org.biojava.bio.structure.scop
public class ScopInstallation extends java.lang.Object implements ScopDatabase
Modifier and Type | Field and Description |
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static java.lang.String |
claFileName |
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 |
protected java.lang.String |
scopDownloadURL |
protected java.lang.String |
scopVersion |
Constructor and Description |
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ScopInstallation()
Create a new SCOP installation, downloading the file to "the right place".
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ScopInstallation(java.lang.String cacheLocation)
Create a new SCOP installation.
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Modifier and Type | Method and Description |
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protected void |
downloadClaFile() |
protected void |
downloadDesFile() |
protected void |
downloadFileFromRemote(java.net.URL remoteURL,
java.io.File localFile) |
protected void |
downloadHieFile() |
void |
ensureClaInstalled() |
void |
ensureDesInstalled() |
void |
ensureHieInstalled() |
java.util.List<ScopDescription> |
filterByClassificationId(java.lang.String query)
Get all scop descriptions that start with a classifcation ID, e.g.
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java.util.List<ScopDescription> |
filterByDescription(java.lang.String query)
Get all scop descriptions that start with a certain name.
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java.util.List<ScopDomain> |
filterByDomainName(java.lang.String query)
search through SCOP and filter based on domain name
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java.util.List<ScopDescription> |
getByCategory(ScopCategory category)
Get all records of a particular classification.
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java.lang.String |
getCacheLocation() |
protected java.lang.String |
getClaFilename() |
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!)
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java.util.List<ScopDomain> |
getDomainsForPDB(java.lang.String pdbId)
Get a list of ScopDomains that have been assigned to a PDB ID
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protected java.lang.String |
getHieFilename() |
ScopDescription |
getScopDescriptionBySunid(int sunid)
Return the SCOP description for a node in the hierarchy by its "sunid" id.
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java.util.List<ScopDomain> |
getScopDomainsBySunid(java.lang.Integer sunid)
Get a SCOP domain by its sunid
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java.lang.String |
getScopDownloadURL() |
ScopNode |
getScopNode(int sunid)
Access a particular ScopNode.
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java.lang.String |
getScopVersion()
Returns the SCOP version
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java.util.List<ScopNode> |
getTree(ScopDomain domain)
get the SCOP sub-tree for a particular domain.
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void |
setCacheLocation(java.lang.String cacheLocation) |
void |
setScopDownloadURL(java.lang.String scopDownloadURL) |
void |
setScopVersion(java.lang.String scopVersion) |
public static final java.lang.String DEFAULT_VERSION
protected java.lang.String scopVersion
public static final java.lang.String claFileName
public static final java.lang.String desFileName
public static final java.lang.String hieFileName
public static final java.lang.String SCOP_DOWNLOAD
protected java.lang.String scopDownloadURL
public static final java.lang.String NEWLINE
public static final java.lang.String FILESPLIT
public ScopInstallation(java.lang.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()
public void ensureClaInstalled()
public void ensureDesInstalled()
public void ensureHieInstalled()
public java.util.List<ScopDescription> getByCategory(ScopCategory category)
ScopDatabase
getByCategory
in interface ScopDatabase
category
- e.g. "superfamily"public java.util.List<ScopDescription> filterByClassificationId(java.lang.String query)
ScopDatabase
filterByClassificationId
in interface ScopDatabase
public java.util.List<ScopNode> getTree(ScopDomain domain)
ScopDatabase
getTree
in interface ScopDatabase
public java.util.List<ScopDomain> filterByDomainName(java.lang.String query)
ScopDatabase
filterByDomainName
in interface ScopDatabase
query
- a (part) of a namepublic java.util.List<ScopDescription> filterByDescription(java.lang.String query)
ScopDatabase
filterByDescription
in interface ScopDatabase
public ScopDescription getScopDescriptionBySunid(int sunid)
ScopDatabase
getScopDescriptionBySunid
in interface ScopDatabase
public java.util.List<ScopDomain> getDomainsForPDB(java.lang.String pdbId)
ScopDatabase
getDomainsForPDB
in interface ScopDatabase
pdbId
- the PDB entrypublic ScopDomain getDomainByScopID(java.lang.String scopId)
ScopDatabase
getDomainByScopID
in interface ScopDatabase
scopId
- e.g. d2bq6a1public ScopNode getScopNode(int sunid)
ScopDatabase
getScopNode
in interface ScopDatabase
sunid
- the scop unique idprotected void downloadClaFile() throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
protected void downloadDesFile() throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
protected void downloadHieFile() throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
protected void downloadFileFromRemote(java.net.URL remoteURL, java.io.File localFile) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
protected java.lang.String getClaFilename()
protected java.lang.String getDesFilename()
protected java.lang.String getHieFilename()
public java.lang.String getCacheLocation()
public void setCacheLocation(java.lang.String cacheLocation)
public java.lang.String getScopVersion()
ScopDatabase
getScopVersion
in interface ScopDatabase
public void setScopVersion(java.lang.String scopVersion)
public java.lang.String getScopDownloadURL()
public void setScopDownloadURL(java.lang.String scopDownloadURL)
public java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.Integer sunid)
ScopDatabase
getScopDomainsBySunid
in interface ScopDatabase
sunid
- the scop unique id