Index of types

alignment [Biocaml_sam]

background [Biocaml_pwm]
Probability distribution over an alphabet
bed_graph_value [Biocaml_wig]

char_seq [Biocaml_fasta]
cigar_op [Biocaml_sam]
collection [Biocaml_jaspar]
comment [Biocaml_wig]
confusion_matrix [Biocaml_roc]
content [Biocaml_track]
The "content" lines of the files.
count_matrix [Biocaml_pwm]
Type to represent gap-free alignments.
counter [Biocaml_accu]
The type of accumulators that count values

database [Biocaml_entrez]
Represents available databases

esearch_answer [Biocaml_entrez]
Represents the result of a request to esearch

fetched [Biocaml_entrez.Fetch]
fixed_step [Biocaml_wig]

idata [Biocaml_cel]
int_seq [Biocaml_fasta]
int_vec [Biocaml_mzData]
Vectors of OCaml ints.
irow [Biocaml_cel]
Represents row in intensity section
item [Biocaml_table.Row]
Type row elements (or “cells”).
item [Biocaml_sam]
item [Biocaml_lines]
item [Biocaml_fastq]
Type of FASTQ items.
item [Biocaml_fasta]
item [Biocaml_bed]
The type of BED data stream items.
item_to_raw [Biocaml_sam.Error]
item_to_raw_error [Biocaml_bam.Transform]
item_type [Biocaml_table.Row]
Definition of the type of a cell.

location [Biocaml_genomeMap]

motif [Biocaml_jaspar]

optional_content [Biocaml_sam]
optional_content_parsing [Biocaml_sam.Error]
optional_content_value [Biocaml_sam]

parse [Biocaml_sam.Error]
Errors possible during parsing.
parse_cigar_error [Biocaml_bam.Transform]
parse_error [Biocaml_wig]
The parsing errors.
parse_error [Biocaml_track]
The possible parsing errors.
parse_error [Biocaml_gff]
The possible parsing errors.
parse_optional_error [Biocaml_bam.Transform]
parsing [Biocaml_bed.Error]
parsing_base [Biocaml_bed.Error]
parsing_buffer [Biocaml_transform.Line_oriented]
parsing_spec [Biocaml_bed]
The specification of how to parse the remaining columns.
probe [Biocaml_bpmap]

range [Biocaml_rSet]
range [Biocaml_genomeMap]
raw_alignment [Biocaml_sam]
The contents of an alignment line.
raw_alignment [Biocaml_bam]
raw_bam_error [Biocaml_bam.Transform]
raw_item [Biocaml_sam]
The "items" of a parsed SAM file stream.
raw_item [Biocaml_fasta.Transform]
Lowest level items parsed by this module:
raw_item [Biocaml_bam]
raw_to_item [Biocaml_sam.Error]
raw_to_item_error [Biocaml_bam.Transform]
reference_sequence [Biocaml_sam]
relation [Biocaml_accu]
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.
stream_item [Biocaml_gff]
The items being output by the parser.
string_to_raw [Biocaml_sam.Error]
The possible errors one can get while parsing SAM files.
string_to_raw_item [Biocaml_fasta.Error]
Errors raised when converting a string to a raw_item.

t [Biocaml_iset]
t [Biocaml_wig]
The most general type that the default parser outputs.
t [Biocaml_transform.Printer_queue]
t [Biocaml_transform]
Type of a buffered transform converting 'inputs to 'outputs.
t [Biocaml_tags]
t [Biocaml_track]
The type of the parser "track" lines.
t [Biocaml_table.Row]
A single row.
t [Biocaml_streamable.S2]
t [Biocaml_streamable.S]
Type of the datastructure.
t [Biocaml_stream]
Type of streams holding values of type 'a.
t [Biocaml_strandName]
Type of strand.
t [Biocaml_solexa_score]
t [Biocaml_sgr]
t [Biocaml_seq]
Type of a sequence
t [Biocaml_sam.Flags]
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_pos]
t [Biocaml_phred_score]
t [Biocaml_msg.Tree]
t [Biocaml_mzData.Precursor]
t [Biocaml_lines.Buffer]
t [Biocaml_lines.Error]
t [Biocaml_line]
A line is simply a string, possibly empty, that does not contain a newline character.
t [Biocaml_interval_tree]
t [Biocaml_histogram]
The type of a histogram whose bin limits are of type 'a.
t [Biocaml_gff]
The type of the GFF records/rows.
t [Biocaml_genomeMap.LMap_spec]
t [Biocaml_genomeMap.Signal]
t [Biocaml_genomeMap.LMap]
t [Biocaml_genomeMap.LSet]
t [Biocaml_genomeMap.Selection]
t [Biocaml_fastq.Error]
t [Biocaml_fasta.Error]
Union of all errors.
t [Biocaml_entrez.Make.Gene]
t [Biocaml_entrez.Make.Pubmed]
t [Biocaml_entrez.Make.PubmedSummary]
t [Biocaml_entrez.Make.Gene_ref]
t [Biocaml_entrez.Make.Dbtag]
t [Biocaml_entrez.Make.Object_id]
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.Relation]
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
t_type [Biocaml_table.Row]
Definition of the type of a row.
tag [Biocaml_wig]
tag [Biocaml_gff]

unzip_error [Biocaml_zip.Transform]
The possible unzipping errors.

variable_step [Biocaml_wig]
vec [Biocaml_mzData]
Vectors of 64 bits floats.