Package org.biojava.nbio.structure.scop

Class Astral

java.lang.Object
org.biojava.nbio.structure.scop.Astral
public class Astral extends Object
Provides programmatic access to ASTRAL representative sets. See the paper by Chandonia et. al. for more information. Example: 
 Set<String> astralSet = Astral.getRepresentatives(Astral.AstralSet.NINETY_FIVE_175B);
This class uses a multiton pattern with soft references for caching. In short: the first time you call the above, it will fetch the data from ASTRAL; the second time will (probably) not have to; and the instances can still be garbage-collected if necessary (meaning they don't require heap memory).
Since:
3.0.6
Author:
dmyerstu

  • Constructor Details

    • Astral

      public Astral(Astral.AstralSet cutoff)
      Constructs a new Astral object. Generally, client code should prefer calling getRepresentatives(AstralSet) instead. This constructor should only be used when an ASTRAL set not included in Astral(AstralSet) is required.
      Parameters:
      cutoff - The ASTRAL sequence-identity cutoff required
      Throws:
      RuntimeException - If the Astral set could not be parsed or accessed for any reason

    • Astral

      public Astral(String id, URL url)
      Constructs a new Astral object. Generally, client code should prefer calling getRepresentatives(AstralSet) instead. This constructor should only be used when an ASTRAL set not included in Astral(AstralSet) is required.
      Throws:
      RuntimeException - If the Astral set could not be parsed or accessed for any reason

    • Astral

      public Astral(String id, Reader reader)
      Constructs a new Astral object. Generally, client code should prefer calling getRepresentatives(AstralSet) instead. This constructor should only be used when an ASTRAL set not included in Astral(AstralSet) is required.
      Throws:
      RuntimeException - If the Astral set could not be parsed or accessed for any reason

  • Method Details

    • getRepresentatives

      public static Set<String> getRepresentatives(Astral.AstralSet cutoff)
      Get a list of representatives' names for the specified ASTRAL cutoff.

    • getRepresentatives

      public static Set<String> getRepresentatives(String id)
      Get a list of representatives' names for the specified ASTRAL cutoff.
      Parameters:
      id - An ASTRAL Id, such as 1.75A_95.

    • getNames

      public Set<String> getNames()
      Returns:
      The names of representatives in this ASTRAL set.

    • getFailedLines

      public LinkedHashMap<Integer,String> getFailedLines()
      Gets a map describing lines read in the file that weren't understood.
      Returns:
      A LinkedHashMap mapping line numbers of failures to the lines themselves