jadex.swing.sequence
Class Contig

java.lang.Object
  |
  +--jadex.swing.sequence.Contig

public class Contig
extends java.lang.Object

A wrapper class for Contig.


Constructor Summary
Contig()
          Creates new Contig
Contig(java.lang.String name)
          Second constructor with name as the arguemnt
Contig(java.lang.String name, java.lang.String map)
          Third constructor with name, map as the arguement
Contig(java.lang.String name, java.lang.String map, MapRange ext, MapRange pm)
          Fourth constructor with all properties as the arguments
 
Method Summary
 jade.db.AceObject getAceObject()
          Get the wrapped AceObject for this Contig.
 MapRange getExtend()
           
 MapRange getExtendF()
           
 java.lang.String getMap()
          Get the name of the Sequence_map this contig is in.
 java.lang.String getName()
          Get the name of the contig.
 MapRange getPMap()
           
 MapRange getRangeFromPMap(MapRange p)
          Transfer the PMap range to SequenceMap range.
 void setAceObject(jade.db.AceObject o)
          Set the wrapped AceObject for this Contig.
 void setExtend(MapRange r)
          Set the MapRange if contig in Sequence_map.
 void setExtendF(MapRange r)
          Set the MapRange of contig in GeneticMap
 void setMap(java.lang.String map)
          Set the name of the Sequence_map this contig is in.
 void setName(java.lang.String name)
          Set the name of the contig.
 void setPMap(MapRange r)
           
 java.lang.String toString()
          For pretty-printing purpose.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Contig

public Contig()
Creates new Contig

Contig

public Contig(java.lang.String name)
Second constructor with name as the arguemnt

Contig

public Contig(java.lang.String name,
              java.lang.String map)
Third constructor with name, map as the arguement

Contig

public Contig(java.lang.String name,
              java.lang.String map,
              MapRange ext,
              MapRange pm)
Fourth constructor with all properties as the arguments
Method Detail

getRangeFromPMap

public MapRange getRangeFromPMap(MapRange p)
Transfer the PMap range to SequenceMap range.
Parameters:
p - the PMap.
Returns:
the MapRange in Sequence_map.

setName

public void setName(java.lang.String name)
Set the name of the contig.
Parameters:
name - the name of the contig.

getName

public java.lang.String getName()
Get the name of the contig.
Returns:
the name of the contig.

setMap

public void setMap(java.lang.String map)
Set the name of the Sequence_map this contig is in.
Parameters:
map - the name of the Sequence_map this contig is in.

getMap

public java.lang.String getMap()
Get the name of the Sequence_map this contig is in.
Returns:
the name of the Sequence_map.

setExtend

public void setExtend(MapRange r)
Set the MapRange if contig in Sequence_map.

getExtend

public MapRange getExtend()

setExtendF

public void setExtendF(MapRange r)
Set the MapRange of contig in GeneticMap

getExtendF

public MapRange getExtendF()

setPMap

public void setPMap(MapRange r)

getPMap

public MapRange getPMap()

setAceObject

public void setAceObject(jade.db.AceObject o)
Set the wrapped AceObject for this Contig.
Parameters:
o - the wrapped AceObject.

getAceObject

public jade.db.AceObject getAceObject()
Get the wrapped AceObject for this Contig.
Returns:
the wrapped AceObject.

toString

public java.lang.String toString()
For pretty-printing purpose.
Overrides:
toString in class java.lang.Object
Following copied from class: java.lang.Object
Returns:
a string representation of the object.