Package org.biojava.nbio.structure.cath

Class CathInstallation

  • All Implemented Interfaces:
    CathDatabase
    public class CathInstallation
extends java.lang.Object
implements CathDatabase
    Author:
    Daniel Asarnow

    • Field Detail

      • 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

      • CATH_DOWNLOAD_URL

        public static final java.lang.String CATH_DOWNLOAD_URL
        See Also:
        Constant Field Values

      • CATH_DOWNLOAD_ALL_RELEASES_DIR

        public static final java.lang.String CATH_DOWNLOAD_ALL_RELEASES_DIR
        See Also:
        Constant Field Values

      • CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR

        public static final java.lang.String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR
        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

      • 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:

      • downloadFileFromRemote

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

      • downloadDomainListFile

        protected void downloadDomainListFile()
                               throws java.io.IOException
        Throws:
        java.io.IOException

      • downloadDomainDescriptionFile

        protected void downloadDomainDescriptionFile()
                                      throws java.io.IOException
        Throws:
        java.io.IOException

      • downloadNodeListFile

        protected void downloadNodeListFile()
                             throws java.io.IOException
        Throws:
        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()

      • setCathVersion

        public void setCathVersion​(java.lang.String cathVersion)