Package org.biojava.nbio.core.sequence.location

Class InsdcParser

  • public class InsdcParser
extends Object
    Parser for working with INSDC style locations. This class supports the full range of location types generated by Genbank, INSDC and ENA.
    Author:
    ayates, jgrzebyta, Paolo Pavan

    • Field Detail

      • singleLocationPattern

        protected static final Pattern singleLocationPattern
        parse a location. if group(1) is null than the feature is on the positive strand, group(2) start position, group(3) end position.

      • genbankSplitPattern

        protected static final Pattern genbankSplitPattern
        Decodes a split pattern. Split patterns are a composition of multiple locationsString qualified by actions: join(location,location, ... location): The indicated elements should be joined (placed end-to-end) to form one contiguous sequence. order(location,location, ... location): The elements can be found in the specified order (5' to 3' direction), nothing is implied about their reasonableness bond(location,location...location): Found in protein files. These generally are used to describe disulfide bonds. complement(location,location...location): consider locations in their complement versus takes in input a comma split location string. The split must be done for outer level commas group(1) is the qualifier group(2) is the location string to getFeatures. In case of complex splits it will contain the nested expression Not really sure that they are not declared obsolete but they are still in several files.

      • locationSplitPattern

        protected static final String locationSplitPattern
        designed to recursively split a location string in tokens. Valid tokens are those divided by coma that are not inside a bracket. I. e. split on the comma only if that comma has zero, or an even number of quotes ahead of it.
        See Also:
        Constant Field Values

      • featureGlobalStart

        protected Integer featureGlobalStart
        these variables are used to compute the global start and end of complex features

      • featureGlobalEnd

        protected Integer featureGlobalEnd
        these variables are used to compute the global start and end of complex features