softparsmap
Class AbstractSequenceData

java.lang.Object
  ooc.LinkedTagInstance
      softparsmap.AbstractSequenceData

All Implemented Interfaces:

Dependencies, SequenceData

Direct Known Subclasses:

SequenceDataXml

public abstract class AbstractSequenceData

extends LinkedTagInstance

implements SequenceData

If the sequences are stored in one file this class can be extended and used together with the class DataSourceXmlGenData.

Constructor Summary

AbstractSequenceData()

Method Summary

PropertyFile	getPropertyFile() Returns the property file.
abstract boolean	moveNextSequence() Move to next sequence in file.
abstract FilePointerPart	newFilePointerPartCurrent() Returns a new FilePointerPart on current position in the file.
abstract void	parseSequence(java.io.RandomAccessFile raf, FilePointerPart fpp) Parse in a sequence given a the file and pointer.
abstract void	setDatabaseFile(java.io.RandomAccessFile raf) Sets the file that contains the sequences.

Methods inherited from class ooc.LinkedTagInstance

containsKey, get, getAttribute, getAttributeBoolean, getAttributeDouble, getAttributeFloat, getAttributeInteger, getAttributeList, getAttributeRef, getAttributeShort, getAttributeString, getAttributeTag, getChildIterator, getChildIteratorByName, getContainer, getContainerTag, getFirstChildTagByName, getTag, getTagId, getTagInstance, getTagInstance, getTagRef, hasAttributeValue, hasChildTagByName, hasChildTags, hasTag, isMutable, keySet, put, remove, setTag, setupInstance

Methods inherited from class java.lang.Object

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

Methods inherited from interface softparsmap.SequenceData

getGiNumber, getIdNumber, getSequenceLength, getSpeciesName, isCompleteSequence

Constructor Detail

AbstractSequenceData

public AbstractSequenceData()

Method Detail

getPropertyFile

public PropertyFile getPropertyFile()

Returns the property file.

Returns:

the property file

See Also:

PropertyFile

newFilePointerPartCurrent

public abstract FilePointerPart newFilePointerPartCurrent()

Returns a new FilePointerPart on current position in the file.

Returns:

a FilePointerPart on current position in file

setDatabaseFile

public abstract void setDatabaseFile(java.io.RandomAccessFile raf)

Sets the file that contains the sequences.

Parameters:

raf - is the file containing the sequences

moveNextSequence

public abstract boolean moveNextSequence()

Move to next sequence in file.

Returns:

true if there is a next sequence and the current pointer is set to this sequence

parseSequence

public abstract void parseSequence(java.io.RandomAccessFile raf,
                                   FilePointerPart fpp)

Parse in a sequence given a the file and pointer.

Parameters:

raf - is the file containing all the sequences

fpp - is the file pointer