ScopFactory (biojava 5.3.0 API)

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`
`static String`	`VERSION_2_0_6`
`static String`	`VERSION_2_0_7`

Constructor Summary

Constructors
Constructor and Description

ScopFactory()

Constructors
Constructor and Description
`ScopFactory()`

Method Summary

All Methods Static Methods Concrete 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_7
```
public static final String VERSION_2_0_7
```
    See Also:
    
    Constant Field Values
  - VERSION_2_0_6
```
public static final String VERSION_2_0_6
```
    See Also:
    
    Constant Field Values
  - VERSION_2_0_5
```
public static final String VERSION_2_0_5
```
    See Also:
    
    Constant Field Values
  - VERSION_2_0_4
```
public static final String VERSION_2_0_4
```
    See Also:
    
    Constant Field Values
  - VERSION_2_0_3
```
public static final String VERSION_2_0_3
```
    See Also:
    
    Constant Field Values
  - VERSION_2_0_2
```
public static final String VERSION_2_0_2
```
    See Also:
    
    Constant Field Values
  - VERSION_2_0_1
```
public static final String VERSION_2_0_1
```
    See Also:
    
    Constant Field Values
  - VERSION_1_75C
```
public static final String VERSION_1_75C
```
    See Also:
    
    Constant Field Values
  - VERSION_1_75B
```
public static final String VERSION_1_75B
```
    See Also:
    
    Constant Field Values
  - VERSION_1_75A
```
public static final String VERSION_1_75A
```
    See Also:
    
    Constant Field Values
  - VERSION_1_75
```
public static final String VERSION_1_75
```
    See Also:
    
    Constant Field Values
  - VERSION_1_73
```
public static final String VERSION_1_73
```
    See Also:
    
    Constant Field Values
  - VERSION_1_71
```
public static final String VERSION_1_71
```
    See Also:
    
    Constant Field Values
  - VERSION_1_69
```
public static final String VERSION_1_69
```
    See Also:
    
    Constant Field Values
  - VERSION_1_67
```
public static final String VERSION_1_67
```
    See Also:
    
    Constant Field Values
  - VERSION_1_65
```
public static final String VERSION_1_65
```
    See Also:
    
    Constant Field Values
  - VERSION_1_63
```
public static final String VERSION_1_63
```
    See Also:
    
    Constant Field Values
  - VERSION_1_61
```
public static final String VERSION_1_61
```
    See Also:
    
    Constant Field Values
  - VERSION_1_59
```
public static final String VERSION_1_59
```
    See Also:
    
    Constant Field Values
  - VERSION_1_57
```
public static final String VERSION_1_57
```
    See Also:
    
    Constant Field Values
  - VERSION_1_55
```
public static final String VERSION_1_55
```
    See Also:
    
    Constant Field Values
  - LATEST_VERSION
```
public static final String LATEST_VERSION
```
    See Also:
    
    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 -

Class ScopFactory

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

VERSION_2_0_7

VERSION_2_0_6

VERSION_2_0_5

VERSION_2_0_4

VERSION_2_0_3

VERSION_2_0_2

VERSION_2_0_1

VERSION_1_75C

VERSION_1_75B

VERSION_1_75A

VERSION_1_75

VERSION_1_73

VERSION_1_71

VERSION_1_69

VERSION_1_67

VERSION_1_65

VERSION_1_63

VERSION_1_61

VERSION_1_59

VERSION_1_57

VERSION_1_55

LATEST_VERSION

Constructor Detail

ScopFactory

Method Detail

getSCOP

getSCOP

getSCOP

getSCOP

setScopDatabase

setScopDatabase

setScopDatabase