com.hfg.bio.seq.alignment.blast

Class BLAST_Database

java.lang.Object

java.io.File

com.hfg.bio.seq.alignment.blast.BLAST_Database

All Implemented Interfaces:

Serializable, Comparable<File>

public class BLAST_Database
extends File

Container for a BLAST database.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static XMLName	XML_DESCRIPTION_ATT
protected static XMLName	XML_DIR_ATT
protected static XMLName	XML_NAME
protected static XMLName	XML_NAME_ATT
protected static XMLName	XML_SEQ_TYPE_ATT

Fields inherited from class java.io.File

pathSeparator, pathSeparatorChar, separator, separatorChar

Constructor Summary

Constructors

Constructor and Description
BLAST_Database(File inParentDir, String inName)
BLAST_Database(String inName)
BLAST_Database(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
String	getDescription()
Integer	getNumSequences()
BioSequenceType	getSeqType()
BLAST_Database	setDescription(String inValue)
BLAST_Database	setSeqType(BioSequenceType inValue)
XMLTag	toXMLTag()

Methods inherited from class java.io.File

canExecute, canRead, canWrite, compareTo, createNewFile, createTempFile, createTempFile, delete, deleteOnExit, equals, exists, getAbsoluteFile, getAbsolutePath, getCanonicalFile, getCanonicalPath, getFreeSpace, getName, getParent, getParentFile, getPath, getTotalSpace, getUsableSpace, hashCode, isAbsolute, isDirectory, isFile, isHidden, lastModified, length, list, list, listFiles, listFiles, listFiles, listRoots, mkdir, mkdirs, renameTo, setExecutable, setExecutable, setLastModified, setReadable, setReadable, setReadOnly, setWritable, setWritable, toPath, toString, toURI, toURL

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

XML_NAME

protected static XMLName XML_NAME

XML_NAME_ATT

protected static XMLName XML_NAME_ATT

XML_SEQ_TYPE_ATT

protected static XMLName XML_SEQ_TYPE_ATT

XML_DIR_ATT

protected static XMLName XML_DIR_ATT

XML_DESCRIPTION_ATT

protected static XMLName XML_DESCRIPTION_ATT

Constructor Detail

BLAST_Database

public BLAST_Database(String inName)

BLAST_Database

public BLAST_Database(File inParentDir,
                      String inName)

BLAST_Database

public BLAST_Database(XMLTag inXMLTag)

Method Detail

toXMLTag

public XMLTag toXMLTag()

setSeqType

public BLAST_Database setSeqType(BioSequenceType inValue)

getSeqType

public BioSequenceType getSeqType()

setDescription

public BLAST_Database setDescription(String inValue)

getDescription

public String getDescription()

getNumSequences

public Integer getNumSequences()