Genoverse.Track.Model functions

The following are functions that exist in the Genoverse.Track.Model object. Any of these can have before/after hooks added to them unless otherwise specified, or be overwritten by supplying them as properties in configuration.

model.setDefaults()

Sets initial properties of the instance. Does not have before/after hooks.

model.features(chr)

Returns an RTree of features for the given chromosome

Argument	Type	Description
chr	String	The name of the chromosome to return features for

model.dataRanges(chr)

Returns an RTree of features for the given chromosome

Argument	Type	Description
chr	String	The name of the chromosome to return data ranges for

model.parseURL(chr, start, end [, url ])

Returns a URL string with placeholders for chromosome, start, end and assembly replaced. Chromosome, start and end placeholders are replaced from input arguments, while the assembly placeholder (if it exists) is replaced with the value of genoverse.assembly.

Argument	Type	Description
chr	String	The name of the chromosome to use in the URL
start	Integer	The start position to use in the URL
end	Integer	The end position to use in the URL
url	String or undefined	The URL to parse. Defaults to the url property

model.getData(chr, start, end [, done ])

Makes jQuery.ajax GET request(s) to get data for the given genomic region (multiple requests may be made if dataRequestLimit is set.

Returns a jQuery deferred object which is resolved when all of the jQuery.ajax requests are complete.

Argument	Type	Description
chr	String	The name of the chromosome to get data for
start	Integer	The start of the region to get data for
end	Integer	The end of the region to get data for
done	Function or undefined	A callback to be executed on completion of each jQuery.ajax request performed

model.receiveData(data, chr, start, end)

Called on successful completion of each successful attempt to get data made by model.getData. Calls model.setDataRange and model.parseData to process the data returned by the request.

Argument	Type	Description
data	Anything	The data returned by the request in model.getData
chr	String	The name of the chromosome used in the request
start	Integer	The start of the region used in the request
end	Integer	The end of the region used in the request

model.parseData(data, chr, start, end)

Converts the data provided into features that Genoverse can use. Calls model.insertFeature for each feature produced from the data. By default, data is expected to be an array of feature objects (the assumption is that the contents of the url is a JSON array). If that is not the case for a particular track, this function will need to be overwritten to handle the data structure being used.

See model.receiveData for argument descriptions.

model.insertFeature(feature)

Inserts the given feature into the features RTree for the feature's chr property

Argument	Type	Description
feature	Object	The feature to be inserted

model.setDataRange(chr, start, end)

Inserts the given start and end into the dataRanges RTree for the given chr. dataRanges are used to check whether data has already been received for a given region, in order to avoid making multiple requests for the same data (see model.checkDataRange).

Argument	Type	Description
chr	String	The name of the chromosome that data has been received for
start	Integer	The start of the region that data has been received for
end	Integer	The end of the region that data has been received for

model.checkDataRange(chr, start, end)

Returns true if the track already has data for the whole of the given genomic region, else returns false.

Argument	Type	Description
chr	String	The name of the chromosome to check
start	Integer	The start of the region to check
end	Integer	The end of the region to check

model.findFeatures(chr, start, end)

Returns an array of sorted features stored in the features RTree for the given chr. If the track has any featureFilters, the returned array will only contain those features which pass all of the filters.

Argument	Type	Description
chr	String	The name of the chromosome to find features in
start	Integer	The start of the region to find features in
end	Integer	The end of the region to find features in

model.sortFeatures(features)

Sorts an array of features based on their sort property, lowest first. By default the value of sort is the feature's start + the index of the feature in the data array received by model.parseData. This means that features are sorted by lowest start, with tie-breaking based on the original data source's ordering.

This function can be overwritten to sort on different criteria.

Argument	Type	Description
features	Array	An array of features to sort

model.updateData(data)

If the track is using the data property, this function allows that data to be updated. The given data argument will completely overwrite the old value of the property, after which the track will be reset.

model.abort()

Aborts all incomplete jQuery.ajax requests currently being made by the model instance