- PosPairMatSet
- PosPairs
- PosPairsHashedPoss
- PosQuad
- PosQuadMat
- PosQuadsHashedLens
- Poss
- Prob
- Prob1dMats
- ProbMat
- ProbMat4d
- ProbMatPair
- ProbMatSetsAvg
- ProbMats
- ProbMatsHashedIds
- Probs
- Probs4dHashedIds
- RawArrayView
- RawArrayViewMut
- RnaId
- RnaIdPair
- Score
- ScoreMat
- ScoreMat4d
- ScorePair
- Seq
- SeqId
- SeqIds
- SeqPair
- SeqSlice
- SeqSlices
- SparsePosSets
- SparsePoss
- SparseProbMat
- SparseProbMatPair
- SparseProbsHashedIds
- SparseScoreMat
- SparseSumMat
- StackScores
- Sum
- Sum4dMat
- SumMat
- SumMat4d
- Sums
- TerminalMismatchScores
Constants
- A
- AA
- AC
- AG
- AU
- A_LOWER
- A_UPPER
- BASEPAIR_LEFT
- BASEPAIR_PROBS_FILE
- BASEPAIR_PROBS_FILE2
- BASEPAIR_RIGHT
- BASEPAIR_SCORES
- BULGE_SCORES_0X1
- BULGE_SCORES_INIT
- BULGE_SCORES_LEN
- BULGE_SCORES_LEN_ATLEAST
- C
- CA
- CC
- CG
- COEFF_HAIRPIN_LEN_EXTRAPOLATION
- COEFF_NUM_BRANCHES
- CONTEXT_INDEX_BASEPAIR
- CONTEXT_INDEX_BULGE
- CONTEXT_INDEX_EXTERNAL
- CONTEXT_INDEX_HAIRPIN
- CONTEXT_INDEX_INTERIOR
- CONTEXT_INDEX_MULTIBRANCH
- CU
- C_LOWER
- C_UPPER
- DANGLING_SCORES_3PRIME
- DANGLING_SCORES_5PRIME
- DANGLING_SCORES_LEFT
- DANGLING_SCORES_RIGHT
- DEFAULT_MIN_BASEPAIR_PROB
- DEFAULT_MIN_MATCH_PROB
- EPSILON
- EXAMPLE_FASTA_FILE_PATH
- EXTERNAL_SCORE_BASEPAIR
- EXTERNAL_SCORE_UNPAIR
- G
- GA
- GAS_CONST
- GC
- GG
- GU
- G_LOWER
- G_UPPER
- HAIRPIN_SCORES_INIT
- HAIRPIN_SCORES_LEN
- HAIRPIN_SCORES_LEN_ATLEAST
- HELIX_AUGU_END_PENALTY
- HELIX_CLOSE_SCORES
- INIT_INSERT_SCORE
- INIT_MATCH_SCORE
- INIT_MULTIBRANCH_BASE
- INSERT2MATCH_SCORE
- INSERT_EXTEND_SCORE
- INSERT_SCORES
- INSERT_SWITCH_SCORE
- INTERIOR_SCORES_1X1
- INTERIOR_SCORES_1X1_CONTRA
- INTERIOR_SCORES_1X2
- INTERIOR_SCORES_2X2
- INTERIOR_SCORES_ASYMMETRIC
- INTERIOR_SCORES_ASYMMETRIC_ATLEAST
- INTERIOR_SCORES_EXPLICIT
- INTERIOR_SCORES_INIT
- INTERIOR_SCORES_LEN
- INTERIOR_SCORES_LEN_ATLEAST
- INTERIOR_SCORES_SYMMETRIC
- INTERIOR_SCORES_SYMMETRIC_ATLEAST
- INVERSE_TEMPERATURE
- K0
- KILO
- LOGSUMEXP_THRESHOLD_UPPER
- LOOPMATCH_PROBS_FILE
- MATCH2INSERT_SCORE
- MATCH2MATCH_SCORE
- MATCH_PROBS_FILE
- MATCH_SCORES
- MAX_2LOOP_LEN
- MAX_HAIRPIN_LEN_EXTRAPOLATION
- MAX_INTERIOR_ASYMMETRIC
- MAX_INTERIOR_EXPLICIT
- MAX_INTERIOR_SYMMETRIC
- MAX_LOOP_LEN
- MIN_HAIRPIN_LEN
- MIN_HAIRPIN_LEN_EXTRAPOLATION
- MIN_SPAN_HAIRPIN_CLOSE
- MULTIBRANCH_SCORE_BASE
- MULTIBRANCH_SCORE_BASEPAIR
- MULTIBRANCH_SCORE_UNPAIR
- NEG_INF
- NEG_INFINITY
- NINIO_COEFF
- NINIO_MAX
- NUM_BASES
- NUM_CONTEXTS
- NUM_SPECIAL_HAIRPINS
- NUM_TRANSITS
- PAIRMATCH_PROBS_FILE
- PROB_BOUND_LOWER
- PROB_BOUND_UPPER
- PSEUDO_BASE
- README_CONTENTS
- README_FILE
- STACK_SCORES
- STACK_SCORES_CONTRA
- TEMPERATURE
- TERMINAL_MISMATCH_SCORES_1XMANY
- TERMINAL_MISMATCH_SCORES_2X3
- TERMINAL_MISMATCH_SCORES_CONTRA
- TERMINAL_MISMATCH_SCORES_HAIRPIN
- TERMINAL_MISMATCH_SCORES_INTERIOR
- TERMINAL_MISMATCH_SCORES_MULTIBRANCH
- U
- UA
- UC
- UG
- UNPAIR
- UNPAIR_PROBS_FILE_BULGE
- UNPAIR_PROBS_FILE_EXTERNAL
- UNPAIR_PROBS_FILE_HAIRPIN
- UNPAIR_PROBS_FILE_INTERIOR
- UNPAIR_PROBS_FILE_MULTIBRANCH
- UU
- U_LOWER
- U_UPPER
- env::consts::ARCH
- env::consts::DLL_EXTENSION
- env::consts::DLL_PREFIX
- env::consts::DLL_SUFFIX
- env::consts::EXE_EXTENSION
- env::consts::EXE_SUFFIX
- env::consts::FAMILY
- env::consts::OS