org.vectorbase.gdav.beans
Class Alignment

java.lang.Object
  extended by org.vectorbase.gdav.beans.Alignment

public class Alignment
extends java.lang.Object

Alignment Javabean

Author:
seth.redmond@imperial.ac.uk Seth Redmond
See Also:
DBConnection

Constructor Summary
Alignment()
          empty constructor
Alignment(java.lang.String newSpp, java.lang.String newChr, int newStart, int newEnd, int newStrand, java.lang.String newCigar, int newScore, java.lang.String newMethod)
          pass basic-info constructor
 
Method Summary
 java.lang.String getChr()
           
 java.lang.String getCigar()
           
 int getEnd()
           
 java.util.List getHSPs()
          use cigar line to split alignment into constituent high-scoring pairs
 java.lang.String getLocation()
           
 java.lang.String getMethod()
           
 int getScore()
           
 java.lang.String getSpp()
           
 int getStart()
           
 int getStrand()
           
 void setChr(java.lang.String newChr)
           
 void setCigar(java.lang.String newCigar)
           
 void setEnd(int newEnd)
           
 void setMethod(java.lang.String newMethod)
           
 void setScore(int newScore)
           
 void setSpp(java.lang.String newSpp)
           
 void setStart(int newStart)
           
 void setStrand(int newStrand)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Alignment

public Alignment()
empty constructor


Alignment

public Alignment(java.lang.String newSpp,
                 java.lang.String newChr,
                 int newStart,
                 int newEnd,
                 int newStrand,
                 java.lang.String newCigar,
                 int newScore,
                 java.lang.String newMethod)
pass basic-info constructor

Method Detail

setMethod

public void setMethod(java.lang.String newMethod)

getMethod

public java.lang.String getMethod()

setSpp

public void setSpp(java.lang.String newSpp)

getSpp

public java.lang.String getSpp()

setChr

public void setChr(java.lang.String newChr)

getChr

public java.lang.String getChr()

setStart

public void setStart(int newStart)

getStart

public int getStart()

setEnd

public void setEnd(int newEnd)

getEnd

public int getEnd()

setStrand

public void setStrand(int newStrand)

getStrand

public int getStrand()

setCigar

public void setCigar(java.lang.String newCigar)

getCigar

public java.lang.String getCigar()

setScore

public void setScore(int newScore)

getScore

public int getScore()

getLocation

public java.lang.String getLocation()

getHSPs

public java.util.List getHSPs()
use cigar line to split alignment into constituent high-scoring pairs