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 Details

  • 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
      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 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)