org.biojava.nbio.structure.scop

Class ScopFactory

java.lang.Object

org.biojava.nbio.structure.scop.ScopFactory

public class ScopFactory
extends Object

Controls the global ScopDatabase being used.

Defaults to a RemoteScopInstallation, which is fast for small numbers of queries. For many queries, using getSCOP(version,true) may be faster, since it makes only one network request.

Example: Fetch the structure corresponding to an old version of scop

 ScopInstallation scop = new ScopInstallation();
 scop.setScopVersion("1.69");
 ScopFactory.setScopDatabase(scop);
 AtomCache cache = new AtomCache();
 cache.setFetchFileEvenIfObsolete(true); //fetch older PDBs
 cache.setStrictSCOP(false); // correct simple errors in domain names
 Structure s = cache.getStructure("d3hbia_");

Author:

sbliven

Field Summary

Fields

Modifier and Type	Field and Description
static String	LATEST_VERSION
static String	VERSION_1_55
static String	VERSION_1_57
static String	VERSION_1_59
static String	VERSION_1_61
static String	VERSION_1_63
static String	VERSION_1_65
static String	VERSION_1_67
static String	VERSION_1_69
static String	VERSION_1_71
static String	VERSION_1_73
static String	VERSION_1_75
static String	VERSION_1_75A
static String	VERSION_1_75B
static String	VERSION_1_75C
static String	VERSION_2_0_1
static String	VERSION_2_0_2
static String	VERSION_2_0_3
static String	VERSION_2_0_4
static String	VERSION_2_0_5

Constructor Summary

Constructors

Constructor and Description
ScopFactory()

Method Summary

Methods

Modifier and Type	Method and Description
static ScopDatabase	getSCOP() Get the current default instance for the default version
static ScopDatabase	getSCOP(boolean forceLocalData)
static ScopDatabase	getSCOP(String version) requests a particular version of SCOP.
static ScopDatabase	getSCOP(String version, boolean forceLocalData) Gets an instance of the specified scop version.
static void	setScopDatabase(ScopDatabase scop) Set the default scop version and instance
static void	setScopDatabase(String version) Set the default scop version
static void	setScopDatabase(String version, boolean forceLocalData) Set the default scop version

Methods inherited from class java.lang.Object

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

Field Detail

VERSION_2_0_5

public static final String VERSION_2_0_5

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Constant Field Values

VERSION_2_0_4

public static final String VERSION_2_0_4

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Constant Field Values

VERSION_2_0_3

public static final String VERSION_2_0_3

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Constant Field Values

VERSION_2_0_2

public static final String VERSION_2_0_2

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Constant Field Values

VERSION_2_0_1

public static final String VERSION_2_0_1

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Constant Field Values

VERSION_1_75C

public static final String VERSION_1_75C

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Constant Field Values

VERSION_1_75B

public static final String VERSION_1_75B

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Constant Field Values

VERSION_1_75A

public static final String VERSION_1_75A

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Constant Field Values

VERSION_1_75

public static final String VERSION_1_75

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Constant Field Values

VERSION_1_73

public static final String VERSION_1_73

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Constant Field Values

VERSION_1_71

public static final String VERSION_1_71

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Constant Field Values

VERSION_1_69

public static final String VERSION_1_69

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Constant Field Values

VERSION_1_67

public static final String VERSION_1_67

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Constant Field Values

VERSION_1_65

public static final String VERSION_1_65

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Constant Field Values

VERSION_1_63

public static final String VERSION_1_63

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Constant Field Values

VERSION_1_61

public static final String VERSION_1_61

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Constant Field Values

VERSION_1_59

public static final String VERSION_1_59

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Constant Field Values

VERSION_1_57

public static final String VERSION_1_57

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Constant Field Values

VERSION_1_55

public static final String VERSION_1_55

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Constant Field Values

LATEST_VERSION

public static final String LATEST_VERSION

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Constant Field Values

Constructor Detail

ScopFactory

public ScopFactory()

Method Detail

getSCOP

public static ScopDatabase getSCOP()

Get the current default instance for the default version

Returns:

getSCOP

public static ScopDatabase getSCOP(boolean forceLocalData)

Parameters:

forceLocalData - Whether to use a local installation or a remote installation

Returns:

See Also:

getSCOP(String, boolean)

getSCOP

public static ScopDatabase getSCOP(String version)

requests a particular version of SCOP. Where possible, this will be the current default instance. Otherwise a new instance will be created.

Parameters:

version -

Returns:

getSCOP

public static ScopDatabase getSCOP(String version,
                   boolean forceLocalData)

Gets an instance of the specified scop version.

The particular implementation returned is influenced by the forceLocalData parameter. When false, the instance returned will generally be a RemoteScopInstallation, although this may be influenced by previous calls to this class. When true, the result is guaranteed to implement LocalScopDatabase (generally a BerkeleyScopInstallation).

Note that

Parameters:

version - A version number, such as VERSION_1_75A

forceLocalData - Whether to use a local installation or a remote installation

Returns:

an

setScopDatabase

public static void setScopDatabase(String version)

Set the default scop version

Parameters:

version - A version number, such as VERSION_1_75A

setScopDatabase

public static void setScopDatabase(String version,
                   boolean forceLocalData)

Set the default scop version

Parameters:

version - A version number, such as VERSION_1_75A

forceLocalData - Whether to use a local installation or a remote installation

setScopDatabase

public static void setScopDatabase(ScopDatabase scop)

Set the default scop version and instance

Parameters:

scop -