org.biojava.bio.structure.cath
Class CathInstallation

java.lang.Object
  org.biojava.bio.structure.cath.CathInstallation

All Implemented Interfaces:

CathDatabase

public class CathInstallation
extends java.lang.Object
implements CathDatabase

Author:

Daniel Asarnow

Field Summary

static java.lang.String	CATH_DOWNLOAD
static java.lang.String	DEFAULT_VERSION
static java.lang.String	domainDescriptionFileName
static java.lang.String	domainListFileName
static java.lang.String	domallFileName
static java.lang.String	FILESPLIT
static java.lang.String	NEWLINE
static java.lang.String	nodeListFileName

Constructor Summary

CathInstallation()

CathInstallation(java.lang.String cacheLocation)

CathInstallation(java.lang.String cacheLocation, boolean usingCDDF, boolean parseCF)

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VERSION

public static final java.lang.String DEFAULT_VERSION

See Also:

Constant Field Values

domainListFileName

public static final java.lang.String domainListFileName

See Also:

Constant Field Values

domainDescriptionFileName

public static final java.lang.String domainDescriptionFileName

See Also:

Constant Field Values

nodeListFileName

public static final java.lang.String nodeListFileName

See Also:

Constant Field Values

domallFileName

public static final java.lang.String domallFileName

See Also:

Constant Field Values

CATH_DOWNLOAD

public static final java.lang.String CATH_DOWNLOAD

See Also:

Constant Field Values

NEWLINE

public static final java.lang.String NEWLINE

FILESPLIT

public static final java.lang.String FILESPLIT

Constructor Detail

CathInstallation

public CathInstallation(java.lang.String cacheLocation,
                        boolean usingCDDF,
                        boolean parseCF)

CathInstallation

public CathInstallation(java.lang.String cacheLocation)

CathInstallation

public CathInstallation()

Method Detail

getDomainListFileName

public java.lang.String getDomainListFileName()

getDomainDescriptionFileName

public java.lang.String getDomainDescriptionFileName()

getNodeListFileName

public java.lang.String getNodeListFileName()

getDomallFileName

public java.lang.String getDomallFileName()

getCathDownloadUrl

public java.lang.String getCathDownloadUrl()

setCathDownloadUrl

public void setCathDownloadUrl(java.lang.String cathDownloadUrl)

getCacheLocation

public java.lang.String getCacheLocation()

setCacheLocation

public void setCacheLocation(java.lang.String cacheLocation)

getInstalledDomainList

public java.util.concurrent.atomic.AtomicBoolean getInstalledDomainList()

setInstalledDomainList

public void setInstalledDomainList(java.util.concurrent.atomic.AtomicBoolean installedDomainList)

getInstalledDomainDescription

public java.util.concurrent.atomic.AtomicBoolean getInstalledDomainDescription()

setInstalledDomainDescription

public void setInstalledDomainDescription(java.util.concurrent.atomic.AtomicBoolean installedDomainDescription)

getInstalledNodeList

public java.util.concurrent.atomic.AtomicBoolean getInstalledNodeList()

getInstalledDomall

public java.util.concurrent.atomic.AtomicBoolean getInstalledDomall()

setInstalledNodeList

public void setInstalledNodeList(java.util.concurrent.atomic.AtomicBoolean installedNodeList)

setInstalledDomall

public void setInstalledDomall(java.util.concurrent.atomic.AtomicBoolean installedDomall)

getCathVersion

public java.lang.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(java.lang.String nodeId)

Description copied from interface: CathDatabase

Return the CathNode for a node ID.

Specified by:

getCathNode in interface CathDatabase

Returns:

CATH node

getByCategory

public java.util.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

Returns:

CATH descriptions

filterByCathCode

public java.util.List<CathDomain> filterByCathCode(java.lang.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

Returns:

CATH descriptions

getTree

public java.util.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

Returns:

CATH sub-tree

filterByNodeName

public java.util.List<CathDomain> filterByNodeName(java.lang.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

Returns:

CATH domains

filterByDescription

public java.util.List<CathDomain> filterByDescription(java.lang.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

Returns:

CATH descriptions

getDescriptionByNodeId

public CathDomain getDescriptionByNodeId(java.lang.String nodeId)

Description copied from interface: CathDatabase

Return CATH description for node representative by node ID.

Specified by:

getDescriptionByNodeId in interface CathDatabase

Returns:

CATH description

getDomainsForPdb

public java.util.List<CathDomain> getDomainsForPdb(java.lang.String pdbId)

Description copied from interface: CathDatabase

Return all CATH domains for a PDB ID.

Specified by:

getDomainsForPdb in interface CathDatabase

Returns:

CATH domains

getDomainByCathId

public CathDomain getDomainByCathId(java.lang.String cathId)

Description copied from interface: CathDatabase

Return CATH domain for CATH domain ID.

Specified by:

getDomainByCathId in interface CathDatabase

Returns:

CATH domain

getDescriptionByCathId

public CathDomain getDescriptionByCathId(java.lang.String cathId)

Description copied from interface: CathDatabase

Return CATH description for CATH domain ID.

Specified by:

getDescriptionByCathId in interface CathDatabase

Returns:

getDomainsByNodeId

public java.util.List<CathDomain> getDomainsByNodeId(java.lang.String nodeId)

Description copied from interface: CathDatabase

Return all CATH domains for a particular CATH node.

Specified by:

getDomainsByNodeId in interface CathDatabase

Returns:

getFragmentsByPdbId

public java.util.List<CathFragment> getFragmentsByPdbId(java.lang.String pdbId)

Specified by:

getFragmentsByPdbId in interface CathDatabase

downloadFileFromRemote

protected void downloadFileFromRemote(java.net.URL remoteURL,
                                      java.io.File localFile)
                               throws java.io.FileNotFoundException,
                                      java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadDomainListFile

protected void downloadDomainListFile()
                               throws java.io.FileNotFoundException,
                                      java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadDomainDescriptionFile

protected void downloadDomainDescriptionFile()
                                      throws java.io.FileNotFoundException,
                                             java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadNodeListFile

protected void downloadNodeListFile()
                             throws java.io.FileNotFoundException,
                                    java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadDomallFile

protected void downloadDomallFile()
                           throws java.io.IOException

Throws:

java.io.IOException

ensureDomainListInstalled

public void ensureDomainListInstalled()

ensureDomainDescriptionInstalled

public void ensureDomainDescriptionInstalled()

ensureNodeListInstalled

public void ensureNodeListInstalled()

ensureDomallInstalled

public void ensureDomallInstalled()