org.geworkbench.bison.datastructure.bioobjects.markers
Interface DSGeneMarker

All Superinterfaces:

java.lang.Cloneable, java.lang.Comparable, DSNamed, DSSequential, java.io.Serializable

All Known Implementing Classes:

CSExpressionMarker, CSGeneMarker, CSGenotypeMarker, SequenceMarker

public interface DSGeneMarker
extends java.lang.Comparable, DSSequential, java.lang.Cloneable, java.io.Serializable

Title: Sequence and Pattern Plugin

Description:

Copyright: Copyright (c) 2003

Company:

Version:

1.0 This class is used to represent any arbitrary genetic marker, such as an Affy probe, a DNA sequence, etc. The accession should be the universal identifier of this data. This should be compatible with caBIO representation

Author:

not attributable

Field Summary

static int	AFFY_TYPE
static int	GENEPIX_TYPE
static int	LOCUSLINK_TYPE
static int	UNIGENE_TYPE

Method Summary

java.lang.Object	clone()
DSGeneMarker	deepCopy() Make a deep copy of this marker.
java.lang.String	getDescription() Returns the textual description of this Marker
int	getDisPlayType()
int	getGeneId() Returns a unique identifier that represent this piece of genetic information
java.lang.String	getGeneName()
java.lang.String	getShortName()
java.lang.String	getShortName(int maxLength)
DSUnigene	getUnigene()
boolean	isEquivalent(DSGeneMarker mInfo)
void	setDescription(java.lang.String label)
void	setDisPlayType(int disPlayType)
void	setGeneId(int x)
void	setGeneName(java.lang.String name)
void	write(java.io.BufferedWriter writer)

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSSequential

getSerial, setSerial

Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSNamed

getLabel, setLabel

Field Detail

AFFY_TYPE

static final int AFFY_TYPE

See Also:

Constant Field Values

GENEPIX_TYPE

static final int GENEPIX_TYPE

See Also:

Constant Field Values

UNIGENE_TYPE

static final int UNIGENE_TYPE

See Also:

Constant Field Values

LOCUSLINK_TYPE

static final int LOCUSLINK_TYPE

See Also:

Constant Field Values

Method Detail

getDescription

java.lang.String getDescription()

Returns the textual description of this Marker

Returns:

a String representing the textual representation

setDescription

void setDescription(java.lang.String label)

getGeneId

int getGeneId()

Returns a unique identifier that represent this piece of genetic information

Returns:

a unique identifier

getUnigene

DSUnigene getUnigene()

getShortName

java.lang.String getShortName()

Returns:

String

getShortName

java.lang.String getShortName(int maxLength)

isEquivalent

boolean isEquivalent(DSGeneMarker mInfo)

deepCopy

DSGeneMarker deepCopy()

Make a deep copy of this marker.

Returns:

write

void write(java.io.BufferedWriter writer)
           throws java.io.IOException

Throws:

java.io.IOException

setDisPlayType

void setDisPlayType(int disPlayType)

getDisPlayType

int getDisPlayType()

setGeneId

void setGeneId(int x)

setGeneName

void setGeneName(java.lang.String name)

getGeneName

java.lang.String getGeneName()

clone

java.lang.Object clone()