CathInstallation (biojava 4.2.1 API)

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 and Description
`static String`	`CATH_DOWNLOAD`
`static String`	`DEFAULT_VERSION`
`static String`	`domainDescriptionFileName`
`static String`	`domainListFileName`
`static String`	`domallFileName`
`static String`	`FILESPLIT`
`static String`	`NEWLINE`
`static String`	`nodeListFileName`

Constructor Summary

Constructors
Constructor and Description
`CathInstallation()`
`CathInstallation(String cacheLocation)`
`CathInstallation(String cacheLocation, boolean usingCDDF, boolean parseCF)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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.
`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 Detail
  - DEFAULT_VERSION
```
public static final String DEFAULT_VERSION
```
  - 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
```
public static final String CATH_DOWNLOAD
```
    See Also:
    
    Constant Field Values
  - NEWLINE
```
public static final String NEWLINE
```
  - FILESPLIT
```
public static final String FILESPLIT
```
- Constructor Detail
  - CathInstallation
```
public CathInstallation(String cacheLocation,
                        boolean usingCDDF,
                        boolean parseCF)
```
  - CathInstallation
```
public CathInstallation(String cacheLocation)
```
  - CathInstallation
```
public CathInstallation()
```
- Method Detail
  - 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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    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
    
    Returns:
  - getFragmentsByPdbId
```
public List<CathFragment> getFragmentsByPdbId(String pdbId)
```
    Specified by:
    
    getFragmentsByPdbId in interface CathDatabase
  - downloadFileFromRemote
```
protected void downloadFileFromRemote(URL remoteURL,
                                      File localFile)
                               throws FileNotFoundException,
                                      IOException
```
    Throws:
    
    FileNotFoundException
    
    IOException
  - downloadDomainListFile
```
protected void downloadDomainListFile()
                               throws FileNotFoundException,
                                      IOException
```
    Throws:
    
    FileNotFoundException
    
    IOException
  - downloadDomainDescriptionFile
```
protected void downloadDomainDescriptionFile()
                                      throws FileNotFoundException,
                                             IOException
```
    Throws:
    
    FileNotFoundException
    
    IOException
  - downloadNodeListFile
```
protected void downloadNodeListFile()
                             throws FileNotFoundException,
                                    IOException
```
    Throws:
    
    FileNotFoundException
    
    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)
```

Class CathInstallation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_VERSION

domainListFileName

domainDescriptionFileName

nodeListFileName

domallFileName

CATH_DOWNLOAD

NEWLINE

FILESPLIT

Constructor Detail

CathInstallation

CathInstallation

CathInstallation

Method Detail

getDomainListFileName

getDomainDescriptionFileName

getNodeListFileName

getDomallFileName

getCathDownloadUrl

setCathDownloadUrl

getCacheLocation

setCacheLocation

getInstalledDomainList

setInstalledDomainList

getInstalledDomainDescription

setInstalledDomainDescription

getInstalledNodeList

getInstalledDomall

setInstalledNodeList

setInstalledDomall

getCathVersion

getCathNode

getByCategory

filterByCathCode

getTree

filterByNodeName

filterByDescription

getDescriptionByNodeId

getDomainsForPdb

getDomainByCathId

getDescriptionByCathId

getDomainsByNodeId

getFragmentsByPdbId

downloadFileFromRemote

downloadDomainListFile

downloadDomainDescriptionFile

downloadNodeListFile

downloadDomallFile

ensureDomainListInstalled

ensureDomainDescriptionInstalled

ensureNodeListInstalled

ensureDomallInstalled

setCathVersion