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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Astral.AstralSet An ASTRAL sequence-identity cutoff with an identifier such as: 1.75A_95 Also contains a URL pointing to a FASTA file containing the representatives.

Constructor Summary

Constructors

Constructor and Description
Astral(Astral.AstralSet cutoff) Constructs a new Astral object.
Astral(String id, Reader reader) Constructs a new Astral object.
Astral(String id, URL url) Constructs a new Astral object.

Method Summary

Modifier and Type	Method and Description
LinkedHashMap<Integer,String>	getFailedLines() Gets a map describing lines read in the file that weren't understood.
Set<String>	getNames()
static Set<String>	getRepresentatives(Astral.AstralSet cutoff) Get a list of representatives' names for the specified ASTRAL cutoff.
static Set<String>	getRepresentatives(String id) Get a list of representatives' names for the specified ASTRAL cutoff.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

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 Detail

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