org.biojava.nbio.structure.ecod

Class EcodInstallation.EcodParser

java.lang.Object

org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser

Enclosing class:

EcodInstallation

public static class EcodInstallation.EcodParser
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	F_UNCLASSIFIED String for unclassified F-groups
static String	IS_DOMAIN_ASSEMBLY Deprecated way of indicating there is an assembly.
static String	IS_REPRESENTATIVE Indicates a manual representative
static String	NOT_DOMAIN_ASSEMBLY String for single-domain assemblies
static String	NOT_REPRESENTATIVE Indicates not a manual representative

Constructor Summary

Constructors

Constructor and Description
EcodParser(BufferedReader reader)
EcodParser(File file)
EcodParser(Reader reader)
EcodParser(String filename)

Method Summary

Modifier and Type	Method and Description
List<EcodDomain>	getDomains()
String	getVersion()

Methods inherited from class java.lang.Object

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

Field Detail

F_UNCLASSIFIED

public static final String F_UNCLASSIFIED

String for unclassified F-groups

See Also:

Constant Field Values

NOT_DOMAIN_ASSEMBLY

public static final String NOT_DOMAIN_ASSEMBLY

String for single-domain assemblies

See Also:

Constant Field Values

IS_DOMAIN_ASSEMBLY

public static final String IS_DOMAIN_ASSEMBLY

Deprecated way of indicating there is an assembly. replaced by the assembly id

See Also:

Constant Field Values

IS_REPRESENTATIVE

public static final String IS_REPRESENTATIVE

Indicates a manual representative

See Also:

Constant Field Values

NOT_REPRESENTATIVE

public static final String NOT_REPRESENTATIVE

Indicates not a manual representative

See Also:

Constant Field Values

Constructor Detail

EcodParser

public EcodParser(String filename)
           throws IOException

Throws:

IOException

EcodParser

public EcodParser(File file)
           throws IOException

Throws:

IOException

EcodParser

public EcodParser(Reader reader)
           throws IOException

Throws:

IOException

EcodParser

public EcodParser(BufferedReader reader)
           throws IOException

Throws:

IOException

Method Detail

getDomains

public List<EcodDomain> getDomains()

Returns:

a list of all EcodDomains

getVersion

public String getVersion()

Returns:

the requestedVersion for this file, or null if none was parsed