ZipChemCompProvider

java.lang.Object
- org.biojava.nbio.structure.io.mmcif.ZipChemCompProvider

All Implemented Interfaces:

ChemCompProvider
```
public class ZipChemCompProvider
extends java.lang.Object
implements ChemCompProvider
```
This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction. If the archive does not contain the record, an attempt is made to download it using DownloadChemCompProvider. The downloaded file is then added to the archive. The class is thread-safe and the same ZipChemCompProvider should be used by all threads to prevent simultaneous read or write to the zip archive. A zip archive will be created if missing.

Since:

12/05/12 updated 3/5/2016 for Java 7 ZipFileSystem

Author:

edlunde, larsonm

Constructor Summary

Constructors
Constructor and Description
`ZipChemCompProvider(java.lang.String chemicalComponentDictionaryFile, java.lang.String tempDir)` ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ChemComp`	`getChemComp(java.lang.String recordName)` Returns a new instance of a chemical component definition.
`static void`	`purgeTempFiles(java.lang.String tempdir)` Cleanup chemical component (.cif.gz) files downloaded to tmpdir.
`void`	`setRemoveCif(boolean doRemove)` Remove downloaded .cif.gz after adding to zip archive? Default is true.

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

- Constructor Detail
  - ZipChemCompProvider
```
public ZipChemCompProvider(java.lang.String chemicalComponentDictionaryFile,
                           java.lang.String tempDir)
                    throws java.io.IOException
```
    ZipChemCompProvider is a Chemical Component provider that stores chemical components in a zip archive. Missing chemical components are downloaded and appended to the archive. If non-existent a new zip archive will be created.
    
    Parameters:
    
    chemicalComponentDictionaryFile - : path to zip archive for chemical components.
    
    tempDir - : path for temporary directory, (null) defaults to path in property "java.io.tmpdir".
    
    Throws:
    
    java.io.IOException
- Method Detail
  - setRemoveCif
```
public void setRemoveCif(boolean doRemove)
```
    Remove downloaded .cif.gz after adding to zip archive? Default is true.
    
    Parameters:
    
    doRemove -
  - getChemComp
```
public ChemComp getChemComp(java.lang.String recordName)
```
    Description copied from interface: ChemCompProvider
    
    Returns a new instance of a chemical component definition.
    
    Specified by:
    
    getChemComp in interface ChemCompProvider
    
    Parameters:
    
    recordName - the ID of the ChemComp
    
    Returns:
    
    a new ChemComp definition.
  - purgeTempFiles
```
public static void purgeTempFiles(java.lang.String tempdir)
```
    Cleanup chemical component (.cif.gz) files downloaded to tmpdir.
    
    Parameters:
    
    tempdir - : path to temporary directory for chemical components

Class ZipChemCompProvider

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ZipChemCompProvider

Method Detail

setRemoveCif

getChemComp

purgeTempFiles