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 final String

lineSplit

static final String

MMCIF_FORMAT

static final String

PDB_CACHE_DIR

static final String

PDB_DIR

static final String

PDB_FORMAT

static final 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)

boolean

getAutoFetch()

Deprecated.
Use getFetchBehavior()

String

getCacheFilePath()

LocalPDBDirectory.FetchBehavior

getFetchBehavior()

String

getFileFormat()

LocalPDBDirectory.ObsoleteBehavior

getObsoleteBehavior()

String

getPdbFilePath()

void

setAutoFetch(boolean autoFetch)

Deprecated.
Use getFetchBehavior()

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 Details
- 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
- PDB_CACHE_DIR
  
  public static final String PDB_CACHE_DIR
  See Also:
  
  Constant Field Values
- lineSplit
  
  public static final String lineSplit
Constructor Details
- UserConfiguration
  
  public UserConfiguration()
  Default UserConfiguration:
  
  split directory
  
  autofetch files
  
  default download location. This is the first specified of:
  "PDB_DIR" system property (for instance, -D"PDB_DIR"=/tmp)
  
  "PDB_DIR" environment variable
  
  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:
  "PDB_CACHE_DIR" system property (for instance, -D"PDB_CACHE_DIR"=/tmp)
  
  "PDB_CACHE_DIR" environment variable
  
  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 Details
- getPdbFilePath
  
  public String getPdbFilePath()
- setPdbFilePath
  
  public void setPdbFilePath(String pdbFilePath)
- getCacheFilePath
  
  public String getCacheFilePath()
- setCacheFilePath
  
  public void setCacheFilePath(String cacheFilePath)
- getAutoFetch
  
  @Deprecated public boolean getAutoFetch()
  
  Deprecated.
  Use getFetchBehavior()
- setAutoFetch
  
  @Deprecated public void setAutoFetch(boolean autoFetch)
  
  Deprecated.
  Use getFetchBehavior()
- 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()

Class UserConfiguration

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

PDB_FORMAT

MMCIF_FORMAT

TMP_DIR

PDB_DIR

PDB_CACHE_DIR

lineSplit

Constructor Details

UserConfiguration

Method Details

getPdbFilePath

setPdbFilePath

getCacheFilePath

setCacheFilePath

getAutoFetch

setAutoFetch

getFetchBehavior

setFetchBehavior

getObsoleteBehavior

setObsoleteBehavior

toXML

toXML

fromStartupParams

setFileFormat

getFileFormat