Package org.biojava.nbio.structure.align.util

Class UserConfiguration

java.lang.Object

org.biojava.nbio.structure.align.util.UserConfiguration

public class UserConfiguration
extends Object

A container to persist config to the file system

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field	Description
static String	BCIF_FORMAT
static String	lineSplit
static String	MMCIF_FORMAT
static String	MMTF_FORMAT
static String	PDB_CACHE_DIR
static String	PDB_DIR
static String	PDB_FORMAT
static String	TMP_DIR

Constructor Summary

Constructors

Constructor	Description
UserConfiguration()	Default UserConfiguration: split directory autofetch files default download location.

Method Summary

Modifier and Type	Method	Description
static UserConfiguration	fromStartupParams(StartupParameters params)
String	getCacheFilePath()
LocalPDBDirectory.FetchBehavior	getFetchBehavior()
String	getFileFormat()
LocalPDBDirectory.ObsoleteBehavior	getObsoleteBehavior()
String	getPdbFilePath()
StructureFiletype	getStructureFiletype()
void	setCacheFilePath(String cacheFilePath)
void	setFetchBehavior(LocalPDBDirectory.FetchBehavior fetchBehavior)
void	setFileFormat(String fileFormat)
void	setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior obsoleteBehavior)
void	setPdbFilePath(String pdbFilePath)
XMLWriter	toXML(PrintWriter pw)	convert Configuration to an XML file so it can be serialized
XMLWriter	toXML(XMLWriter xw)	convert Configuration to an XML file so it can be serialized add to an already existing xml file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

PDB_FORMAT

public static final String PDB_FORMAT

See Also:

Constant Field Values

MMCIF_FORMAT

public static final String MMCIF_FORMAT

See Also:

Constant Field Values

MMTF_FORMAT

public static final String MMTF_FORMAT

See Also:

Constant Field Values

BCIF_FORMAT

public static final String BCIF_FORMAT

See Also:

Constant Field Values

TMP_DIR

public static final String TMP_DIR

See Also:

Constant Field Values

PDB_DIR

public static final String PDB_DIR

See Also:

Constant Field Values

PDB_CACHE_DIR

public static final String PDB_CACHE_DIR

See Also:

Constant Field Values

lineSplit

public static final String lineSplit

Constructor Detail

UserConfiguration

public UserConfiguration()

Default UserConfiguration:

• split directory
• autofetch files
• default download location. This is the first specified of:
  1. "PDB_DIR" system property (for instance, -D"PDB_DIR"=/tmp)
  2. "PDB_DIR" environment variable
  3. System temp directory (java.io.tmpdir property)
  if the provided path is not a directory then the system's temp directory is used. A non-writable path is allowed, only a warning will be logged.
• default cache location. This is the first specified of:
  1. "PDB_CACHE_DIR" system property (for instance, -D"PDB_CACHE_DIR"=/tmp)
  2. "PDB_CACHE_DIR" environment variable
  3. the value set for "PDB_DIR"
  if the provided path is not a directory or is not writable then the system's temp directory is used.

Method Detail

getPdbFilePath

public String getPdbFilePath()

setPdbFilePath

public void setPdbFilePath(String pdbFilePath)

getCacheFilePath

public String getCacheFilePath()

setCacheFilePath

public void setCacheFilePath(String cacheFilePath)

getFetchBehavior

public LocalPDBDirectory.FetchBehavior getFetchBehavior()

setFetchBehavior

public void setFetchBehavior(LocalPDBDirectory.FetchBehavior fetchBehavior)

getObsoleteBehavior

public LocalPDBDirectory.ObsoleteBehavior getObsoleteBehavior()

setObsoleteBehavior

public void setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior obsoleteBehavior)

toXML

public XMLWriter toXML(PrintWriter pw)
                throws IOException

convert Configuration to an XML file so it can be serialized

Parameters:

pw -

Returns:

XMLWriter

Throws:

IOException

toXML

public XMLWriter toXML(XMLWriter xw)
                throws IOException

convert Configuration to an XML file so it can be serialized add to an already existing xml file.

Parameters:

xw - the XML writer to use

Returns:

the writer again

Throws:

IOException

See Also:

ConfigXMLHandler

fromStartupParams

public static UserConfiguration fromStartupParams(StartupParameters params)

setFileFormat

public void setFileFormat(String fileFormat)

getFileFormat

public String getFileFormat()

getStructureFiletype

public StructureFiletype getStructureFiletype()