FlatFileInstallation (BioJava-1.7.1 API)

java.lang.Object
- org.biojava.bio.structure.server.FlatFileInstallation

All Implemented Interfaces:

PDBInstallation
```
public class FlatFileInstallation
extends java.lang.Object
implements PDBInstallation
```
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:
- pdbinfo.txt - contains resolution, experimetnal technique, deposition and modification date, biological description of the structure
- chaininfo.txt - contains information about every chain, like the compound information from the header, the nr of amino acids in chain, The alignment to the SEQRES residues
In order to create these index files for this PDB installation, please see the PrepareIndexFile class.
Author:

Andreas Prlic

See Also:
PrepareIndexFile

Field Summary

Fields
Modifier and Type	Field and Description
`static java.text.SimpleDateFormat`	`dateFormat`
`static java.lang.String`	`DEFAUL_CHAIN_FILE`
`static java.lang.String`	`DEFAULT_INDEX_FILE`
`static java.util.logging.Logger`	`logger`

Constructor Summary

Constructors
Constructor and Description

FlatFileInstallation(java.io.File filePath)
create a new FlatFile Installation and point it to the directory that contains all PDB files

Constructors
Constructor and Description
`FlatFileInstallation(java.io.File filePath)` create a new FlatFile Installation and point it to the directory that contains all PDB files

Method Summary

Methods
Modifier and Type	Method and Description
`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
`java.util.List<PDBHeader>`	`getAll()` get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
`java.io.File`	`getChainInfoFile()`
`java.io.File`	`getFilePath()`
`PDBHeader`	`getPDBHeader(java.lang.String pdbId)` get the PDB header for a single protein structure
`java.io.File`	`getPDBInfoFile()`
`Structure`	`getStructure(java.lang.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(java.io.File chainInfoFile)`
`void`	`setFilePath(java.io.File filePath)`
`void`	`setPDBInfoFile(java.io.File indexFile)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - logger
```
public static final java.util.logging.Logger logger
```
  - DEFAULT_INDEX_FILE
```
public static final java.lang.String DEFAULT_INDEX_FILE
```
    See Also:
    Constant Field Values
  - DEFAUL_CHAIN_FILE
```
public static final java.lang.String DEFAUL_CHAIN_FILE
```
    See Also:
    Constant Field Values
  - dateFormat
```
public static java.text.SimpleDateFormat dateFormat
```
- Constructor Detail
  - FlatFileInstallation
```
public FlatFileInstallation(java.io.File filePath)
```
    create a new FlatFile Installation and point it to the directory that contains all PDB files
    
    Parameters:
    filePath -
- Method Detail
  - getPDBInfoFile
```
public java.io.File getPDBInfoFile()
```
  - setPDBInfoFile
```
public void setPDBInfoFile(java.io.File indexFile)
```
  - getChainInfoFile
```
public java.io.File getChainInfoFile()
```
  - setChainInfoFile
```
public void setChainInfoFile(java.io.File chainInfoFile)
```
  - getFilePath
```
public java.io.File getFilePath()
```
  - setFilePath
```
public void setFilePath(java.io.File filePath)
```
  - addPDBFilter
```
public void addPDBFilter(PDBFilter filter)
```
    Description copied from interface: PDBInstallation
    
    add a filter for PDB files. THis can be used to request, e.g. all X-ray structures, or all structures with a given resolution, all proteins with a certain function, etc.
    
    Specified by:
    
    addPDBFilter in interface PDBInstallation
    
    Parameters:
    filter - the filter to apply when getAll is being called.
    See Also:
    PDBInstallation.getAll()
  - clearFilters
```
public void clearFilters()
```
    Description copied from interface: PDBInstallation
    
    remove all filters, next time getAll is called, it will return all available PDBs
    
    Specified by:
    
    clearFilters in interface PDBInstallation
  - applyFilters
```
public void applyFilters()
```
  - getAll
```
public java.util.List<PDBHeader> getAll()
```
    Description copied from interface: PDBInstallation
    
    get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
    
    Specified by:
    
    getAll in interface PDBInstallation
    
    Returns:
    a list of PDBHeader objects
  - getPDBHeader
```
public PDBHeader getPDBHeader(java.lang.String pdbId)
```
    Description copied from interface: PDBInstallation
    
    get the PDB header for a single protein structure
    
    Specified by:
    
    getPDBHeader in interface PDBInstallation
    
    Returns:
    the PDB header object
  - getStructure
```
public Structure getStructure(java.lang.String pdbId)
```
    Description copied from interface: PDBInstallation
    
    request a structure by its PDB identifier
    
    Specified by:
    
    getStructure in interface PDBInstallation
    
    Returns:
    the structure for the pdbId
  - hasNext
```
public boolean hasNext()
```
    Description copied from interface: PDBInstallation
    
    return if the iteration over all structures will return another structure
    
    Specified by:
    
    hasNext in interface PDBInstallation
    
    Returns:
    true if there is another structure that has not been iterated over yet
  - next
```
public Structure next()
```
    Description copied from interface: PDBInstallation
    
    iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
    
    Specified by:
    
    next in interface PDBInstallation
    
    Returns:
    the next structure

Class FlatFileInstallation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

logger

DEFAULT_INDEX_FILE

DEFAUL_CHAIN_FILE

dateFormat

Constructor Detail

FlatFileInstallation

Method Detail

getPDBInfoFile

setPDBInfoFile

getChainInfoFile

setChainInfoFile

getFilePath

setFilePath

addPDBFilter

clearFilters

applyFilters

getAll

getPDBHeader

getStructure

hasNext

next