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

All Superinterfaces:
java.lang.Cloneable, java.lang.Comparable<DSGeneMarker>, DSNamed, DSSequential, java.io.Serializable
All Known Implementing Classes:
CSExpressionMarker, CSGeneMarker, SequenceMarker

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

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

Copyright: Copyright (c) 2003

Company:

Version:
$Id$
Author:
not attributable

Method Summary
 java.lang.Object clone()
           
 DSGeneMarker deepCopy()
          Make a deep copy of this marker.
 java.lang.String getAnnotation()
           
 java.lang.String getDescription()
          Returns the textual description of this Marker
 int getGeneId()
          Returns a unique identifier that represent this piece of genetic information
 int[] getGeneIds()
          return all entrez ID's for this 'marker' (probe set) from annotation file
 java.lang.String getGeneName()
           
 java.lang.String getShortName()
           
 java.lang.String[] getShortNames()
          return all gene symbols for this 'marker' (probe set) from annotation file
 DSUnigene getUnigene()
           
 void setAnnotation(java.lang.String annot)
           
 void setDescription(java.lang.String label)
           
 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
 

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

getGeneIds

int[] getGeneIds()
return all entrez ID's for this 'marker' (probe set) from annotation file

Returns:

getUnigene

DSUnigene getUnigene()

getShortName

java.lang.String getShortName()
Returns:
String

getShortNames

java.lang.String[] getShortNames()
return all gene symbols for this 'marker' (probe set) from annotation file

Returns:

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

setGeneId

void setGeneId(int x)

setGeneName

void setGeneName(java.lang.String name)

getGeneName

java.lang.String getGeneName()

clone

java.lang.Object clone()

setAnnotation

void setAnnotation(java.lang.String annot)

getAnnotation

java.lang.String getAnnotation()