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
Constructor Summary |
UserConfiguration()
Default UserConfiguration:
split directory
autofetch files
default download location. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
UserConfiguration
public UserConfiguration()
- Default UserConfiguration:
- split directory
- autofetch files
- default download location. This is the first specified of:
- PDB_DIR system property (for instance, -DPDB_DIR=/tmp)
- PDB_DIR environment variable
- System temp directory (java.io.tmpdir property)
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()