pairwise-logo.gif (1266 bytes)

All Packages  Class Hierarchy  This Package  Previous  Next  Index

Class PairwiseComparativeMap.PairwiseComparativeMapData 

java.lang.Object
   |
   +----PairwiseComparativeMap.PairwiseComparativeMapData
public class PairwiseComparativeMapData
extends Object
This is the highest level class in the Pairwise Comparative Map component data structure. It contains two Pairwise Maps and a PairwiseHomologys data structure describing the homologys between the two maps. You are advised to use the homology processing method to create your PairwiseHomologys data structure.

Version:
1.0

Author:
Written by Jeremy Dickson for the UK Crop Plant Bioinformatics Network, October 1998.

See Also:
PCM_FileParser, PairwiseLocus, PairwiseMap, PairwiseHomologys, LocusNoAndMap

Constructor Index

o PairwiseComparativeMapData(PairwiseMap, PairwiseMap)
Default constructor.
o PairwiseComparativeMapData(PairwiseMap, PairwiseMap, PairwiseHomologys)
This constructor allows you to enter the PairwiseHomologys object yourself.

Method Index

o getLHS_map()
Returns the map on the left-hand side.
o getPairwiseHomologys()
Returns the PairwiseHomologys object.
o getRHS_map()
Returns the map on the right-hand side.
o processHomologys(Array)
This method creates the data necessary to describe the homologys between the two maps.
o setLHS_Map(PairwiseMap)
Sets the map on the left-hand side.
o setRHS_Map(PairwiseMap)
Sets the map on the left-hand side.
o setSausageColour1(Color)
Sets the colour of the sausages of the first database to be encountered in the data
o setSausageColour2(Color)
Sets the colour of the sausages of the second database to be encountered in the data

Constructors

o PairwiseComparativeMapData 
 public PairwiseComparativeMapData(PairwiseMap leftMap,
                                   PairwiseMap rightMap)
Default constructor.

Parameters:
leftMap - The map on the left-hand side.
rightMap - The map on the right-hand side. If you are creating a PCM with only one map rather than two, feed null in to the second map.
o PairwiseComparativeMapData 
 public PairwiseComparativeMapData(PairwiseMap leftMap,
                                   PairwiseMap rightMap,
                                   PairwiseHomologys homologys)
This constructor allows you to enter the PairwiseHomologys object yourself. Advice- don't! Use the previous constructor and call the method processHomologys(Array).

Parameters:
leftMap - The map on the left-hand side.
rightMap - The map on the right-hand side. If you are creating a PCM with only one map rather than two, feed null in to the second map.
homologys - The PairwiseHomologys object.

Methods

o processHomologys 
 public void processHomologys(Array rawHomologys) throws PCMFileParsingException
This method creates the data necessary to describe the homologys between the two maps. An array of String arrays is fed in to the method.

THIS METHOD IS CALLED AUTOMATICALLY BY THE FILE PARSER.

Parameters:
rawHomologys - This array contains lots of String[2] arrays containing the name of the locus on the LHS map and on the RHS map that a relationship should be set up between.
See Also:
PCM_FileParser
o getPairwiseHomologys 
 public PairwiseHomologys getPairwiseHomologys()
Returns the PairwiseHomologys object.

o getLHS_map 
 public PairwiseMap getLHS_map()
Returns the map on the left-hand side.

o getRHS_map 
 public PairwiseMap getRHS_map()
Returns the map on the right-hand side.

o setLHS_Map 
 public void setLHS_Map(PairwiseMap LHS_Map)
Sets the map on the left-hand side.

o setRHS_Map 
 public void setRHS_Map(PairwiseMap RHS_Map)
Sets the map on the left-hand side.

o setSausageColour1 
 public void setSausageColour1(Color sausageColour1)
Sets the colour of the sausages of the first database to be encountered in the data

o setSausageColour2 
 public void setSausageColour2(Color sausageColour2)
Sets the colour of the sausages of the second database to be encountered in the data 

All Packages  Class Hierarchy  This Package  Previous  Next  Index