ScopInstallation

java.lang.Object
- org.biojava.nbio.structure.scop.ScopInstallation

All Implemented Interfaces:

LocalScopDatabase, ScopDatabase

Direct Known Subclasses:

BerkeleyScopInstallation
```
public class ScopInstallation
extends java.lang.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 java.lang.String`	`claFileName`
`static java.lang.String`	`comFileName`
`static java.lang.String`	`DEFAULT_VERSION`
`static java.lang.String`	`desFileName`
`static java.lang.String`	`FILESPLIT`
`static java.lang.String`	`hieFileName`
`static java.lang.String`	`NEWLINE`
`static java.lang.String`	`SCOP_DOWNLOAD`
`static java.lang.String`	`SCOP_DOWNLOAD_ALTERNATE`
`protected java.lang.String`	`scopVersion`

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addMirror(java.lang.String scopDownloadURL)`
`protected void`	`downloadClaFile()`
`protected void`	`downloadComFile()`
`protected void`	`downloadDesFile()`
`protected void`	`downloadFileFromRemote(java.net.URL remoteURL, java.io.File localFile)`
`protected void`	`downloadHieFile()`
`void`	`ensureClaInstalled()`
`void`	`ensureComInstalled()`
`void`	`ensureDesInstalled()`
`void`	`ensureHieInstalled()`
`java.util.List<ScopDescription>`	`filterByClassificationId(java.lang.String query)` Get all scop descriptions that start with a classification ID, e.g.
`java.util.List<ScopDescription>`	`filterByDescription(java.lang.String query)` Get all scop descriptions that start with a certain name.
`java.util.List<ScopDomain>`	`filterByDomainName(java.lang.String query)` search through SCOP and filter based on domain name
`java.util.List<ScopDescription>`	`getByCategory(ScopCategory category)` Get all records of a particular classification.
`java.lang.String`	`getCacheLocation()`
`protected java.lang.String`	`getClaFilename()`
`protected java.lang.String`	`getComFilename()`
`java.util.List<java.lang.String>`	`getComments(int sunid)` Get comments about a SCOP domain by its sunid
`protected java.lang.String`	`getDesFilename()`
`ScopDomain`	`getDomainByScopID(java.lang.String scopId)` get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
`java.util.List<ScopDomain>`	`getDomainsForPDB(java.lang.String pdbId)` Get a list of ScopDomains that have been assigned to a PDB ID
`protected java.lang.String`	`getHieFilename()`
`java.util.List<ScopMirror>`	`getMirrors()`
`ScopDescription`	`getScopDescriptionBySunid(int sunid)` Return the SCOP description for a node in the hierarchy by its "sunid" id.
`java.util.List<ScopDomain>`	`getScopDomainsBySunid(java.lang.Integer sunid)` Get a SCOP domain by its sunid
`java.lang.String`	`getScopDownloadURL()` Deprecated.
`ScopNode`	`getScopNode(int sunid)` Access a particular ScopNode.
`java.lang.String`	`getScopVersion()` Returns the SCOP version
`java.util.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(java.lang.String cacheLocation)`
`void`	`setScopDownloadURL(java.lang.String scopDownloadURL)` Deprecated. Use `addMirror(java.lang.String)` instead
`void`	`setScopVersion(java.lang.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 java.lang.String DEFAULT_VERSION
```
    See Also:
    
    Constant Field Values
  - scopVersion
```
protected java.lang.String scopVersion
```
  - claFileName
```
public static final java.lang.String claFileName
```
    See Also:
    
    Constant Field Values
  - desFileName
```
public static final java.lang.String desFileName
```
    See Also:
    
    Constant Field Values
  - hieFileName
```
public static final java.lang.String hieFileName
```
    See Also:
    
    Constant Field Values
  - comFileName
```
public static final java.lang.String comFileName
```
    See Also:
    
    Constant Field Values
  - SCOP_DOWNLOAD
```
public static final java.lang.String SCOP_DOWNLOAD
```
    See Also:
    
    Constant Field Values
  - SCOP_DOWNLOAD_ALTERNATE
```
public static final java.lang.String SCOP_DOWNLOAD_ALTERNATE
```
    See Also:
    
    Constant Field Values
  - NEWLINE
```
public static final java.lang.String NEWLINE
```
  - FILESPLIT
```
public static final java.lang.String FILESPLIT
```
- Constructor Detail
  - ScopInstallation
```
public ScopInstallation(java.lang.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 java.io.IOException
```
    Throws:
    
    java.io.IOException
  - ensureDesInstalled
```
public void ensureDesInstalled()
                        throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - ensureComInstalled
```
public void ensureComInstalled()
                        throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - ensureHieInstalled
```
public void ensureHieInstalled()
                        throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - getByCategory
```
public java.util.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 java.util.List<ScopDescription> filterByClassificationId(java.lang.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 java.util.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 java.util.List<ScopDomain> filterByDomainName(java.lang.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 java.util.List<ScopDescription> filterByDescription(java.lang.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 java.util.List<ScopDomain> getDomainsForPDB(java.lang.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(java.lang.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 java.io.FileNotFoundException,
                               java.io.IOException
```
    Throws:
    
    java.io.FileNotFoundException
    
    java.io.IOException
  - downloadDesFile
```
protected void downloadDesFile()
                        throws java.io.FileNotFoundException,
                               java.io.IOException
```
    Throws:
    
    java.io.FileNotFoundException
    
    java.io.IOException
  - downloadHieFile
```
protected void downloadHieFile()
                        throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - downloadComFile
```
protected void downloadComFile()
                        throws java.io.FileNotFoundException,
                               java.io.IOException
```
    Throws:
    
    java.io.FileNotFoundException
    
    java.io.IOException
  - downloadFileFromRemote
```
protected void downloadFileFromRemote(java.net.URL remoteURL,
                                      java.io.File localFile)
                               throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - getClaFilename
```
protected java.lang.String getClaFilename()
```
  - getDesFilename
```
protected java.lang.String getDesFilename()
```
  - getHieFilename
```
protected java.lang.String getHieFilename()
```
  - getComFilename
```
protected java.lang.String getComFilename()
```
  - getCacheLocation
```
public java.lang.String getCacheLocation()
```
  - setCacheLocation
```
public void setCacheLocation(java.lang.String cacheLocation)
```
  - getScopVersion
```
public java.lang.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(java.lang.String scopVersion)
```
    Description copied from interface: ScopDatabase
    
    Sets the scop version used.
    
    Specified by:
    
    setScopVersion in interface ScopDatabase
  - getScopDownloadURL
```
@Deprecated
public java.lang.String getScopDownloadURL()
```
    Deprecated.
    
    Get the URL of the first scop mirror being used
    
    Returns:
  - setScopDownloadURL
```
@Deprecated
public void setScopDownloadURL(java.lang.String scopDownloadURL)
```
    Deprecated. Use addMirror(java.lang.String) instead
    
    Parameters:
    
    scopDownloadURL - URL to load
  - addMirror
```
public void addMirror(java.lang.String scopDownloadURL)
```
  - getMirrors
```
public java.util.List<ScopMirror> getMirrors()
```
  - getScopDomainsBySunid
```
public java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.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 java.util.List<java.lang.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:

Class ScopInstallation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_VERSION

scopVersion

claFileName

desFileName

hieFileName

comFileName

SCOP_DOWNLOAD

SCOP_DOWNLOAD_ALTERNATE

NEWLINE

FILESPLIT

Constructor Detail

ScopInstallation

ScopInstallation

Method Detail

nullifyComments

ensureClaInstalled

ensureDesInstalled

ensureComInstalled

ensureHieInstalled

getByCategory

filterByClassificationId

getTree

filterByDomainName

filterByDescription

getScopDescriptionBySunid

getDomainsForPDB

getDomainByScopID

getScopNode

downloadClaFile

downloadDesFile

downloadHieFile

downloadComFile

downloadFileFromRemote

getClaFilename

getDesFilename

getHieFilename

getComFilename

getCacheLocation

setCacheLocation

getScopVersion

setScopVersion

getScopDownloadURL

setScopDownloadURL

addMirror

getMirrors

getScopDomainsBySunid

getComments