Index of types

alignment [Biocaml_sam]
attribute [Biocaml_gff]

background [Biocaml_pwm]
Probability distribution over an alphabet
block [Biocaml_track]
A block of information.

columns [Biocaml_table]
All column names occurring in a file, in order that they occur.
confusion_matrix [Biocaml_roc]
count_matrix [Biocaml_pwm]
Type to represent gap-free alignments.
counter [Biocaml_accu]
The type of accumulators that count values

format [Biocaml_wig]

getter [Biocaml_table]
A function get of type getter can be used as get r c to get the value of the column named c in row r.

header [Biocaml_sam]
header_line [Biocaml_sam]

idata [Biocaml_cel]
int_vec [Biocaml_mzData]
Vectors of OCaml ints.
irow [Biocaml_cel]
Represents row in intensity section

location [Biocaml_genomeMap]

probe [Biocaml_bpmap]
pt [Biocaml_wig]
A data point is a 4-tuple (chr,lo,hi,x), where x is the value assigned to interval [lo, hi], inclusive of end-points, on chromosome chr.

range [Biocaml_rSet]
range [Biocaml_genomeMap]
record [Biocaml_fastq]
Each record in a fastq file consists of 4 fields: title, sequence, another title, and a quality score.
record [Biocaml_fasta]
Header and content.
record_type_code [Biocaml_sam]
String is exactly three characters, matching the regular expression '@A-Za-zA-Za-z'.
recordi [Biocaml_fasta]
Header and integers.
row [Biocaml_table]
Data row.
row [Biocaml_gff]
Type of information on a row.
row [Biocaml_bpmap]
Type of information on one data row.

sb_algebraic_rule [Biocaml_sbml]
sb_compartment [Biocaml_sbml]
sb_delay [Biocaml_sbml]
sb_event [Biocaml_sbml]
sb_event_assignment [Biocaml_sbml]
sb_function_definition [Biocaml_sbml]
sb_generic_rule [Biocaml_sbml]
sb_initial_assignment [Biocaml_sbml]
sb_kinetic_law [Biocaml_sbml]
sb_math [Biocaml_sbml]
sb_math_container [Biocaml_sbml]
sb_math_operator [Biocaml_sbml]
sb_model [Biocaml_sbml]
sb_parameter [Biocaml_sbml]
sb_reaction [Biocaml_sbml]
sb_rule [Biocaml_sbml]
sb_species [Biocaml_sbml]
sb_species_ref [Biocaml_sbml]
sb_trigger [Biocaml_sbml]
sb_unit [Biocaml_sbml]
sb_unit_definition [Biocaml_sbml]
section [Biocaml_bar]
spectrum [Biocaml_mzData]
Individual mass spectrum.
strand [Biocaml_gff]

t [Biocaml_mzData.Precursor]
t [Biocaml_intervalTree]
t [Biocaml_pos]
t [Biocaml_msg.Tree]
t [Biocaml_wig]
Type of WIG data.
t [Biocaml_tags]
Collection of tags, which classify a data format.
t [Biocaml_table]
A table consists of: comments (optional), column names, a getter function, an enumeration of the rows in the table
t [Biocaml_track.BrowserLines]
Type of a sequence of browser lines.
t [Biocaml_track.TrackLine]
Type of a track line.
t [Biocaml_track]
Type of a track file.
t [Biocaml_strandName]
Type of strand.
t [Biocaml_solexaScore]
t [Biocaml_sgr]
t [Biocaml_seq]
Type of a sequence
t [Biocaml_rSet]
Type of a set of integers.
t [Biocaml_romanNum]
Type of a roman numeral.
t [Biocaml_range]
Type of a range.
t [Biocaml_pwm]
Representation of a PWM
t [Biocaml_phredScore]
t [Biocaml_histogram]
The type of a histogram whose bin limits are of type 'a.
t [Biocaml_gff]
The type representing a GFF file.
t [Biocaml_genomeMap.LMap_spec]
t [Biocaml_genomeMap.LSet]
t [Biocaml_genomeMap.Signal]
t [Biocaml_genomeMap.LMap]
t [Biocaml_genomeMap.Selection]
t [Biocaml_comments]
Sequence of comment lines.
t [Biocaml_cel]
The type of a CEL file.
t [Biocaml_bpmap]
Type of a BPMAP file.
t [Biocaml_bar]
Type of a BAR file, which can be thought of as a header plus set of sections.
t [Biocaml_accu.Counter]
t [Biocaml_accu]
General type for accumulators: 'instances are mapped to 'bins, and the 'accumulated value for a 'bin is updated with an 'increment

vec [Biocaml_mzData]
Vectors of 64 bits floats.