org.biojava.bio.program.das.dasalignment
Class Alignment

java.lang.Object
  org.biojava.bio.program.das.dasalignment.Alignment

public class Alignment

extends Object

Alignment object to contain/manage a DAS alignment. the description of the alignment objects is an ArrayList of HashMaps

Author:

Andreas Prlic

See Also:

DAS specification at http://www.sanger.ac.uk/Users/ap3/DAS/new_spec.html

Each objects is described by a HashMap that has the following keys:

 mandatory: 
 * id      
 * version 
 * type    
 * coordinateSystem
 * optional:
 * description
 * sequence
 ArrayList notes (a list of strings)
 

scores is an ArrayList of HashMaps (can be empty) keys: mandatory: scorename scorevalue

blocks: ArrayList consisting of ArrayList block. block: ArrayList of hashMaps with the following keys: mandatory: id start end optional: orientation cigarstring

Constructor Summary

Alignment()

Method Summary

void	addBlock(ArrayList segment)
void	addObject(HashMap object)
void	addScore(HashMap score)
ArrayList	getBlocks()
ArrayList	getObjects()
ArrayList	getScores()
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Alignment

public Alignment()

Method Detail

addObject

public void addObject(HashMap object)
               throws DASException

Throws:

DASException

getObjects

public ArrayList getObjects()

addScore

public void addScore(HashMap score)
              throws DASException

Throws:

DASException

getScores

public ArrayList getScores()

addBlock

public void addBlock(ArrayList segment)
              throws DASException

Throws:

DASException

getBlocks

public ArrayList getBlocks()

toString

public String toString()