+
+ -
+
+ <constant> CDCCOICanAutoExpand
+
+
+ -
+
+ CDCCOITrackingOptions: Available tracking options for
+ Clusters of Interest Used as drop-downs for COI editors
+ and automatic filling
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOIConciseTrackingOptions
+
+
+ -
+
+ CDCCOITrackingOptionsDateFilter: A filtering option
+ applied to cluster nodes when computing COI membership
+ under different tracking options Specifies the maximum
+ number of MONTHS (relative to the reference data) that a
+ node age must fall into
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOICreatedBySystem
+
+
+ -
+
+ CDCCOINodeKind: Available options for how a COI member was
+ identified Used as drop-downs for COI editors and
+ automatic filling
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOICreatedManually
+
+
+ -
+
+ CDCCOICreatedBySystem: The value of "createdBy" in a COI
+ record when the COI was created by the system
+ (automatically)
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOIKind
+
+
+ -
+
+ ShapeOrdering: The range to which values for
+ categorical/ordinal variables will be mapped using the
+ "Shape" dropdown
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOIKindAutomaticCreation
+
+
+ -
+
+ CDCJurisdictionLowMorbidity: The set of low-morbidity
+ jurisdictions for Secure HIV TRACE
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOINodeKind
+
+
+ -
+
+ CDCCOIConciseTrackingOptions: Available shorter tracking
+ options for Clusters of Interest Used for COI exports
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOINodeKindDefault
+
+
+ -
+
+ CDCCOIKindAutomaticCreation: The kind of COI that is
+ automatically created by the system
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOITrackingOptions
+
+
+ -
+
+ CDCCOIKind: Available creation options for Clusters of
+ Interest
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOITrackingOptionsDateFilter
+
+
+ -
+
+ CDCCOITrackingOptionsFilter: A filtering option is applied
+ to cluster edges when computing COI membership under
+ different tracking options Selects edges of different
+ lengths (0.5% vs 1.5%)
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOITrackingOptionsDefault
+
+
+ -
+
+ CDCCOICanAutoExpand: The types of tracking modes which are
+ subject to automatic growth tracking
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOITrackingOptionsDistanceFilter
+
+
+ -
+
+ CDCCOITrackingOptionsNone: The "no-tracking" option
+ assigned for COI
+
+
+
+
+
+
+ -
+
+ <constant> CDCCOITrackingOptionsNone
+
+
+ -
+
+ CDCCOITrackingOptionsDefault: The default tracking option
+ assigned to COI
+
+
+
+
+
+
+ -
+
+ <constant> CDCJurisdictionCodes
+
+
+ -
+
+ CDCCOICreatedManually: The value of "createdBy" in a COI
+ record when the COI was created manually
+
+
+
+
+
+
+ -
+
+ <constant> CDCJurisdictionLowMorbidity
+
+
+ -
+
+ CDCJurisdictionCodes: Mapping from full names to
+ two-letter codes for various Secure HIV-TRACE
+ jurisdictions
+
+
+
+
+
+
+ -
+
+ <constant> CDCNPMember
+
+
+ -
+
+ CDCCOINodeKindDefault: The method of node identification
+ used by default (and it automatically created COI)
+
+
+
+
+
+
+ -
+
+ <constant> Categorical
+
+
+ -
+
+ CategoricalBase: The default set of colors used for
+ displaying colors of categorical attributes
+
+
+
+
+
+
+ -
+
+
+ -
+
+ Used to generate pop-over labels for node displays, and
+ COI views
+
+
+
+
+
+
+ -
+
+ <constant> DateUpperBoundYear
+
+
+ -
+
+ Used in many places where alpha-numerically sorted dates
+ are desired
+
+
+
+
+
+
+ -
+
+
+ -
+
+ Used to generate legend labels for date-valued attributes
+ for network displayes
+
+
+
+
+
+
+ -
+
+
+ -
+
+ Maximum year value (no future dates)
+
+
+
+
+
+
+ -
+
+
+ -
+
+ this is currently used to display node addition dates to
+ COI
+
+
+
+
+
+
+ -
+
+
+ -
+
+ List of accepted time formats for attribute values
+
+
+
+
+
+
+ -
+
+ <constant> EdgeColorBase
+
+
+ -
+
+ MaximumValuesInCategories: Maximum # of distinct values
+ that can be rendered for categorical variables
+
+
+
+
+
+
+ -
+
+ <constant> MaximumValuesInCategories
+
+
+ -
+
+ Categorical: Expanded color range using darker shades
+ based on `CategoricalBase`
+
+
+
+
+
+
+ -
+
+ <constant> PresetColorSchemes
+
+
+ -
+
+ EdgeColorBase: The default color range for shading network
+ EDGES
+
+
+
+
+
+
+ -
+
+ <constant> PresetShapeSchemes
+
+
+ -
+
+ PresetColorSchemes: Predefined (hard-coded) color schemes
+ for specific attribute fields. Keys are exactly matched by
+ categorical variable names These should be updated if a
+ specific attribute needs to use a particular color scheme
+ for value rendering
+
+
+
+
+
+
+ -
+
+ <constant> SequentialColor
+
+
+ -
+
+ PresetShapeSchemes: Predefined (hard-coded) shape schemes
+ for specific attribute fields. Keys are exactly matched by
+ categorical variable names These should be updated if a
+ specific attribute needs to use a particular shape scheme
+ for value rendering
+
+
+
+
+
+
+ -
+
+ <constant> ShapeOrdering
+
+
+ -
+
+ SequentialColor: The default color ranges for a fixed
+ number of values
+
+
+
+
+
+
+ -
+
+ <constant> SubclusterSeparator
+
+
+ -
+
+ network: Attributes and string constants for the network
+ object
+
+
+
+
+
+
+ -
+
+ cluster_time_scale
+
+
+ -
+
+ used as a part of auto-named COI, e.g. NC_202105_44.1
+
+
+
+
+
+
+ -
+
+ d3
+
+
+ -
+
+ A collection of table column definitions
+
+
+
+
+
+
+ -
+
+ d3
+
+
+ -
+
+ Combined definitions and presets for various network
+ components.
+
+
+
+
+
+
+ -
+
+ d3
+
+
+ -
+
+ Functions that help manipulate network JSON and perform
+ other utility operations
+
+
+
+
+
+
+ -
+
+
+ -
+
+ missing: Values to use when displaying missing values
+
+
+
+
+
+
+ -
+
+ <constant> missing
+
+
+ -
+
+ CDCNPMember: The label for the auto-generated node
+ attribute (ever in NP CoI)
+
+
+
+
+
+
+ -
+
+ <constant> network
+
+
+ -
+
+ formats: Various formatters for numerical values
+
+
+
+
+
+
+
+
+ -
+
+ _action_drop_down(self, pg)
+
+
+ -
+
+ Generates a dropdown menu for actions on a cluster of
+ interest (COI).
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The main network visualization object.
+ |
+
+
+
+ pg |
+
+
+ Object
+ |
+
+
+ The cluster of interest data.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ An array of dropdown menu options.
+
+
+
+ - Type
+ -
+ Array
+
+
+
+
+
+ -
+
+ add_a_sortable_table(container, headers, content [,
+ overwrite] [, caption] [, priority_set_editor])
+
+
+ -
+
+ Adds a sortable table to a D3 selection container.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ container |
+
+
+ d3.selection
+ |
+
+ |
+
+
+ The D3 selection representing the container element
+ for the table.
+ |
+
+
+
+ headers |
+
+
+ Array.<string>
+ |
+
+ |
+
+
+ An array of strings representing the table headers.
+ |
+
+
+
+ content |
+
+
+ Array.<Object>
+ |
+
+ |
+
+
+ An array of objects representing the table content.
+ Each object should have properties that map to table
+ cells.
+ |
+
+
+
+ overwrite |
+
+
+ boolean
+ |
+
+ <optional>
|
+
+
+ An optional flag indicating whether to overwrite any
+ existing table content (default: false).
+ |
+
+
+
+ caption |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ An optional caption for the table.
+ |
+
+
+
+ priority_set_editor |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional function used to customize cell
+ formatting based on priority sets. The function
+ should accept four arguments: - `d`: The data object
+ for the current cell. - `i`: The index of the
+ current cell within its row. - `cell`: The D3
+ selection of the current cell element (a `
+ |
+
+
+ ` element). - `priority_set_editor`: The
+ `priority_set_editor` function passed to
+ `add_a_sortable_table`.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ b64toBlob(b64,
+ onsuccess [, onerror])
+
+
+ -
+
+ Converts a base64-encoded string to a Blob object.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ b64 |
+
+
+ string
+ |
+
+ |
+
+
+ The base64-encoded string.
+ |
+
+
+
+ onsuccess |
+
+
+ function
+ |
+
+ |
+
+
+ A callback function to be called when the conversion
+ is successful.
+ |
+
+
+
+ onerror |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional callback function to be called if an
+ error occurs.
+ |
+
+
+
+
+
+
+
+
+ -
+
+ collapseLargeCategories(nodes, schema)
+
+
+ -
+
+ Collapses rare categories to "Other" category if there are
+ >CATEGORY_UNIQUE_VALUE_LIMIT categories
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ nodes |
+
+
+ Array.<Object>
+ |
+
+
+ An array of node objects, each containing patient
+ attributes.
+ |
+
+
+
+ schema |
+
+
+ Object
+ |
+
+
+ An object defining the schema for the patient
+ attributes.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ True if any categories were collapsed, false otherwise.
+
+
+
+ - Type
+ -
+ boolean
+
+
+
+
+
+ -
+
+
+ -
+
+ Creates a color picker input element with a label.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ id |
+
+
+ string
+ |
+
+
+ The ID for the color picker input element.
+ |
+
+
+
+ colorizer |
+
+
+ function
+ |
+
+
+ A colorizer function that maps values to colors.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ The HTML markup for the color picker input element with
+ the label.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+
+ -
+
+ Creates a color picker input element with a label for
+ continuous values.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ id |
+
+
+ string
+ |
+
+
+ The ID for the color picker input element.
+ |
+
+
+
+ color |
+
+
+ string
+ |
+
+
+ The initial color value for the color picker.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ The HTML markup for the color picker input element with
+ the label.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+ colorStops(id, number)
+
+
+ -
+
+ Creates a color stop input element with a label.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ id |
+
+
+ string
+ |
+
+
+ The ID for the color stop input element.
+ |
+
+
+
+ number |
+
+
+ number
+ |
+
+
+ The initial value for the color stop.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ The HTML markup for the color stop input element with the
+ label.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+ copyToClipboard(text)
+
+
+ -
+
+ Copies the given text to the clipboard.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ text |
+
+
+ string
+ |
+
+
+ The text to be copied.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ datamonkey_describe_vector(vector [, as_list])
+
+
+ -
+
+ Calculates descriptive statistics for a numerical vector.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ vector |
+
+
+ Array.<number>
+ |
+
+ |
+
+
+ An array of numbers representing the data.
+ |
+
+
+
+ as_list |
+
+
+ boolean
+ |
+
+ <optional>
|
+
+
+ An optional flag indicating whether to return the
+ statistics as a formatted string.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - If `as_list` is false, returns an object with the
+ following properties: - `min`: The minimum value. - `max`:
+ The maximum value. - `median`: The median value. - `Q1`:
+ The first quartile. - `Q3`: The third quartile. - `mean`:
+ The mean value. - If `as_list` is true, returns a
+ formatted string representing the statistics.
+
+
+
+ - Type
+ -
+ Object
+ |
+
+ string
+
+
+
+
+
+ -
+
+
+ -
+
+ Creates a downloadable CSV file for the provided data and
+ adds a button to trigger the download.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ data |
+
+
+ Array.<Object>
+ |
+
+ |
+
+
+ An array of objects representing the data to be
+ exported.
+ |
+
+
+
+ name |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ An optional name for the exported CSV file. If not
+ provided, defaults to "export.csv".
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ datamonkey_export_handler(data [, filename] [, mimeType])
+
+
+ -
+
+ Handles exporting data to a file based on browser
+ capabilities.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ data |
+
+
+ string
+ |
+
+ |
+
+
+ The data to be exported.
+ |
+
+
+
+ filename |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ The desired filename for the downloaded file.
+ Defaults to "download.tsv".
+ |
+
+
+
+ mimeType |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ The MIME type of the data. Defaults to "text/plain"
+ if not provided.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+
+ -
+
+ Creates a downloadable JSON file for the provided data and
+ adds a button to trigger the download.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ data |
+
+
+ Object
+ |
+
+ Array.<Object>
+ |
+
+ |
+
+
+ The data to be exported, either a single object or
+ an array of objects.
+ |
+
+
+
+ title |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ An optional title for the exported JSON file. If not
+ provided, defaults to "export".
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ datamonkey_save_image(type, container)
+
+
+ -
+
+ Saves the contents of an SVG element as an image file.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ type |
+
+
+ string
+ |
+
+
+ The desired image format (either "svg" or "png").
+ |
+
+
+
+ container |
+
+
+ jQuery
+ |
+
+ HTMLElement
+ |
+
+
+ A jQuery selector or element reference containing
+ the SVG element.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ draw_priority_set_table(self, container, priority_groups)
+
+
+ -
+
+ Draws a table of priority sets (clusters of interest).
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The main network visualization object.
+ |
+
+
+
+ container |
+
+
+ HTMLElement
+ |
+
+
+ The HTML element where the table will be displayed
+ (optional).
+ |
+
+
+
+ priority_groups |
+
+
+ Array
+ |
+
+
+ An array of objects representing the priority sets
+ (optional).
+ |
+
+
+
+
+
+
+
+
+ -
+
+ edge_typer(e,
+ edge_types, T)
+
+
+ -
+
+ Determines the type of an edge based on its length and
+ predefined edge types.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ e |
+
+
+ Object
+ |
+
+
+ The edge object to be classified.
+ |
+
+
+
+ edge_types |
+
+
+ Array.<string>
+ |
+
+
+ An array of two edge types. The first type is used
+ for edges shorter than or equal to `T`, and the
+ second type is used for edges longer than `T`.
+ |
+
+
+
+ T |
+
+
+ number
+ |
+
+
+ The threshold value for edge length classification.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ The edge type corresponding to the edge's length.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+ ensure_node_attributes_exist()
+
+
+ -
+
+ ensure_node_attributes_exist Iterate over nodes in the
+ network. If a node does not have an array of attributes or
+ data dictionary records, create an empty one. This makes
+ error checking less complex downstream.
+
+
+
+
+
+
+ -
+
+ exportColorScheme(uniqValues, colorizer)
+
+
+ -
+
+ Exports a color scheme based on unique values and a
+ colorizer function.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ uniqValues |
+
+
+ Object
+ |
+
+
+ An object containing unique values for each
+ attribute, as returned by `getUniqueValues`.
+ |
+
+
+
+ colorizer |
+
+
+ function
+ |
+
+
+ A colorizer function that maps values to colors.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ An object where the keys are unique values and the values
+ are the corresponding colors.
+
+
+
+ - Type
+ -
+ Object
+
+
+
+
+
+ -
+
+ filter_parse(filter_value)
+
+
+ -
+
+ Parses a filter string into an array of filter objects.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ filter_value |
+
+
+ string
+ |
+
+
+ The filter string to be parsed.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ An array of filter objects, each with a `type` property
+ and a corresponding `value` property. The `type` can be
+ "re" for regular expression, "date" for date range, or
+ "distance" for numerical comparison.
+
+
+
+ - Type
+ -
+ Array.<Object>
+
+
+
+
+
+ -
+
+ filter_table(element)
+
+
+ -
+
+ Filters a D3 table based on user-defined filters in column
+ headers.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ element |
+
+
+ d3.selection
+ |
+
+ HTMLElement
+ |
+
+
+ The D3 selection or HTML element representing a
+ table header cell that triggered the filter
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ filter_table_by_column_handler(datum, conditions)
+
+
+ -
+
+ Filters a table based on specified conditions applied to a
+ column.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ datum |
+
+
+ *
+ |
+
+
+ The data object representing a row in the table.
+ |
+
+
+
+ conditions |
+
+
+ Array.<Object>
+ |
+
+
+ An array of condition objects, each with the
+ following properties: - `type`: The type of
+ condition ("re" for regular expression, "date" for
+ date range, "distance" for numerical comparison). -
+ `value`: The value or range for the condition: - For
+ "re": A regular expression object. - For "date": An
+ array of two Date objects representing the start and
+ end dates. - For "distance": A number representing
+ the threshold value. - `greater_than` (optional): A
+ boolean indicating whether to use greater-than
+ comparison for "distance" conditions.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ True if the row matches at least one condition, false
+ otherwise.
+
+
+
+ - Type
+ -
+ boolean
+
+
+
+
+
+ -
+
+
+ -
+
+ Formats a cell in a table based on provided data.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ data |
+
+
+ Object
+ |
+
+ |
+
+
+ The data object representing the table cell. It
+ should have properties like: - `value`: The cell
+ value. - `format` (optional): A function used to
+ format the value. - `html` (optional): A flag
+ indicating whether the value should be set as HTML.
+ - `callback` (optional): A function used to
+ customize cell content and behavior. - `filter`
+ (optional): A flag indicating whether to enable
+ filtering for the column. - `column_id` (optional):
+ The index of the column (used for filtering). -
+ `sort` (optional): A flag indicating whether to
+ enable sorting for the column. - `presort`
+ (optional): A string ("asc" or "desc") for initial
+ sort direction. - `actions` (optional): An array of
+ button configurations for cell actions. - `help`
+ (optional): A string describing the cell content
+ (used as a tooltip).
+ |
+
+
+
+ index |
+
+
+ number
+ |
+
+ |
+
+
+ The index of the cell within its row.
+ |
+
+
+
+ item |
+
+
+ d3.selection
+ |
+
+ |
+
+
+ The D3 selection of the table cell element (a `
+ |
+ ` element). |
+
+
+
+ priority_set_editor |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional function used for priority set
+ functionality (internal).
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ getUniqueValues(nodes,
+ schema)
+
+
+ -
+
+ Retrieves unique values for each attribute in a given
+ dataset.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ nodes |
+
+
+ Array.<Object>
+ |
+
+
+ An array of node objects, each containing patient
+ attributes.
+ |
+
+
+
+ schema |
+
+
+ Object
+ |
+
+
+ An object defining the schema for the patient
+ attributes.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ An object where each key represents an attribute name and
+ the corresponding value is an array of unique values for
+ that attribute.
+
+
+
+ - Type
+ -
+ Object
+
+
+
+
+
+ -
+
+ get_editor()
+
+
+ -
+
+ Gets the current priority set editor object.
+
+
+
+
+ Returns:
+
+
+ The priority set editor object, or null if not open.
+
+
+
+ - Type
+ -
+ Object
+
+
+
+
+
+ -
+
+ get_ui_element_selector_by_role(role)
+
+
+ -
+
+ Retrieves a CSS selector for UI elements based on their
+ `data-hivtrace-ui-role` attribute.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ role |
+
+
+ string
+ |
+
+
+ The value of the `data-hivtrace-ui-role` attribute.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ A CSS selector string targeting elements with the
+ specified role.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+ handle_cluster_click(self:, cluster, release)
+
+
+ -
+
+ handle_cluster_click Handle contextual menus for clusters
+ and cluster drag
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self: |
+
+ |
+
+ network object |
+
+
+
+ cluster |
+
+ |
+
+
+ [optional]: the cluster object to act on
+ |
+
+
+
+ release |
+
+ |
+
+
+ [optional]: the cluster object to release the
+ "fixed" flag from
+ |
+
+
+
+
+
+
+
+
+ -
+
+ handle_inline_confirm(this_button, generator, text,
+ action, disabled)
+
+
+ -
+
+ Handles inline confirmation popovers.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ this_button |
+
+
+ HTMLElement
+ |
+
+
+ The button element that triggers the popover.
+ |
+
+
+
+ generator |
+
+
+ function
+ |
+
+
+ A function that generates the HTML content for the
+ popover body.
+ |
+
+
+
+ text |
+
+
+ string
+ |
+
+
+ The initial text to display in the popover's text
+ area (optional).
+ |
+
+
+
+ action |
+
+
+ function
+ |
+
+
+ A callback function to be executed when the user
+ confirms the action. Takes the value from the text
+ area as input.
+ |
+
+
+
+ disabled |
+
+
+ boolean
+ |
+
+
+ A flag indicating if the text area should be
+ disabled (optional).
+ |
+
+
+
+
+
+
+
+
+ -
+
+ hiv_trace_export_table_to_text(parent_id, table_id, csv
+ [, file_name_placeholder])
+
+
+ -
+
+ This function creates a download button that, when
+ clicked, exports the data from the specified table as
+ either a CSV or TSV file. It uses D3 for DOM manipulation
+ and assumes the existence of a `helpers` object with
+ `table_to_text` and `export_handler` methods.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ parent_id |
+
+
+ string
+ |
+
+ |
+
+
+ The selector for the parent element where the button
+ will be appended.
+ |
+
+
+
+ table_id |
+
+
+ string
+ |
+
+ |
+
+
+ The selector for the table to be exported.
+ |
+
+
+
+ csv |
+
+
+ boolean
+ |
+
+ |
+
+
+ If true, exports as CSV; if false, exports as TSV.
+ |
+
+
+
+
+ file_name_placeholder
+ |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ The base name for the exported file. If not
+ provided, it defaults to the table_id without the
+ first character.
+ |
+
+
+
+
+
+
+ Requires:
+
+ - module:d3
+
+ - module:helpers
+
+
+ Returns:
+
+
+ The D3 selection of the created button.
+
+
+
+ - Type
+ -
+ d3.Selection
+
+
+
+ Example
+
+
+hiv_trace_export_table_to_text("#parent-div", "#data-table", true, "export-data");
+
+
+
+ -
+
+ hivtraceClusterGraphSummary()
+
+
+ -
+
+ ## hivtraceClusterGraphSummary Function Creates and
+ populates a summary table for an HIV trace cluster graph.
+ #### Parameters `graph`: The input graph data. `tag`: The
+ HTML element to append the summary table to. `not_CDC`: A
+ flag indicating whether to include CDC-specific statistics
+ or not (optional). #### Returns None
+
+
+
+
+
+
+ -
+
+ hivtrace_cluster_depthwise_traversal(nodes, edges [,
+ edge_filter] [, save_edges] [, seed_nodes] [, white_list])
+
+
+ -
+
+ Performs a depth-wise traversal on a cluster of nodes,
+ considering edges and optional filters.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ nodes |
+
+
+ Array.<Object>
+ |
+
+ |
+
+
+ An array of node objects. Each node should have an
+ `id` property.
+ |
+
+
+
+ edges |
+
+
+ Array.<Object>
+ |
+
+ |
+
+
+ An array of edge objects. Each edge should have
+ `source` and `target` properties referencing node
+ IDs.
+ |
+
+
+
+ edge_filter |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional filtering function applied to edges
+ before traversal. The function should accept an edge
+ object and return a boolean indicating whether to
+ include the edge.
+ |
+
+
+
+ save_edges |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional function used to store traversed edges.
+ It should be called with an array where each element
+ represents the edges within a cluster.
+ |
+
+
+
+ seed_nodes |
+
+
+ Array.<Object>
+ |
+
+ <optional>
|
+
+
+ An optional array of node objects to use as starting
+ points for traversal. If not provided, all nodes
+ will be considered.
+ |
+
+
+
+ white_list |
+
+
+ Set
+ |
+
+ <optional>
|
+
+
+ An optional set of node IDs restricting traversal to
+ nodes within the set.
+ |
+
+
+
+
+
+
+ Throws:
+
+
+ -
+
+ If an edge references non-existent nodes.
+
+
+ -
+
+ - Type
+ -
+ Error
+
+
+
+
+
+ Returns:
+
+
+ An array of clusters, where each cluster is an array of
+ node objects.
+
+
+
+ - Type
+ -
+ Array.<Array.<Object>>
+
+
+
+
+
+ -
+
+ hivtrace_coi_timeseries(cluster, element [, plot_width])
+
+
+ -
+
+ This function creates a detailed time series visualization
+ for a cluster of interest (COI). It displays nodes and
+ events over time, with interactive features for
+ highlighting and displaying additional information. The
+ visualization includes: - A time axis - Lines representing
+ nodes - Circles representing events - Interactive
+ highlighting and tooltips - Time range boxes for context
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Default |
+
+ Description |
+
+
+
+
+
+ cluster |
+
+
+ Object
+ |
+
+ |
+
+ |
+
+
+ The cluster object containing node and event
+ information.
+
+ Properties
+
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ node_info |
+
+
+ Object
+ |
+
+
+ Information about nodes in the cluster.
+ |
+
+
+
+ event_info |
+
+
+ Object
+ |
+
+
+ Information about events in the cluster.
+ |
+
+
+
+ |
+
+
+
+ element |
+
+
+ d3.Selection
+ |
+
+ |
+
+ |
+
+
+ The D3 selection of the element where the
+ visualization will be rendered.
+ |
+
+
+
+ plot_width |
+
+
+ number
+ |
+
+ <optional>
|
+
+ 1000 |
+
+
+ The width of the plot in pixels.
+ |
+
+
+
+
+
+
+ Requires:
+
+ - module:d3
+
+ - module:lodash
+
+
+ Example
+
+
+const cluster = {
+ node_info: {...},
+ event_info: {...}
+};
+const element = d3.select("#visualization-container");
+hivtrace_coi_timeseries(cluster, element, 1200);
+
+
+
+ -
+
+ hivtrace_compute_node_degrees(obj)
+
+
+ -
+
+ This function modifies the input object by adding a
+ 'degree' property to each node. The degree of a node is
+ the number of edges connected to it.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ obj |
+
+
+ Object
+ |
+
+
+ The graph object containing nodes and edges.
+
+ Properties
+
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ Nodes |
+
+
+ Object
+ |
+
+
+ An object representing the nodes of the
+ graph.
+ |
+
+
+
+ Edges |
+
+
+ Object
+ |
+
+
+ An object representing the edges of the
+ graph.
+ |
+
+
+
+
+ Edges[].source
+ |
+
+
+ string
+ |
+
+
+ The source node of an edge.
+ |
+
+
+
+
+ Edges[].target
+ |
+
+
+ string
+ |
+
+
+ The target node of an edge.
+ |
+
+
+
+ |
+
+
+
+
+
+
+ Example
+
+
+const graph = {
+ Nodes: {
+ "1": {},
+ "2": {}
+ },
+ Edges: {
+ "e1": { source: "1", target: "2" }
+ }
+};
+hivtrace_compute_node_degrees(graph);
+// graph.Nodes["1"].degree === 1
+// graph.Nodes["2"].degree === 1
+
+
+
+ -
+
+ hivtrace_date_or_na_if_missing(date [, formatter])
+
+
+ -
+
+ Formats a date using a specified formatter, or returns
+ "N/A" if the date is missing.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ date |
+
+
+ Date
+ |
+
+ |
+
+
+ The date object to be formatted.
+ |
+
+
+
+ formatter |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional formatter function used to format the
+ date. If not provided, `DateViewFormatExport` is
+ used.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ The formatted date string, or "N/A" if the date is
+ missing.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+ hivtrace_generate_svg_symbol(type)
+
+
+ -
+
+ Generates an SVG symbol based on the specified type.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ type |
+
+
+ string
+ |
+
+
+ The type of symbol to generate. Possible values are:
+ - "circle" - "cross" - "diamond" - "square" -
+ "triangle-down" - "triangle-up" - "triangle" -
+ "pentagon" - "hexagon" - "septagon" - "octagon" -
+ "ellipse"
+ |
+
+
+
+
+
+
+ Requires:
+
+ - module:d3
+
+ - module:hivtrace_generate_svg_polygon
+
+ - module:hivtrace_generate_svg_ellipse
+
+
+ Returns:
+
+
+ A D3 symbol generator or a custom polygon/ellipse
+ generator. - For "circle", "cross", "diamond", "square",
+ "triangle-down", "triangle-up": Returns a D3 symbol
+ generator of the specified type. - For "triangle",
+ "pentagon", "hexagon", "septagon", "octagon": Returns a
+ custom polygon generator with the specified number of
+ sides. - For "ellipse": Returns a custom ellipse
+ generator. - For any other input: Returns a D3 symbol
+ generator of type "circle" as default.
+
+
+
+ - Type
+ -
+ Object
+
+
+
+
+
+ -
+
+ hivtrace_histogram(graph, histogram_tag, histogram_label)
+
+
+ -
+
+ Renders a histogram for a graph property and displays a
+ descriptive label.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ graph |
+
+
+ Object
+ |
+
+
+ An object containing graph data, including
+ distribution and fitted data for the property.
+ |
+
+
+
+ histogram_tag |
+
+
+ string
+ |
+
+
+ The ID of the HTML element where the histogram will
+ be rendered.
+ |
+
+
+
+ histogram_label |
+
+
+ string
+ |
+
+
+ The ID of the HTML element where the descriptive
+ label will be displayed.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ hivtrace_histogram_distances(graph, histogram_tag,
+ histogram_label)
+
+
+ -
+
+ Renders a histogram for edge lengths (genetic distances)
+ and displays a label.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ graph |
+
+
+ Object
+ |
+
+
+ An object containing graph data, including edges.
+ |
+
+
+
+ histogram_tag |
+
+
+ string
+ |
+
+
+ The ID of the HTML element where the histogram will
+ be rendered.
+ |
+
+
+
+ histogram_label |
+
+
+ string
+ |
+
+
+ The ID of the HTML element where the descriptive
+ label will be displayed.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ hivtrace_plot_cluster_dynamics(time_series, container,
+ x_title, y_title [, y_scale] [, bin_by] [, options])
+
+
+ -
+
+ Generates a plot visualizing cluster dynamics over time.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ time_series |
+
+
+ Array.<Object>
+ |
+
+ |
+
+
+ An array of data points, each with a required `time`
+ property (a date object) and optional properties
+ representing attributes.
+ |
+
+
+
+ container |
+
+
+ d3.selection
+ |
+
+ |
+
+
+ A D3 selection representing the container element
+ for the plot.
+ |
+
+
+
+ x_title |
+
+
+ string
+ |
+
+ |
+
+
+ The title for the x-axis.
+ |
+
+
+
+ y_title |
+
+
+ string
+ |
+
+ |
+
+
+ The title for the y-axis.
+ |
+
+
+
+ y_scale |
+
+
+ d3.scale
+ |
+
+ <optional>
|
+
+
+ An optional D3 scale for the y-axis. If not
+ provided, a linear scale will be used.
+ |
+
+
+
+ bin_by |
+
+
+ function
+ |
+
+ <optional>
|
+
+
+ An optional function used to bin data points into
+ time intervals. The function should accept a date
+ object and return an array with three elements: -
+ The bin label (e.g., "Q1 2023"). - The start date of
+ the bin. - The middle date of the bin (used for
+ x-axis positioning). If not provided, a default
+ function that bins by quarters is used.
+ |
+
+
+
+ options |
+
+
+ Object
+ |
+
+ <optional>
|
+
+
+ An optional configuration object for the plot. -
+ `base_line`: (number, default: 20) The baseline
+ value for the y-axis. - `top`: (number, default: 40)
+ The top padding for the plot. - `right`: (number,
+ default: 30) The right padding for the plot. -
+ `bottom`: (number, default: 60) The bottom padding
+ for the plot. - `left`: (number, default: 100) The
+ left padding for the plot. - `font_size`: (number,
+ default: 18) The font size for labels and text
+ elements. - `rect_size`: (number, default: 22) The
+ size of rectangles used in the legend. - `width`:
+ (number, default: 1024) The width of the plot
+ container. - `height`: (number, default: 600) The
+ height of the plot container. - `barchart`:
+ (boolean, default: false) If true, the plot will be
+ displayed as a bar chart. - `skip_cumulative`:
+ (boolean, default: false) If true, the cumulative
+ area will not be displayed. - `x-tick-format`:
+ (Function) An optional function for formatting
+ x-axis tick labels. - `prefix`: (string) An optional
+ prefix to add to attribute names displayed in the
+ legend. - `colorizer`: (Object) An optional
+ colorizer object for attributes. Keys should be
+ attribute names, and values should be D3 scales used
+ for coloring lines/bars. - `drag`: (Object) An
+ optional drag object for enabling dragging the plot.
+ |
+
+
+
+
+
+
+ Throws:
+
+
+ -
+
+ If no data points are provided.
+
+
+ -
+
+ - Type
+ -
+ Error
+
+
+
+
+
+
+
+ -
+
+ hivtrace_render_histogram(counts [, fit], w, h, id)
+
+
+ -
+
+ Renders a histogram for discrete data using D3.js.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ counts |
+
+
+ Array.<number>
+ |
+
+ |
+
+
+ An array of counts for each category.
+ |
+
+
+
+ fit |
+
+
+ Array.<number>
+ |
+
+ <optional>
|
+
+
+ (optional) - An array of fitted values for each
+ category.
+ |
+
+
+
+ w |
+
+
+ number
+ |
+
+ |
+
+
+ The width of the plot area.
+ |
+
+
+
+ h |
+
+
+ number
+ |
+
+ |
+
+
+ The height of the plot area.
+ |
+
+
+
+ id |
+
+
+ string
+ |
+
+ |
+
+
+ The ID of the HTML element where the histogram will
+ be rendered.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ hivtrace_render_histogram_continuous(data, w, h, id)
+
+
+ -
+
+ Renders a histogram for continuous data using D3.js.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ data |
+
+
+ Array.<number>
+ |
+
+
+ An array of numerical values.
+ |
+
+
+
+ w |
+
+
+ number
+ |
+
+
+ The width of the plot area.
+ |
+
+
+
+ h |
+
+
+ number
+ |
+
+
+ The height of the plot area.
+ |
+
+
+
+ id |
+
+
+ string
+ |
+
+
+ The ID of the HTML element where the histogram will
+ be rendered.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ hivtrace_render_scatterplot(points, w, h, id, labels [,
+ dates])
+
+
+ -
+
+ Renders a scatter plot using D3.js.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Default |
+
+ Description |
+
+
+
+
+
+ points |
+
+
+ Array.<Object>
+ |
+
+ |
+
+ |
+
+
+ An array of data points, each with x and y
+ coordinates (and optionally a title).
+ |
+
+
+
+ w |
+
+
+ number
+ |
+
+ |
+
+ |
+
+
+ The width of the plot area.
+ |
+
+
+
+ h |
+
+
+ number
+ |
+
+ |
+
+ |
+
+
+ The height of the plot area.
+ |
+
+
+
+ id |
+
+
+ string
+ |
+
+ |
+
+ |
+
+
+ The ID of the HTML element where the plot will be
+ rendered.
+ |
+
+
+
+ labels |
+
+
+ Object
+ |
+
+ |
+
+ |
+
+
+ An object containing labels for the x and y axes.
+ |
+
+
+
+ dates |
+
+
+ boolean
+ |
+
+ <optional>
|
+
+ false |
+
+
+ A flag indicating whether the x-axis should
+ represent dates.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ init(self)
+
+
+ -
+
+ Initializes the component, setting up event listeners and
+ UI elements.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The component object itself.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ n_months_ago(reference_date, months)
+
+
+ -
+
+ Calculates a date that is `months` months ago from a given
+ reference date.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ reference_date |
+
+
+ Date
+ |
+
+
+ The reference date from which to calculate the past
+ date.
+ |
+
+
+
+ months |
+
+
+ number
+ |
+
+
+ The number of months to go back.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ A new Date object representing the date `months` months
+ ago from the reference date.
+
+
+
+ - Type
+ -
+ Date
+
+
+
+
+
+ -
+
+ normalize_node_attributes()
+
+
+ -
+
+ normalize_node_attributes Iterate over node attributes,
+ lower case all the keys for mapping. If attributes are
+ found that are not in the data dictionary, attempt to map
+ them using "labels".
+
+
+
+
+
+
+ -
+
+ open_editor(self,
+ node_set, name, description, cluster_kind, kind_options,
+ validation_mode, existing_set, cluster_tracking,
+ created_by)
+
+
+ -
+
+ Opens a priority node set editor.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The main network visualization object.
+ |
+
+
+
+ node_set |
+
+
+ Array
+ |
+
+
+ An existing priority node set (optional).
+ |
+
+
+
+ name |
+
+
+ string
+ |
+
+
+ Name of the priority node set (optional for new
+ sets).
+ |
+
+
+
+ description |
+
+
+ string
+ |
+
+
+ Description of the priority node set (optional).
+ |
+
+
+
+ cluster_kind |
+
+
+ string
+ |
+
+
+ The method used to identify the cluster (optional).
+ |
+
+
+
+ kind_options |
+
+
+ Array
+ |
+
+
+ Available options for cluster identification
+ methods.
+ |
+
+
+
+ validation_mode |
+
+
+ string
+ |
+
+
+ Indicates the mode (create, validate, revise).
+ |
+
+
+
+ existing_set |
+
+
+ Object
+ |
+
+
+ Reference to the existing priority node set (for
+ revisions).
+ |
+
+
+
+ cluster_tracking |
+
+
+ string
+ |
+
+
+ Method for tracking cluster growth (optional).
+ |
+
+
+
+ created_by |
+
+
+ string
+ |
+
+
+ Who created the node set (system or manual).
+ |
+
+
+
+
+
+
+
+
+ -
+
+ priority_groups_add_set(self, nodeset, update_table,
+ not_validated, prior_name, op_code)
+
+
+ -
+
+ Adds a new priority set to the network visualization.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The main network visualization object.
+ |
+
+
+
+ nodeset |
+
+
+ Object
+ |
+
+
+ The object representing the new priority set.
+ |
+
+
+
+ update_table |
+
+
+ boolean
+ |
+
+
+ Flag indicating whether to update the priority set
+ table. (optional)
+ |
+
+
+
+ not_validated |
+
+
+ boolean
+ |
+
+
+ Flag indicating whether to perform validation before
+ adding. (optional)
+ |
+
+
+
+ prior_name |
+
+
+ string
+ |
+
+
+ Optional name of an existing priority set to
+ replace.
+ |
+
+
+
+ op_code |
+
+
+ string
+ |
+
+
+ Optional operation code (defaults to "insert").
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ True if the set was added successfully, false otherwise.
+
+
+
+ - Type
+ -
+ boolean
+
+
+
+
+
+ -
+
+ priority_groups_check_name(defined_priority_groups,
+ string [, prior_name])
+
+
+ -
+
+ A valid name must: - Have a length between 1 and 35
+ characters. - Not be a duplicate among existing priority
+ groups (excluding itself if editing).
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+
+ defined_priority_groups
+ |
+
+
+ Array.<Object>
+ |
+
+ |
+
+
+ An array of existing priority group objects.
+ |
+
+
+
+ string |
+
+
+ string
+ |
+
+ |
+
+
+ The name to be validated.
+ |
+
+
+
+ prior_name |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ (optional) - The previous name of the priority group
+ (used for edit case).
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ True if the name is valid, false otherwise.
+
+
+
+ - Type
+ -
+ boolean
+
+
+
+
+
+ -
+
+ priority_set_inject_node_attibutes(self, nodes,
+ node_attributes)
+
+
+ -
+
+ Injects priority set related attributes into network
+ nodes.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The main network visualization object.
+ |
+
+
+
+ nodes |
+
+
+ Array
+ |
+
+
+ Array of network nodes.
+ |
+
+
+
+ node_attributes |
+
+
+ Array
+ |
+
+
+ Array of priority set attributes for specific nodes
+ (identified by name).
+ |
+
+
+
+
+
+
+
+
+ -
+
+ priority_set_view(self, priority_set, options)
+
+
+ -
+
+ Creates a subcluster view for a specific priority set.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ The main network visualization object.
+ |
+
+
+
+ priority_set |
+
+
+ Object
+ |
+
+
+ The priority set object.
+ |
+
+
+
+ options |
+
+
+ Object
+ |
+
+
+ Optional configuration options for the view.
+ |
+
+
+
+
+
+
+
+
+ -
+
+ random_id( [alphabet]
+ [, length])
+
+
+ -
+
+ Generates a random ID string using a specified alphabet
+ and length.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ alphabet |
+
+
+ Array.<string>
+ |
+
+ <optional>
|
+
+
+ An optional array of characters to use in the ID. If
+ not provided, a default alphabet of letters "a" to
+ "g" is used.
+ |
+
+
+
+ length |
+
+
+ number
+ |
+
+ <optional>
|
+
+
+ An optional length for the ID. If not provided, a
+ default length of 32 is used.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ A randomly generated ID string.
+
+
+
+ - Type
+ -
+ string
+
+
+
+
+
+ -
+
+ secure_hiv_trace_subcluster_columns(self)
+
+
+ -
+
+ Defines secure column definitions for HIV Trace subcluster
+ data.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ self |
+
+
+ Object
+ |
+
+
+ (optional) - The object containing context for
+ calculations (presumably the component using this
+ function).
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ An array of column definition objects. Each object has the
+ following properties: - `description`: - `value`: (string)
+ The human-readable name of the column. - `sort`:
+ (function) A function used to sort the column data. -
+ `presort` (string, optional): The default sort direction
+ ("asc" or "desc"). - `help`: (string) Help text displayed
+ when hovering over the column header. - `generator`:
+ (function) A function that generates the value and actions
+ for each cluster based on the provided cluster object. -
+ The generator function receives the cluster object as an
+ argument. - It should return an object with the following
+ properties: - `html`: (boolean) Whether the column value
+ should be rendered as HTML. - `value`: (array|string) The
+ actual data for the column. - `volatile`: (boolean,
+ optional) Whether the value needs to be recalculated
+ frequently. - `format`: (function, optional) A function
+ used to format the column value for display. - `actions`:
+ (function, optional) A function used to generate actions
+ for the column. - The actions function receives two
+ arguments: - `item`: (object) The current cluster object.
+ - `value`: (array|string) The value of the column for the
+ current cluster. - It should return an array of action
+ objects, each with the following properties: - `icon`:
+ (string) The icon class name to display for the action. -
+ `action`: (function) The function executed when the action
+ is clicked. - The action function receives two arguments:
+ - `button`: (jQuery object) The button element
+ representing the action. - `v`: (array|string) The value
+ of the column for the current cluster. - `help`: (string)
+ The help text displayed when hovering over the action
+ icon.
+
+
+
+ - Type
+ -
+ Array.<Object>
+
+
+
+
+
+ -
+
+ sort_table_by_column(element, datum)
+
+
+ -
+
+ Sorts a D3 table based on the clicked column header.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ element |
+
+
+ d3.selection
+ |
+
+ HTMLElement
+ |
+
+
+ HTML element representing the clicked column header.
+ |
+
+
+
+ datum |
+
+
+ *
+ |
+
+
+ (optional) - The data object associated with the
+ table (used internally).
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - Type
+ -
+ void
+
+
+
+
+
+ -
+
+ sort_table_toggle_icon(element [, value])
+
+
+ -
+
+ Toggles the sort icon on a column header and returns a
+ sorting function.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Argument |
+
+ Description |
+
+
+
+
+
+ element |
+
+
+ d3.selection
+ |
+
+ HTMLElement
+ |
+
+ |
+
+
+ The D3 selection or HTML element representing the
+ column header.
+ |
+
+
+
+ value |
+
+
+ string
+ |
+
+ <optional>
|
+
+
+ (optional) - The desired sort direction ("asc",
+ "desc", or "unsorted").
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ - If `value` is provided, returns nothing. - If `value` is
+ not provided, returns a sorting function (`d3.ascending`
+ or `d3.descending`) based on the current sort state.
+
+
+
+ - Type
+ -
+ function
+ |
+
+ void
+
+
+
+
+
+ -
+
+ table_get_cell_value(data)
+
+
+ -
+
+ Retrieves the value of a cell in a table data object.
+
+
+ Parameters:
+
+
+
+
+ | Name |
+
+ Type |
+
+ Description |
+
+
+
+
+
+ data |
+
+
+ Object
+ |
+
+
+ The data object representing the table cell. It
+ should have a `value` property.
+ |
+
+
+
+
+
+
+ Returns:
+
+
+ The value of the cell, or the result of calling
+ `data.value()` if it's a function.
+
+
+
+ - Type
+ -
+ *
+
+
+
+
+
+ -
+
+ unpack_compact_json()
+
+
+ -
+
+ unpack_compact_json: If the input network JSON is in
+ compact form, i.e. instead of storing key : value it
+ stores key : integer index of value unique_values: list of
+ values convert it to key: value The operation is performed
+ in place on the `json` argument
+
+
+
+
+
+