org.geworkbench.bison.datastructure.bioobjects.markers
Class CSGeneMarker

java.lang.Object
  extended by org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<DSGeneMarker>, DSGeneMarker, DSNamed, DSSequential
Direct Known Subclasses:
CSExpressionMarker, SequenceMarker

public class CSGeneMarker
extends java.lang.Object
implements DSGeneMarker, java.io.Serializable

Title: Bioworks

Description: Modular Application Framework for Gene Expession, Sequence and Genotype Analysis

Copyright: Copyright (c) 2003 -2004

Company: Columbia University

Version:
$Id: CSGeneMarker.java 10604 2013-05-30 16:09:40Z wangmen $
Author:
not attributable
See Also:
Serialized Form

Field Summary
protected  java.lang.String abrev
           
protected  java.lang.String description
           
protected  int geneId
           
protected  int[] geneIds
           
protected  java.lang.String label
           
protected  int markerId
           
protected  DSUnigene unigene
           
 
Constructor Summary
CSGeneMarker()
           
CSGeneMarker(java.lang.String label)
           
 
Method Summary
 java.lang.Object clone()
           
 int compareTo(DSGeneMarker marker)
          Implementation of the Comparable interface.
 DSGeneMarker deepCopy()
          Make a deep copy of this marker.
 boolean equals(java.lang.Object marker)
           
 java.lang.String getAnnotation()
           
 java.lang.String getDescription()
          getLabel
 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 getLabel()
          getAccession
 int getSerial()
          getSerial
 java.lang.String getShortName()
           
 java.lang.String[] getShortNames()
          return all gene symbols for this 'marker' (probe set) from annotation file
 DSUnigene getUnigene()
           
 int hashCode()
           
 void setAnnotation(java.lang.String annot)
           
 void setDescription(java.lang.String label)
           
 void setGeneId(int locusLink)
           
 void setGeneName(java.lang.String geneName)
           
 void setLabel(java.lang.String label)
          Sets the label for this object.
 void setSerial(int id)
          Sets the serial for this object
 java.lang.String toString()
           
 void write(java.io.BufferedWriter writer)
           
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

label

protected java.lang.String label

description

protected java.lang.String description

abrev

protected java.lang.String abrev

markerId

protected int markerId

geneId

protected int geneId

geneIds

protected int[] geneIds

unigene

protected DSUnigene unigene
Constructor Detail

CSGeneMarker

public CSGeneMarker()

CSGeneMarker

public CSGeneMarker(java.lang.String label)
Method Detail

clone

public java.lang.Object clone()
Specified by:
clone in interface DSGeneMarker
Overrides:
clone in class java.lang.Object

getDescription

public java.lang.String getDescription()
getLabel

Specified by:
getDescription in interface DSGeneMarker
Returns:
String

setDescription

public void setDescription(java.lang.String label)
Specified by:
setDescription in interface DSGeneMarker

getLabel

public java.lang.String getLabel()
getAccession

Specified by:
getLabel in interface DSNamed
Returns:
String

getGeneId

public int getGeneId()
Description copied from interface: DSGeneMarker
Returns a unique identifier that represent this piece of genetic information

Specified by:
getGeneId in interface DSGeneMarker
Returns:
a unique identifier

setLabel

public void setLabel(java.lang.String label)
Description copied from interface: DSNamed
Sets the label for this object.

Specified by:
setLabel in interface DSNamed
Parameters:
label - the new label for this object.

setGeneId

public void setGeneId(int locusLink)
Specified by:
setGeneId in interface DSGeneMarker

setGeneName

public void setGeneName(java.lang.String geneName)
Specified by:
setGeneName in interface DSGeneMarker

getSerial

public int getSerial()
getSerial

Specified by:
getSerial in interface DSSequential
Returns:
int

setSerial

public void setSerial(int id)
Description copied from interface: DSSequential
Sets the serial for this object

Specified by:
setSerial in interface DSSequential
Parameters:
id - the new serial.

equals

public boolean equals(java.lang.Object marker)
Overrides:
equals in class java.lang.Object

compareTo

public int compareTo(DSGeneMarker marker)
Implementation of the Comparable interface.

Specified by:
compareTo in interface java.lang.Comparable<DSGeneMarker>
Parameters:
o -
Returns:

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

getShortName

public java.lang.String getShortName()
Specified by:
getShortName in interface DSGeneMarker
Returns:
String

hashCode

public int hashCode()
Overrides:
hashCode in class java.lang.Object

write

public void write(java.io.BufferedWriter writer)
           throws java.io.IOException
Specified by:
write in interface DSGeneMarker
Throws:
java.io.IOException

getUnigene

public DSUnigene getUnigene()
Specified by:
getUnigene in interface DSGeneMarker

getGeneName

public java.lang.String getGeneName()
Specified by:
getGeneName in interface DSGeneMarker

deepCopy

public DSGeneMarker deepCopy()
Description copied from interface: DSGeneMarker
Make a deep copy of this marker.

Specified by:
deepCopy in interface DSGeneMarker
Returns:

getGeneIds

public int[] getGeneIds()
Description copied from interface: DSGeneMarker
return all entrez ID's for this 'marker' (probe set) from annotation file

Specified by:
getGeneIds in interface DSGeneMarker
Returns:

getShortNames

public java.lang.String[] getShortNames()
Description copied from interface: DSGeneMarker
return all gene symbols for this 'marker' (probe set) from annotation file

Specified by:
getShortNames in interface DSGeneMarker
Returns:

setAnnotation

public void setAnnotation(java.lang.String annot)
Specified by:
setAnnotation in interface DSGeneMarker

getAnnotation

public java.lang.String getAnnotation()
Specified by:
getAnnotation in interface DSGeneMarker