org.biojava.nbio.structure.ecod

Class EcodInstallation

java.lang.Object

org.biojava.nbio.structure.ecod.EcodInstallation

All Implemented Interfaces:

EcodDatabase

public class EcodInstallation
extends Object
implements EcodDatabase

Provides access to the Evolutionary Classification of Protein Domains (ECOD). The preferred mechanism for obtaining instances of this class is through the EcodFactory class. Reference: H. Cheng, R. D. Schaeffer, Y. Liao, L. N. Kinch, J. Pei, S. Shi, B. H.\ Kim, N. V. Grishin. (2014) ECOD: An evolutionary classification of protein domains. PLoS Comput Biol 10(12): e1003926. http://prodata.swmed.edu/ecod/

Author:

Spencer Bliven

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	EcodInstallation.EcodParser

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_VERSION
static String	DOMAINS_PATH
static Pattern	ECOD_RE
static String	ECOD_URL

Constructor Summary

Constructors

Constructor and Description
EcodInstallation()
EcodInstallation(String cacheLocation, String version) Use EcodFactory to create instances.

Method Summary

Modifier and Type	Method and Description
void	clear() Clears all domains, requiring the file to be reparsed for subsequent accesses
void	ensureDomainsFileInstalled() Blocks until ECOD domains file has been downloaded and parsed.
List<EcodDomain>	filterByHierarchy(String hierarchy) Get a list of domains within a particular level of the hierarchy
List<EcodDomain>	getAllDomains() Get all ECOD domains
String	getCacheLocation() Get the location of the cache directory (usually set to the PDB_CACHE_DIR property).
EcodDomain	getDomainsById(String ecodId) Get a particular ECOD domain by the domain ID (e.g.
List<EcodDomain>	getDomainsForPdb(String pdbId) public EcodInstallation(String cacheLocation) { this( cacheLocation, DEFAULT_VERSION ); } /** Get a list of all ECOD domains for a particular PDB ID
Integer	getUpdateFrequency() The expected ECOD update frequency determines whether the version "latest" should be re-downloaded
String	getUrl() Get the top-level ECOD server URL.
String	getVersion() Return the ECOD version, as parsed from the file.
static void	main(String[] args)
void	setCacheLocation(String cacheLocation) Set an alternate download location for files
void	setUpdateFrequency(Integer updateFrequency) The "latest" version will be re-downloaded if it is older than getUpdateFrequency() days.
void	setUrl(String url) Specify a different mirror for the ECOD server.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VERSION

public static final String DEFAULT_VERSION

See Also:

Constant Field Values

ECOD_URL

public static final String ECOD_URL

See Also:

Constant Field Values

DOMAINS_PATH

public static final String DOMAINS_PATH

See Also:

Constant Field Values

ECOD_RE

public static final Pattern ECOD_RE

Constructor Detail

EcodInstallation

public EcodInstallation(String cacheLocation,
                        String version)

Use EcodFactory to create instances. The instantiation of multiple installations at the same path can lead to race conditions when downloading files.

Parameters:

cacheLocation - Location to save files, typically from the PDB_CACHE_DIR parameter

requestedVersion - ECOD requestedVersion to fetch

EcodInstallation

public EcodInstallation()

See Also:

EcodFactory.getEcodDatabase()

Method Detail

getDomainsForPdb

public List<EcodDomain> getDomainsForPdb(String pdbId)
                                  throws IOException

public EcodInstallation(String cacheLocation) { this( cacheLocation, DEFAULT_VERSION ); } /** Get a list of all ECOD domains for a particular PDB ID

Specified by:

getDomainsForPdb in interface EcodDatabase

Parameters:

pdbId -

Returns:

the list of domains, or null if no matching domains were found

Throws:

IOException

filterByHierarchy

public List<EcodDomain> filterByHierarchy(String hierarchy)
                                   throws IOException

Get a list of domains within a particular level of the hierarchy

Specified by:

filterByHierarchy in interface EcodDatabase

Parameters:

hierarchy - A dot-separated list giving the X-group, H-group, and/or T-group (e.g. "1.1" for all members of the RIFT-related H-group)

Returns:

Throws:

IOException

getDomainsById

public EcodDomain getDomainsById(String ecodId)
                          throws IOException

Get a particular ECOD domain by the domain ID (e.g. "e4hhbA1")

Specified by:

getDomainsById in interface EcodDatabase

Parameters:

ecodId -

Returns:

Throws:

IOException

getAllDomains

public List<EcodDomain> getAllDomains()
                               throws IOException

Get all ECOD domains

Specified by:

getAllDomains in interface EcodDatabase

Returns:

Throws:

IOException

clear

public void clear()

Clears all domains, requiring the file to be reparsed for subsequent accesses

getVersion

public String getVersion()
                  throws IOException

Return the ECOD version, as parsed from the file. Note that this may differ from the version requested in the constructor for the special case of "latest"

Specified by:

getVersion in interface EcodDatabase

Returns:

the ECOD version

Throws:

IOException - If an error occurs while downloading or parsing the file

getUrl

public String getUrl()

Get the top-level ECOD server URL. Defaults to "http://prodata.swmed.edu"

Returns:

the url to the ecod server

setUrl

public void setUrl(String url)

Specify a different mirror for the ECOD server.

Parameters:

urlFormat - the urlFormat to set

getCacheLocation

public String getCacheLocation()

Get the location of the cache directory (usually set to the PDB_CACHE_DIR property). ECOD files will be downloaded to this directory

Returns:

setCacheLocation

public void setCacheLocation(String cacheLocation)

Set an alternate download location for files

Parameters:

cacheLocation -

ensureDomainsFileInstalled

public void ensureDomainsFileInstalled()
                                throws IOException

Blocks until ECOD domains file has been downloaded and parsed. This may be useful in multithreaded environments.

Throws:

IOException

getUpdateFrequency

public Integer getUpdateFrequency()

The expected ECOD update frequency determines whether the version "latest" should be re-downloaded

Returns:

the expected ECOD update frequency, in days

setUpdateFrequency

public void setUpdateFrequency(Integer updateFrequency)

The "latest" version will be re-downloaded if it is older than getUpdateFrequency() days. Setting this to null disables re-downloading (delete $PDB_CACHE_DIR/ecod.latest.domains.txt manually to force updating). Setting to 0 will force downloading for every program execution.

Parameters:

updateFrequency - the updateFrequency to set

toString

public String toString()

Overrides:

toString in class Object

main

public static void main(String[] args)