org.biojava.nbio.structure.scop

Class ScopInstallation

java.lang.Object

org.biojava.nbio.structure.scop.ScopInstallation

All Implemented Interfaces:

LocalScopDatabase, ScopDatabase

Direct Known Subclasses:

BerkeleyScopInstallation

public class ScopInstallation
extends Object
implements LocalScopDatabase

This class provides access to the SCOP protein structure classification. For more information about SCOP see here:

• SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/
• Introduction: http://scop.mrc-lmb.cam.ac.uk/scop/intro.html
• SCOP parsable files: http://scop.mrc-lmb.cam.ac.uk/scop/parse/

This class can automatically download missing files from the SCOP classification.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	claFileName
static String	comFileName
static String	DEFAULT_VERSION
static String	desFileName
static String	FILESPLIT
static String	hieFileName
static String	NEWLINE
static String	SCOP_DOWNLOAD
static String	SCOP_DOWNLOAD_ALTERNATE
protected String	scopVersion

Constructor Summary

Constructors

Constructor and Description
ScopInstallation() Create a new SCOP installation, downloading the file to "the right place".
ScopInstallation(String cacheLocation) Create a new SCOP installation.

Method Summary

Modifier and Type	Method and Description
void	addMirror(String scopDownloadURL)
protected void	downloadClaFile()
protected void	downloadComFile()
protected void	downloadDesFile()
protected void	downloadFileFromRemote(URL remoteURL, File localFile)
protected void	downloadHieFile()
void	ensureClaInstalled()
void	ensureComInstalled()
void	ensureDesInstalled()
void	ensureHieInstalled()
List<ScopDescription>	filterByClassificationId(String query) Get all scop descriptions that start with a classification ID, e.g.
List<ScopDescription>	filterByDescription(String query) Get all scop descriptions that start with a certain name.
List<ScopDomain>	filterByDomainName(String query) search through SCOP and filter based on domain name
List<ScopDescription>	getByCategory(ScopCategory category) Get all records of a particular classification.
String	getCacheLocation()
protected String	getClaFilename()
protected String	getComFilename()
List<String>	getComments(int sunid) Get comments about a SCOP domain by its sunid
protected String	getDesFilename()
ScopDomain	getDomainByScopID(String scopId) get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
List<ScopDomain>	getDomainsForPDB(String pdbId) Get a list of ScopDomains that have been assigned to a PDB ID
protected String	getHieFilename()
List<ScopMirror>	getMirrors()
ScopDescription	getScopDescriptionBySunid(int sunid) Return the SCOP description for a node in the hierarchy by its "sunid" id.
List<ScopDomain>	getScopDomainsBySunid(Integer sunid) Get a SCOP domain by its sunid
String	getScopDownloadURL() Deprecated.
ScopNode	getScopNode(int sunid) Access a particular ScopNode.
String	getScopVersion() Returns the SCOP version
List<ScopNode>	getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.
void	nullifyComments() Removes all of the comments (dir.com file) in order to free memory.
void	setCacheLocation(String cacheLocation)
void	setScopDownloadURL(String scopDownloadURL) Deprecated. Use addMirror(java.lang.String) instead
void	setScopVersion(String scopVersion) Sets the scop version used.

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

See Also:

Constant Field Values

scopVersion

protected String scopVersion

claFileName

public static final String claFileName

See Also:

Constant Field Values

desFileName

public static final String desFileName

See Also:

Constant Field Values

hieFileName

public static final String hieFileName

See Also:

Constant Field Values

comFileName

public static final String comFileName

See Also:

Constant Field Values

SCOP_DOWNLOAD

public static final String SCOP_DOWNLOAD

See Also:

Constant Field Values

SCOP_DOWNLOAD_ALTERNATE

public static final String SCOP_DOWNLOAD_ALTERNATE

See Also:

Constant Field Values

NEWLINE

public static final String NEWLINE

FILESPLIT

public static final String FILESPLIT

Constructor Detail

ScopInstallation

public ScopInstallation(String cacheLocation)

Create a new SCOP installation.

Parameters:

cacheLocation - where the SCOP files are stored. If they can't be found at that location they will get automatically downloaded and installed there.

ScopInstallation

public ScopInstallation()

Create a new SCOP installation, downloading the file to "the right place". This will first check for system properties or environmental variables called UserConfiguration.PDB_CACHE_DIR, or else will use a temporary directory

Method Detail

nullifyComments

public void nullifyComments()

Removes all of the comments (dir.com file) in order to free memory. The file will need to be reloaded if getComments(int) is called subsequently.

ensureClaInstalled

public void ensureClaInstalled()
                        throws IOException

Throws:

IOException

ensureDesInstalled

public void ensureDesInstalled()
                        throws IOException

Throws:

IOException

ensureComInstalled

public void ensureComInstalled()
                        throws IOException

Throws:

IOException

ensureHieInstalled

public void ensureHieInstalled()
                        throws IOException

Throws:

IOException

getByCategory

public List<ScopDescription> getByCategory(ScopCategory category)

Description copied from interface: ScopDatabase

Get all records of a particular classification.

Specified by:

getByCategory in interface ScopDatabase

Parameters:

category - e.g. "superfamily"

Returns:

all records of this type

filterByClassificationId

public List<ScopDescription> filterByClassificationId(String query)

Description copied from interface: ScopDatabase

Get all scop descriptions that start with a classification ID, e.g. b.1.18

Specified by:

filterByClassificationId in interface ScopDatabase

Returns:

list of scop descriptions

getTree

public List<ScopNode> getTree(ScopDomain domain)

Description copied from interface: ScopDatabase

get the SCOP sub-tree for a particular domain.

Specified by:

getTree in interface ScopDatabase

Returns:

list of ScopNodes providing the path to this domain

filterByDomainName

public List<ScopDomain> filterByDomainName(String query)

Description copied from interface: ScopDatabase

search through SCOP and filter based on domain name

Specified by:

filterByDomainName in interface ScopDatabase

Parameters:

query - a (part) of a name

Returns:

list of matchin ScopDomains

filterByDescription

public List<ScopDescription> filterByDescription(String query)
                                          throws ScopIOException

Description copied from interface: ScopDatabase

Get all scop descriptions that start with a certain name. e.g. Globin

Specified by:

filterByDescription in interface ScopDatabase

Returns:

list of scop descriptions

Throws:

ScopIOException

getScopDescriptionBySunid

public ScopDescription getScopDescriptionBySunid(int sunid)

Description copied from interface: ScopDatabase

Return the SCOP description for a node in the hierarchy by its "sunid" id.

Specified by:

getScopDescriptionBySunid in interface ScopDatabase

Returns:

a ScopDescription object

getDomainsForPDB

public List<ScopDomain> getDomainsForPDB(String pdbId)

Description copied from interface: ScopDatabase

Get a list of ScopDomains that have been assigned to a PDB ID

Specified by:

getDomainsForPDB in interface ScopDatabase

Parameters:

pdbId - the PDB entry

Returns:

a list of ScopDomains

getDomainByScopID

public ScopDomain getDomainByScopID(String scopId)

Description copied from interface: ScopDatabase

get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)

Specified by:

getDomainByScopID in interface ScopDatabase

Parameters:

scopId - e.g. d2bq6a1

Returns:

a ScopDomain or null if no domain with the particular ID could be found

getScopNode

public ScopNode getScopNode(int sunid)

Description copied from interface: ScopDatabase

Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...

Specified by:

getScopNode in interface ScopDatabase

Parameters:

sunid - the scop unique id

Returns:

a ScopNode that matches this sunid

downloadClaFile

protected void downloadClaFile()
                        throws FileNotFoundException,
                               IOException

Throws:

FileNotFoundException

IOException

downloadDesFile

protected void downloadDesFile()
                        throws FileNotFoundException,
                               IOException

Throws:

FileNotFoundException

IOException

downloadHieFile

protected void downloadHieFile()
                        throws IOException

Throws:

IOException

downloadComFile

protected void downloadComFile()
                        throws FileNotFoundException,
                               IOException

Throws:

FileNotFoundException

IOException

downloadFileFromRemote

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

Throws:

IOException

getClaFilename

protected String getClaFilename()

getDesFilename

protected String getDesFilename()

getHieFilename

protected String getHieFilename()

getComFilename

protected String getComFilename()

getCacheLocation

public String getCacheLocation()

setCacheLocation

public void setCacheLocation(String cacheLocation)

getScopVersion

public String getScopVersion()

Description copied from interface: ScopDatabase

Returns the SCOP version

Specified by:

getScopVersion in interface ScopDatabase

Returns:

version of SCOP

setScopVersion

public void setScopVersion(String scopVersion)

Description copied from interface: ScopDatabase

Sets the scop version used.

Specified by:

setScopVersion in interface ScopDatabase

getScopDownloadURL

@Deprecated
public String getScopDownloadURL()

Deprecated.

Get the URL of the first scop mirror being used

Returns:

setScopDownloadURL

@Deprecated
public void setScopDownloadURL(String scopDownloadURL)

Deprecated. Use addMirror(java.lang.String) instead

Parameters:

scopDownloadURL - URL to load

addMirror

public void addMirror(String scopDownloadURL)

getMirrors

public List<ScopMirror> getMirrors()

getScopDomainsBySunid

public List<ScopDomain> getScopDomainsBySunid(Integer sunid)

Description copied from interface: ScopDatabase

Get a SCOP domain by its sunid

Specified by:

getScopDomainsBySunid in interface ScopDatabase

Parameters:

sunid - the scop unique id

Returns:

a list of scop domains that match this sunid

getComments

public List<String> getComments(int sunid)

Description copied from interface: ScopDatabase

Get comments about a SCOP domain by its sunid

Specified by:

getComments in interface ScopDatabase

Returns: