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java.lang.Objectorg.biojava.bio.structure.server.FlatFileInstallation
public class FlatFileInstallation
a PDB installation that reads all files from one directory in the file system.
and keeps several files with the information parsed from the PDB headers for
easier data access.
In particular these files are:
PrepareIndexFile
Field Summary | |
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static SimpleDateFormat |
dateFormat
|
static String |
DEFAUL_CHAIN_FILE
|
static String |
DEFAULT_INDEX_FILE
|
static Logger |
logger
|
Constructor Summary | |
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FlatFileInstallation(File filePath)
create a new FlatFile Installation and point it to the directory that contains all PDB files |
Method Summary | |
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void |
addPDBFilter(PDBFilter filter)
add a filter for PDB files. |
void |
applyFilters()
|
void |
clearFilters()
remove all filters, next time getAll is called, it will return all available PDBs |
List<PDBHeader> |
getAll()
get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs |
File |
getChainInfoFile()
|
File |
getFilePath()
|
PDBHeader |
getPDBHeader(String pdbId)
get the PDB header for a single protein structure |
File |
getPDBInfoFile()
|
Structure |
getStructure(String pdbId)
request a structure by its PDB identifier |
boolean |
hasNext()
return if the iteration over all structures will return another structure |
Structure |
next()
iterate over all structures in this Installation that pass the provided filters and return the next one in the list. |
void |
setChainInfoFile(File chainInfoFile)
|
void |
setFilePath(File filePath)
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void |
setPDBInfoFile(File indexFile)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final Logger logger
public static final String DEFAULT_INDEX_FILE
public static final String DEFAUL_CHAIN_FILE
public static SimpleDateFormat dateFormat
Constructor Detail |
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public FlatFileInstallation(File filePath)
filePath
- Method Detail |
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public File getPDBInfoFile()
public void setPDBInfoFile(File indexFile)
public File getChainInfoFile()
public void setChainInfoFile(File chainInfoFile)
public File getFilePath()
public void setFilePath(File filePath)
public void addPDBFilter(PDBFilter filter)
PDBInstallation
addPDBFilter
in interface PDBInstallation
filter
- the filter to apply when getAll is being called.PDBInstallation.getAll()
public void clearFilters()
PDBInstallation
clearFilters
in interface PDBInstallation
public void applyFilters()
public List<PDBHeader> getAll()
PDBInstallation
getAll
in interface PDBInstallation
public PDBHeader getPDBHeader(String pdbId)
PDBInstallation
getPDBHeader
in interface PDBInstallation
public Structure getStructure(String pdbId)
PDBInstallation
getStructure
in interface PDBInstallation
public boolean hasNext()
PDBInstallation
hasNext
in interface PDBInstallation
public Structure next()
PDBInstallation
next
in interface PDBInstallation
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