Package org.biojava.nbio.structure.cath

Class CathInstallation

java.lang.Object

org.biojava.nbio.structure.cath.CathInstallation

All Implemented Interfaces:

CathDatabase

public class CathInstallation
extends Object
implements CathDatabase

Author:

Daniel Asarnow

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CATH_DOWNLOAD_ALL_RELEASES_DIR
static final String	CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR
static final String	CATH_DOWNLOAD_URL
static final String	DEFAULT_VERSION
static final String	domainDescriptionFileName
static final String	domainListFileName
static final String	domallFileName
static final String	FILESPLIT
static final String	NEWLINE
static final String	nodeListFileName

Constructor Summary

Constructors

Constructor	Description
CathInstallation()
CathInstallation(String cacheLocation)
CathInstallation(String cacheLocation, boolean usingCDDF, boolean parseCF)

Method Summary

Modifier and Type	Method	Description
protected void	downloadDomainDescriptionFile()
protected void	downloadDomainListFile()
protected void	downloadDomallFile()
protected void	downloadFileFromRemote(URL remoteURL, File localFile)
protected void	downloadNodeListFile()
void	ensureDomainDescriptionInstalled()
void	ensureDomainListInstalled()
void	ensureDomallInstalled()
void	ensureNodeListInstalled()
List<CathDomain>	filterByCathCode(String query)	Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query.
List<CathDomain>	filterByDescription(String query)	Return list of CATH descriptions whose descriptions (name field) starts with the query.
List<CathDomain>	filterByNodeName(String query)	Return list of CATH domains whose node name (e.g.
List<CathDomain>	getByCategory(CathCategory category)	Return list of CATH descriptions for node representatives at a CATH category (e.g.
String	getCacheLocation()
String	getCathDownloadUrl()
CathNode	getCathNode(String nodeId)	Return the CathNode for a node ID.
String	getCathVersion()	Return the CATH release version.
CathDomain	getDescriptionByCathId(String cathId)	Return CATH description for CATH domain ID.
CathDomain	getDescriptionByNodeId(String nodeId)	Return CATH description for node representative by node ID.
CathDomain	getDomainByCathId(String cathId)	Return CATH domain for CATH domain ID.
String	getDomainDescriptionFileName()
String	getDomainListFileName()
List<CathDomain>	getDomainsByNodeId(String nodeId)	Return all CATH domains for a particular CATH node.
List<CathDomain>	getDomainsForPdb(String pdbId)	Return all CATH domains for a PDB ID.
String	getDomallFileName()
List<CathFragment>	getFragmentsByPdbId(String pdbId)
AtomicBoolean	getInstalledDomainDescription()
AtomicBoolean	getInstalledDomainList()
AtomicBoolean	getInstalledDomall()
AtomicBoolean	getInstalledNodeList()
String	getNodeListFileName()
List<CathNode>	getTree(CathDomain domain)	Return the CATH sub-tree for a particular domain.
void	setCacheLocation(String cacheLocation)
void	setCathDownloadUrl(String cathDownloadUrl)
void	setCathVersion(String cathVersion)
void	setInstalledDomainDescription(AtomicBoolean installedDomainDescription)
void	setInstalledDomainList(AtomicBoolean installedDomainList)
void	setInstalledDomall(AtomicBoolean installedDomall)
void	setInstalledNodeList(AtomicBoolean installedNodeList)

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_VERSION

public static final String DEFAULT_VERSION

See Also:

• Constant Field Values

domainListFileName

public static final String domainListFileName

See Also:

• Constant Field Values

domainDescriptionFileName

public static final String domainDescriptionFileName

See Also:

• Constant Field Values

nodeListFileName

public static final String nodeListFileName

See Also:

• Constant Field Values

domallFileName

public static final String domallFileName

See Also:

• Constant Field Values

CATH_DOWNLOAD_URL

public static final String CATH_DOWNLOAD_URL

See Also:

• Constant Field Values

CATH_DOWNLOAD_ALL_RELEASES_DIR

public static final String CATH_DOWNLOAD_ALL_RELEASES_DIR

See Also:

• Constant Field Values

CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR

public static final String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR

See Also:

• Constant Field Values

NEWLINE

public static final String NEWLINE

FILESPLIT

public static final String FILESPLIT

Constructor Details

CathInstallation

public CathInstallation(String cacheLocation,
 boolean usingCDDF,
 boolean parseCF)

CathInstallation

public CathInstallation(String cacheLocation)

CathInstallation

public CathInstallation()

Method Details

getDomainListFileName

public String getDomainListFileName()

getDomainDescriptionFileName

public String getDomainDescriptionFileName()

getNodeListFileName

public String getNodeListFileName()

getDomallFileName

public String getDomallFileName()

getCathDownloadUrl

public String getCathDownloadUrl()

setCathDownloadUrl

public void setCathDownloadUrl(String cathDownloadUrl)

getCacheLocation

public String getCacheLocation()

setCacheLocation

public void setCacheLocation(String cacheLocation)

getInstalledDomainList

public AtomicBoolean getInstalledDomainList()

setInstalledDomainList

public void setInstalledDomainList(AtomicBoolean installedDomainList)

getInstalledDomainDescription

public AtomicBoolean getInstalledDomainDescription()

setInstalledDomainDescription

public void setInstalledDomainDescription(AtomicBoolean installedDomainDescription)

getInstalledNodeList

public AtomicBoolean getInstalledNodeList()

getInstalledDomall

public AtomicBoolean getInstalledDomall()

setInstalledNodeList

public void setInstalledNodeList(AtomicBoolean installedNodeList)

setInstalledDomall

public void setInstalledDomall(AtomicBoolean installedDomall)

getCathVersion

public String getCathVersion()

Description copied from interface: CathDatabase

Return the CATH release version.

Specified by:

getCathVersion in interface CathDatabase

Returns:

CATH version

getCathNode

public CathNode getCathNode(String nodeId)

Description copied from interface: CathDatabase

Return the CathNode for a node ID.

Specified by:

getCathNode in interface CathDatabase

Parameters:

nodeId -

Returns:

CATH node

getByCategory

public List<CathDomain> getByCategory(CathCategory category)

Description copied from interface: CathDatabase

Return list of CATH descriptions for node representatives at a CATH category (e.g. "T").

Specified by:

getByCategory in interface CathDatabase

Parameters:

category -

Returns:

CATH descriptions

filterByCathCode

public List<CathDomain> filterByCathCode(String query)

Description copied from interface: CathDatabase

Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query. This is currently redundant with getDescriptionsByNodeId.

Specified by:

filterByCathCode in interface CathDatabase

Parameters:

query -

Returns:

CATH descriptions

getTree

public List<CathNode> getTree(CathDomain domain)

Description copied from interface: CathDatabase

Return the CATH sub-tree for a particular domain.

Specified by:

getTree in interface CathDatabase

Parameters:

domain -

Returns:

CATH sub-tree

filterByNodeName

public List<CathDomain> filterByNodeName(String query)

Description copied from interface: CathDatabase

Return list of CATH domains whose node name (e.g. Orthogonal Bundle) starts with the query.

Specified by:

filterByNodeName in interface CathDatabase

Parameters:

query -

Returns:

CATH domains

filterByDescription

public List<CathDomain> filterByDescription(String query)

Description copied from interface: CathDatabase

Return list of CATH descriptions whose descriptions (name field) starts with the query.

Specified by:

filterByDescription in interface CathDatabase

Parameters:

query -

Returns:

CATH descriptions

getDescriptionByNodeId

public CathDomain getDescriptionByNodeId(String nodeId)

Description copied from interface: CathDatabase

Return CATH description for node representative by node ID.

Specified by:

getDescriptionByNodeId in interface CathDatabase

Parameters:

nodeId -

Returns:

CATH description

getDomainsForPdb

public List<CathDomain> getDomainsForPdb(String pdbId)

Description copied from interface: CathDatabase

Return all CATH domains for a PDB ID.

Specified by:

getDomainsForPdb in interface CathDatabase

Parameters:

pdbId -

Returns:

CATH domains

getDomainByCathId

public CathDomain getDomainByCathId(String cathId)

Description copied from interface: CathDatabase

Return CATH domain for CATH domain ID.

Specified by:

getDomainByCathId in interface CathDatabase

Parameters:

cathId -

Returns:

CATH domain

getDescriptionByCathId

public CathDomain getDescriptionByCathId(String cathId)

Description copied from interface: CathDatabase

Return CATH description for CATH domain ID.

Specified by:

getDescriptionByCathId in interface CathDatabase

Parameters:

cathId -

Returns:

getDomainsByNodeId

public List<CathDomain> getDomainsByNodeId(String nodeId)

Description copied from interface: CathDatabase

Return all CATH domains for a particular CATH node.

Specified by:

getDomainsByNodeId in interface CathDatabase

Parameters:

nodeId -

Returns:

getFragmentsByPdbId

public List<CathFragment> getFragmentsByPdbId(String pdbId)

Specified by:

getFragmentsByPdbId in interface CathDatabase

downloadFileFromRemote

protected void downloadFileFromRemote(URL remoteURL,
 File localFile)
                               throws IOException

Throws:

IOException

downloadDomainListFile

protected void downloadDomainListFile()
                               throws IOException

Throws:

IOException

downloadDomainDescriptionFile

protected void downloadDomainDescriptionFile()
                                      throws IOException

Throws:

IOException

downloadNodeListFile

protected void downloadNodeListFile()
                             throws IOException

Throws:

IOException

downloadDomallFile

protected void downloadDomallFile()
                           throws IOException

Throws:

IOException

ensureDomainListInstalled

public void ensureDomainListInstalled()

ensureDomainDescriptionInstalled

public void ensureDomainDescriptionInstalled()

ensureNodeListInstalled

public void ensureNodeListInstalled()

ensureDomallInstalled

public void ensureDomallInstalled()

setCathVersion

public void setCathVersion(String cathVersion)