public class ScopInstallation extends java.lang.Object implements LocalScopDatabase
Modifier and Type | Field and Description |
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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 and Description |
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ScopInstallation()
Create a new SCOP installation, downloading the file to "the right place".
|
ScopInstallation(java.lang.String cacheLocation)
Create a new SCOP installation.
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Modifier and Type | Method and Description |
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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.
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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 |
getComFilename() |
java.util.List<java.lang.String> |
getComments(int sunid)
Get comments about a SCOP domain by its sunid
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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() |
java.util.List<ScopMirror> |
getMirrors() |
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()
Deprecated.
|
ScopNode |
getScopNode(int sunid)
Access a particular ScopNode.
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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.
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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 comFileName
public static final java.lang.String SCOP_DOWNLOAD
public static final java.lang.String SCOP_DOWNLOAD_ALTERNATE
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()
UserConfiguration.PDB_CACHE_DIR
, or else will use a temporary directorypublic void nullifyComments()
getComments(int)
is called subsequently.public void ensureClaInstalled() throws java.io.IOException
java.io.IOException
public void ensureDesInstalled() throws java.io.IOException
java.io.IOException
public void ensureComInstalled() throws java.io.IOException
java.io.IOException
public void ensureHieInstalled() throws java.io.IOException
java.io.IOException
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) throws ScopIOException
ScopDatabase
filterByDescription
in interface ScopDatabase
ScopIOException
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.IOException
java.io.IOException
protected void downloadComFile() 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.IOException
java.io.IOException
protected java.lang.String getClaFilename()
protected java.lang.String getDesFilename()
protected java.lang.String getHieFilename()
protected java.lang.String getComFilename()
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)
ScopDatabase
setScopVersion
in interface ScopDatabase
@Deprecated public java.lang.String getScopDownloadURL()
@Deprecated public void setScopDownloadURL(java.lang.String scopDownloadURL)
addMirror(java.lang.String)
insteadscopDownloadURL
- URL to loadpublic void addMirror(java.lang.String scopDownloadURL)
public java.util.List<ScopMirror> getMirrors()
public java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.Integer sunid)
ScopDatabase
getScopDomainsBySunid
in interface ScopDatabase
sunid
- the scop unique idpublic java.util.List<java.lang.String> getComments(int sunid)
ScopDatabase
getComments
in interface ScopDatabase