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 Description

static class EcodInstallation.EcodParser

Field Summary

Fields
Modifier and Type Field Description

static String DEFAULT_VERSION

static String DOMAINS_PATH

static Pattern ECOD_RE

static String ECOD_URL

Constructor Summary

Constructors
Constructor Description

EcodInstallation()

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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)
```

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

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

Class EcodInstallation

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_VERSION

ECOD_URL

DOMAINS_PATH

ECOD_RE

Constructor Detail

EcodInstallation

EcodInstallation

Method Detail

getDomainsForPdb

filterByHierarchy

getDomainsById

getAllDomains

clear

getVersion

getUrl

setUrl

getCacheLocation

setCacheLocation

ensureDomainsFileInstalled

getUpdateFrequency

setUpdateFrequency

toString

main