Crate consprob_trained Copy item path Source env Inspection and manipulation of the process’s environment. trained_alignfold_scores trained_alignfold_scores_randinit array Create an Array azip Array zip macro: lock step function application across several arrays and
producers. env Inspects an environment variable at compile time. s Slice argument constructor. Align AlignScores AlignSums AlignfoldProbMats AlignfoldProbMatsAvg AlignfoldScores AlignfoldSums ArrayBase An n -dimensional array. Axis An axis index. BufReader The BufReader<R> struct adds buffering to any reader. BufWriter Wraps a writer and buffers its output. Dim Dimension description. DirEntry Entries returned by the ReadDir FastaRecord File An object providing access to an open file on the filesystem. FoldScoreSets FoldScores FoldScoresTrained FoldSums HAIRPIN_SCORES_SPECIAL HashMap A hash map implemented with quadratic probing and SIMD lookup. HashSet A hash set implemented as a HashMap where the value is (). Index A FASTA index as created by SAMtools (.fai). IndexedReader A FASTA reader with an index as created by SAMtools (.fai). IndexedReaderIterator Interval An Interval wraps the std::ops::Range from the stdlib and is defined by a start and end field
where end should be >= start. LoopSums MatchProbMats NewAxis Token to represent a new axis in a slice description. Normal The normal distribution N(mean, std_dev**2). Options A description of the options that a program can handle. PairAlignfold Path A slice of a path (akin to str Pool A threadpool that acts as a handle to a number
of threads spawned at construction. RangeInsertScores Reader A FASTA reader. Record A FASTA record. Records An iterator over the records of a Fasta file. Sequence A sequence record returned by the FASTA index. TrainDatum Writer A Fasta writer. TrainType 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_BASEPAIR_PROB_TRAIN DEFAULT_LEARNING_TOLERANCE DEFAULT_MATCH_PROB_TRAIN DEFAULT_MIN_BASEPAIR_PROB DEFAULT_MIN_MATCH_PROB DEFAULT_TRAIN_TYPE EPSILON EXAMPLE_FASTA_FILE_PATH EXTERNAL_SCORE_BASEPAIR EXTERNAL_SCORE_UNPAIR G GA GAMMA_DISTRO_ALPHA GAMMA_DISTRO_BETA GAS_CONST GC GG GROUP_SIZE_EXTERNAL GROUP_SIZE_INSERT_TRANSITION GROUP_SIZE_MATCH_TRANSITION GROUP_SIZE_MULTIBRANCH GU G_LOWER G_UPPER HAIRPIN_SCORES_INIT HAIRPIN_SCORES_LEN HAIRPIN_SCORES_LEN_ATLEAST HELIX_AUGU_END_PENALTY HELIX_CLOSE_SCORES INFINITY Deprecation planned Infinity (∞).
Use f32::INFINITY INIT_INSERT_SCORE INIT_MATCH_SCORE INIT_MULTIBRANCH_BASE INSERT2MATCH_SCORE INSERT_EXTEND_SCORE INSERT_SCORES INSERT_SWITCH_SCORE INTERIOR_SCORES_1X1 INTERIOR_SCORES_1X2 INTERIOR_SCORES_1X1_CONTRA 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 Deprecation planned Negative infinity (−∞).
Use f32::NEG_INFINITY NINIO_COEFF NINIO_MAX NUM_BASEPAIRS 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 TRAINED_SCORES_FILE TRAINED_SCORES_FILE_RANDINIT 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 AsArray Argument conversion into an array view Bounded Numbers which have upper and lower bounds BufRead A BufRead is a type of Reader which has an internal buffer, allowing it
to perform extra ways of reading. Dimension Array shape and index trait. Display Format trait for an empty format, {}. Distribution Types (distributions) that can be used to create a random instance of T. FastExp This trait adds a fast approximation of exp to float types. FastaRead Trait for FASTA readers. FromPrimitive A generic trait for converting a number to a value. Hash A hashable type. HashIndex Integer NdFloat Floating-point element types f32 and f64. One Defines a multiplicative identity element for Self. Ord Trait for types that form a total order . PrimInt Generic trait for primitive integers. RandomExt Constructors for n-dimensional arrays with random elements. Read The Read trait allows for reading bytes from a source. Seek The Seek trait provides a cursor which can be moved within a stream of
bytes. Send Types that can be transferred across thread boundaries. ShapeBuilder A trait for Shape and D where D: Dimension that allows
customizing the memory layout (strides) of an array shape. Sync Types for which it is safe to share references between threads. ToPrimitive A generic trait for converting a value to a number. Unsigned A trait for values which cannot be negative Write A trait for objects which are byte-oriented sinks. Zero Defines an additive identity element for Self. Dim Create a new dimension value. Ix0 Create a zero-dimensional index Ix1 Create a one-dimensional index Ix2 Create a two-dimensional index Ix3 Create a three-dimensional index Ix4 Create a four-dimensional index Ix5 Create a five-dimensional index Ix6 Create a six-dimensional index IxDyn Create a dynamic-dimensional index align_char2base arr0 Create a zero-dimensional array with the element x. arr1 Create a one-dimensional array with elements from xs. arr2 Create a two-dimensional array with elements from xs. aview0 Create a zero-dimensional array view borrowing x. aview1 Create a one-dimensional array view with elements borrowing xs. aview2 Create a two-dimensional array view with elements borrowing xs. aview_mut1 Create a one-dimensional read-write array view with elements borrowing xs. bfgs Returns a value of x that should minimize f. f must be convex and twice-differentiable. bfgs_scores2scores bytes2seq bytes2seq_gapped char2base consprob consprob_core consprob_trained constrain convert_char copy_alignfold_scores_align copy_alignfold_scores_fold create_dir Creates a new, empty directory at the provided path durbin_algo expf filter_basepair_probs filter_fold_scores filter_match_probs from_utf8_unchecked ⚠ Converts a slice of bytes to a string slice without checking
that the string contains valid UTF-8. gapped2ungapped get_2loop_len_pair get_2loop_score get_2loop_score_contra get_2loop_sums get_abs_diff get_accessible_score get_accuracy_expected get_align_sums get_alignfold_probs get_alignfold_sums get_basepair_probs get_basepair_probs_contra get_bulge_score get_bulge_score_contra get_dict_min_pair get_dict_min_stack get_diff get_fold_sums get_fold_sums_contra get_hairpin_len get_hairpin_score get_hairpin_score_contra get_helix_close_score get_interior_score get_interior_score_contra get_junction_score get_junction_score_single get_loop_sums get_max_basepair_span get_mismatch_pair get_multibranch_close_score get_num_unpairs_external get_num_unpairs_multibranch get_regularizer get_sparse_poss get_special_hairpin_score get_stack_score get_stack_score_contra get_terminal_mismatch_score get_twoloop_score has_canonical_basepair has_valid_sums invert_basepair ln_exp_1p logsumexp matches_augu max Compares and returns the maximum of two values. mccaskill_algo min Compares and returns the minimum of two values. multizip An iterator that generalizes .zip() and allows running multiple iterators in lockstep. pair_probs2avg_probs prescan print_program_usage print_train_info range Returns an iterator over the given range [start, stop) (that is, starting
at start (inclusive), and ending at stop (exclusive)). range_inclusive Return an iterator over the range [start, stop] read_align_clustal read_align_fasta read_align_stockholm read_dir Returns an iterator over the entries within a directory. scale scan In place implementation of scan over a slice. scores2bfgs_scores stdout Constructs a new handle to the standard output of the current process. struct2vec thread_rng Retrieve the lazily-initialized thread-local random number generator,
seeded by the system. Intended to be used in method chaining style,
e.g. thread_rng().gen::<i32>(), or cached locally, e.g.
let mut rng = thread_rng();. Invoked by the Default trait, making
ThreadRng::default() equivalent. trim_newline Remove a trailing newline from the given string in place. vec2struct write_alignfold_prob_mats write_alignfold_scores_trained write_logs write_readme AlignfoldProbsHashedIds ArcArray An array where the data has shared ownership and is copy on write. Arg Args Array An array that owns its data uniquely. Array0 zero-dimensional array Array1 one-dimensional array Array2 two-dimensional array Array3 three-dimensional array Array4 four-dimensional array Array5 five-dimensional array Array6 six-dimensional array ArrayD dynamic-dimensional array ArrayView A read-only array view. ArrayView0 zero-dimensional array view ArrayView1 one-dimensional array view ArrayView2 two-dimensional array view ArrayView3 three-dimensional array view ArrayView4 four-dimensional array view ArrayView5 five-dimensional array view ArrayView6 six-dimensional array view ArrayViewD dynamic-dimensional array view ArrayViewMut A read-write array view. ArrayViewMut0 zero-dimensional read-write array view ArrayViewMut1 one-dimensional read-write array view ArrayViewMut2 two-dimensional read-write array view ArrayViewMut3 three-dimensional read-write array view ArrayViewMut4 four-dimensional read-write array view ArrayViewMut5 five-dimensional read-write array view ArrayViewMut6 six-dimensional read-write array view ArrayViewMutD dynamic-dimensional read-write array view Base Basepair BasepairScores BfgsScore BfgsScores BoolsHashedPoss BulgeScores0x1 BulgeScoresInit BulgeScoresLen Char Col Cols ContextProf ContextProfSetPair ContextProfs CowArray An array with copy-on-write behavior. DanglingScores FastaId FastaRecords FoldChar FoldScoreSetPair FoldScoresPairTrained FoldStr HairpinScoresInit HairpinScoresLen HairpinScoresSpecial HelixCloseScores Inputs2loopSumsGetter InputsAlignfoldProbsGetter InputsConsprobCore InputsInsideSumsGetter InputsLoopSumsGetter InsertScores Interior1x2 Interior2x2 InteriorScores1x1 InteriorScores1x2 InteriorScores1x1Contra InteriorScores2x2 InteriorScoresAsymmetric InteriorScoresBonus InteriorScoresExplicit InteriorScoresInit InteriorScoresLen InteriorScoresSymmetric Ix0 zero-dimensionial Ix1 one-dimensional Ix2 two-dimensional Ix3 three-dimensional Ix4 four-dimensional Ix5 five-dimensional Ix6 six-dimensional IxDyn dynamic-dimensional LoopStruct 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 A read-only array view without a lifetime. RawArrayViewMut A mutable array view without a lifetime. RealSeqPair RefFoldScoresPair Regularizer Regularizers RnaId RnaIdPair Score ScoreMat ScoreMat4d ScorePair Scores Seq SeqId SeqIds SeqPair SeqSlice SeqSlices SparsePosMat SparsePosSets SparsePoss SparseProbMat SparseProbMatPair SparseProbsHashedIds SparseScoreMat SparseSumMat StackScores Sum Sum4dMat SumMat SumMat4d Sums TerminalMismatchScores Text Type alias for an owned text, i.e. Vec<u8>. TextSlice Type alias for a text slice, i.e. &[u8]. TrainData Hash Derive macro generating an impl of the trait Hash. Ord Derive macro generating an impl of the trait Ordhere .