|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.structure.scop.ScopInstallation
public class ScopInstallation
This class provides access to the SCOP protein structure classification. For more information about SCOP see here:
Field Summary | |
---|---|
static String |
claFileName
|
static String |
DEFAULT_VERSION
|
static String |
desFileName
|
static String |
FILESPLIT
|
static String |
hieFileName
|
static String |
NEWLINE
|
static String |
SCOP_DOWNLOAD
|
protected String |
scopDownloadURL
|
protected String |
scopVersion
|
Constructor Summary | |
---|---|
ScopInstallation()
Create a new SCOP installation, downloading the file to "the right place". |
|
ScopInstallation(String cacheLocation)
Create a new SCOP installation. |
Method Summary | |
---|---|
protected void |
downloadClaFile()
|
protected void |
downloadDesFile()
|
protected void |
downloadFileFromRemote(URL remoteURL,
File localFile)
|
protected void |
downloadHieFile()
|
void |
ensureClaInstalled()
|
void |
ensureDesInstalled()
|
void |
ensureHieInstalled()
|
List<ScopDescription> |
filterByClassificationId(String query)
Get all scop descriptions that start with a classifcation 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 |
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()
|
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()
|
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 |
setCacheLocation(String cacheLocation)
|
void |
setScopDownloadURL(String scopDownloadURL)
|
void |
setScopVersion(String scopVersion)
|
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final String DEFAULT_VERSION
protected String scopVersion
public static final String claFileName
public static final String desFileName
public static final String hieFileName
public static final String SCOP_DOWNLOAD
protected String scopDownloadURL
public static final String NEWLINE
public static final String FILESPLIT
Constructor Detail |
---|
public ScopInstallation(String cacheLocation)
cacheLocation
- where the SCOP files are stored. If they can't be found at that location they will get automatically downloaded and installed there.public ScopInstallation()
Method Detail |
---|
public void ensureClaInstalled()
public void ensureDesInstalled()
public void ensureHieInstalled()
public List<ScopDescription> getByCategory(ScopCategory category)
ScopDatabase
getByCategory
in interface ScopDatabase
category
- e.g. "superfamily"
public List<ScopDescription> filterByClassificationId(String query)
ScopDatabase
filterByClassificationId
in interface ScopDatabase
public List<ScopNode> getTree(ScopDomain domain)
ScopDatabase
getTree
in interface ScopDatabase
public List<ScopDomain> filterByDomainName(String query)
ScopDatabase
filterByDomainName
in interface ScopDatabase
query
- a (part) of a name
public List<ScopDescription> filterByDescription(String query)
ScopDatabase
filterByDescription
in interface ScopDatabase
public ScopDescription getScopDescriptionBySunid(int sunid)
ScopDatabase
getScopDescriptionBySunid
in interface ScopDatabase
public List<ScopDomain> getDomainsForPDB(String pdbId)
ScopDatabase
getDomainsForPDB
in interface ScopDatabase
pdbId
- the PDB entry
public ScopDomain getDomainByScopID(String scopId)
ScopDatabase
getDomainByScopID
in interface ScopDatabase
scopId
- e.g. d2bq6a1
public ScopNode getScopNode(int sunid)
ScopDatabase
getScopNode
in interface ScopDatabase
sunid
- the scop unique id
protected void downloadClaFile() throws FileNotFoundException, IOException
FileNotFoundException
IOException
protected void downloadDesFile() throws FileNotFoundException, IOException
FileNotFoundException
IOException
protected void downloadHieFile() throws FileNotFoundException, IOException
FileNotFoundException
IOException
protected void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException
FileNotFoundException
IOException
protected String getClaFilename()
protected String getDesFilename()
protected String getHieFilename()
public String getCacheLocation()
public void setCacheLocation(String cacheLocation)
public String getScopVersion()
ScopDatabase
getScopVersion
in interface ScopDatabase
public void setScopVersion(String scopVersion)
public String getScopDownloadURL()
public void setScopDownloadURL(String scopDownloadURL)
public List<ScopDomain> getScopDomainsBySunid(Integer sunid)
ScopDatabase
getScopDomainsBySunid
in interface ScopDatabase
sunid
- the scop unique id
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |