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

Class InsdcParser<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.location.InsdcParser<S,C>
public class InsdcParser<S extends AbstractSequence<C>,C extends Compound> 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 Details

    • 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 splitted 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:

    • 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

  • Constructor Details

    • InsdcParser

      public InsdcParser()

    • InsdcParser

      public InsdcParser(DataSource dataSource)

  • Method Details

    • setComplexFeaturesAppendMode

      public void setComplexFeaturesAppendMode(org.biojava.nbio.core.sequence.location.InsdcParser.complexFeaturesAppendEnum complexFeaturesAppendMode)

    • getDataSource

      public DataSource getDataSource()

    • parse

      public Location parse(String locationString) throws ParserException
      Main method for parsing a location from a String instance
      Parameters:
      locationString - Represents a logical location
      Returns:
      The parsed location
      Throws:
      ParserException - thrown in the event of any error during parsing

    • parse

      public List<AbstractLocation> parse(Reader reader) throws IOException, ParserException
      Reader based version of the parse methods.
      Parameters:
      reader - The source of the data; assumes that end of the reader stream is the end of the location string to parse
      Returns:
      The parsed location
      Throws:
      IOException - Thrown with any reader error
      ParserException - Thrown with any error with parsing locations

    • main

      public static void main(String[] args)