Data / BioEntities#

The methods contained within ‘Data / BioEntities’ are used to access/modify data on content/drugs/chemicals entities, as well as markers drawn on the map: pins, surfaces, lines, polygons, texts and images.

Below is a description of the methods, as well as the types they return.

Available data access methods include:

• getAllChemicals
  • gets list of searched chemicals
  • returns array of Chemical
• getAllContent
  • gets list of searched content
  • returns array of BioEntity
• getAllDrugs
  • gets list of searched drugs
  • returns array of Drug
• getAllMarkers
  • gets list of added markers
  • returns array of Marker
• getShownElements

  • gets list of all currently shown content/chemicals/drugs BioEntities + markers

  • returns object of

    {
        content: BioEntity[]
        drugs: BioEntity[]
        chemicals: BioEntity[]
        markers: Marker[]
    }

Available data modify methods include:

clearAllElements#

• accepts single argument

  • array of string which includes one or more of: 'drugs', 'chemicals', 'content', 'marker'

• clears all elements of provided type(s)

• returns nothing

• example:

  window.minerva.data.bioEntities.clearAllElements(['drugs', 'chemicals']);

addSingleMarker#

• accepts single argument: a marker object

  • fields common to all marker types:

    {
        type: 'pin' OR 'surface' OR 'line' OR 'polygon' OR 'text' OR 'image'
        id: string [optional]
        opacity: number
        modelId: number [optional]
    }

  • id - optional, if not provided uuidv4 is generated; a plugin can choose its own ids to recognise its markers in click events

  • opacity - should be a float between 0 and 1 (example: 0.54)

  • modelId - if marker should be visible only on single map, modelId should be provided

  • colors should be provided in hex format with hash (example: #FF0000)

• fields specific to the marker type:

  type	fields
  pin	color, x, y, number [optional] - number presented on the pin, width [optional], height [optional]
  surface	color, x, y, width, height
  line	color, start: { x, y }, end: { x, y }
  polygon	fillColor, borderColor, borderWidth, points: [{ x, y }, ...] - ordered list of the polygon vertices
  text	color, x, y, text, fontName [optional] - one of 'ARIAL', 'HELVETICA', 'TIMES_NEW_ROMAN', 'COURIER_NEW', 'GEORGIA', 'VERDANA' (default 'ARIAL'), fontSize [optional] (default 12)
  image	x, y, width, height, url - source of the image

  • x, y, start, end and points are coordinates on the map

• adds one marker to markers list

• returns created Marker

• throws an error when a marker with the given id is already shown; use updateSingleMarker to change an existing marker

• clicking a marker on the map triggers an event, see Events

• examples:

  window.minerva.data.bioEntities.addSingleMarker({
    type: 'surface',
    color: '#106AD7',
    opacity: 0.67,
    x: 4438,
    y: 1124,
    width: 200,
    height: 300,
    modelId: 52,
  });

  window.minerva.data.bioEntities.addSingleMarker({
    type: 'pin',
    color: '#106AD7',
    opacity: 1,
    x: 8723,
    y: 4322,
    number: 43,
  });
  window.minerva.data.bioEntities.addSingleMarker({
    type: 'line',
    color: '#106AD7',
    opacity: 1,
    modelId: 52,
    start: {
      x: 8723,
      y: 4322,
    },
    end: {
      x: 4438,
      y: 1124,
    },
  });

  window.minerva.data.bioEntities.addSingleMarker({
    type: 'polygon',
    fillColor: '#106AD7',
    borderColor: '#000000',
    borderWidth: 2,
    opacity: 0.5,
    points: [
      { x: 8723, y: 4322 },
      { x: 4438, y: 1124 },
      { x: 5000, y: 6000 },
    ],
    modelId: 52,
  });
  window.minerva.data.bioEntities.addSingleMarker({
    type: 'text',
    color: '#106AD7',
    opacity: 1,
    x: 8723,
    y: 4322,
    text: 'Hello map',
    fontSize: 24,
    modelId: 52,
  });
  window.minerva.data.bioEntities.addSingleMarker({
    type: 'image',
    opacity: 1,
    x: 8723,
    y: 4322,
    width: 200,
    height: 200,
    url: 'https://example.com/image.png',
    modelId: 52,
  });

updateSingleMarker#

• accepts single argument: a marker object with the same fields as in addSingleMarker; id is required and identifies the marker to change

• replaces the shown marker with the given id and keeps its id; the whole marker is replaced (not patched), so all fields required by the marker type must be provided, and the type itself may change

• returns updated Marker

• throws an error when no marker with the given id is shown

• example:

  window.minerva.data.bioEntities.addSingleMarker({
    id: 'gene-TP53',
    type: 'pin',
    color: '#106AD7',
    opacity: 1,
    x: 8723,
    y: 4322,
  });
  window.minerva.data.bioEntities.updateSingleMarker({
    id: 'gene-TP53',
    type: 'pin',
    color: '#D71010',
    opacity: 1,
    x: 8723,
    y: 4322,
  });

removeSingleMarker#

• accepts single argument of string which represents marker id

• removes one marker from markers list

• returns nothing

• example:

  window.minerva.data.bioEntities.removeSingleMarker('f4c068d1-9695-4f1b-928c-d0cff92164b2');

removeAllMarkers#

• removes all markers from markers list

• returns nothing

• example:

  window.minerva.data.bioEntities.removeAllMarkers();