softparsmap
Class SequenceDataXml

java.lang.Object
  ooc.LinkedTagInstance
      softparsmap.AbstractSequenceData
          softparsmap.SequenceDataXml

All Implemented Interfaces:

Dependencies, SequenceData

public class SequenceDataXml

extends AbstractSequenceData

This class is used by DataSourceXmlNcbiTaxonomy to extract sequence data from one file in XML-format. The format is flexible within limits, see the def.xml file for more information.

Constructor Summary

SequenceDataXml()

Method Summary

int	getGiNumber() Returns the GI number.
int	getIdNumber() Returns the identity number for this sequence.
int	getSequenceLength() Returns the length of the sequence.
java.lang.String	getSpeciesName() Returns the species name that harbor this sequence.
boolean	isCompleteSequence() Returns true if the sequence is complete, otherwise false.
boolean	moveNextSequence() Move to next sequence in file.
FilePointerPart	newFilePointerPartCurrent() Returns a new FilePointerPart on current position in the file.
void	parseSequence(java.io.RandomAccessFile raf, FilePointerPart fpp) Parse in a sequence given a the file and pointer.
void	setDatabaseFile(java.io.RandomAccessFile raf) Sets the file that contains the sequences.

Methods inherited from class softparsmap.AbstractSequenceData

getPropertyFile

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

Constructor Detail

SequenceDataXml

public SequenceDataXml()

Method Detail

setDatabaseFile

public void setDatabaseFile(java.io.RandomAccessFile raf)

Description copied from class: AbstractSequenceData

Sets the file that contains the sequences.

Specified by:

setDatabaseFile in class AbstractSequenceData

Parameters:

raf - is the file containing the sequences

moveNextSequence

public boolean moveNextSequence()

Description copied from class: AbstractSequenceData

Move to next sequence in file.

Specified by:

moveNextSequence in class AbstractSequenceData

Returns:

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

newFilePointerPartCurrent

public FilePointerPart newFilePointerPartCurrent()

Description copied from class: AbstractSequenceData

Returns a new FilePointerPart on current position in the file.

Specified by:

newFilePointerPartCurrent in class AbstractSequenceData

Returns:

a FilePointerPart on current position in file

parseSequence

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

Description copied from class: AbstractSequenceData

Parse in a sequence given a the file and pointer.

Specified by:

parseSequence in class AbstractSequenceData

Parameters:

raf - is the file containing all the sequences

fpp - is the file pointer

getIdNumber

public int getIdNumber()

Description copied from interface: SequenceData

Returns the identity number for this sequence.

Returns:

the identity number for this sequence

isCompleteSequence

public boolean isCompleteSequence()

Description copied from interface: SequenceData

Returns true if the sequence is complete, otherwise false.

Returns:

true if sequence is complete

getGiNumber

public int getGiNumber()

Description copied from interface: SequenceData

Returns the GI number. For more information see NCBI . If the NCBI Taxonomy database is not used, let this method return -1.

Returns:

the GI number

getSequenceLength

public int getSequenceLength()

Description copied from interface: SequenceData

Returns the length of the sequence.

Returns:

the length of the sequence.

getSpeciesName

public java.lang.String getSpeciesName()

Description copied from interface: SequenceData

Returns the species name that harbor this sequence.

Returns:

the species name that harbor this sequence