org.biojava.bio.structure.align.util

Class UserConfiguration

java.lang.Object

org.biojava.bio.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 and Description
static String	MMCIF_FORMAT
static String	PDB_DIR
static String	PDB_FORMAT
static String	TMP_DIR

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
static UserConfiguration	fromStartupParams(StartupParameters params)
boolean	getAutoFetch()
String	getFileFormat()
String	getPdbFilePath()
boolean	isSplit()
void	setAutoFetch(boolean autoFetch)
void	setFileFormat(String fileFormat)
void	setPdbFilePath(String pdbFilePath)
void	setSplit(boolean isSplit)
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

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

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, -DPDB_DIR=/tmp)
  2. PDB_DIR environment variable
  3. System temp directory (java.io.tmpdir property)

Method Detail

getPdbFilePath

public String getPdbFilePath()

setPdbFilePath

public void setPdbFilePath(String pdbFilePath)

isSplit

public boolean isSplit()

setSplit

public void setSplit(boolean isSplit)

getAutoFetch

public boolean getAutoFetch()

setAutoFetch

public void setAutoFetch(boolean autoFetch)

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

fromStartupParams

public static UserConfiguration fromStartupParams(StartupParameters params)

setFileFormat

public void setFileFormat(String fileFormat)

getFileFormat

public String getFileFormat()