org.blackbox.shell
Class BBX_Annotation

java.lang.Object
  extended by org.blackbox.model.Hypothesis
      extended by org.blackbox.hypothesis.HAnnotation
          extended by org.blackbox.shell.BBX_Annotation
All Implemented Interfaces:
java.lang.Comparable, Interval, ObservableEntity

public class BBX_Annotation
extends HAnnotation


Field Summary
 
Fields inherited from class org.blackbox.model.Hypothesis
curEvent
 
Constructor Summary
BBX_Annotation(HSequence seq, Domain home, KnowledgeSource creator, java.util.Map annotations, boolean strand, int from, int to)
           
 
Method Summary
 java.lang.String asTab()
           
 java.lang.Object clone()
           
 org.biojava.bio.seq.FramedFeature.ReadingFrame featureFrame(int from, int to, boolean strand, HSequence seq)
           
 int getFrame()
          Frame of this interval.
 int getLength()
          Retourne la taille de cet intervalle.
 int getMax()
          Retourne la plus grande des deux coordonnees.
 int getMin()
          Retourne la plus petite des deux coordonnees.
 HSequence getSequence()
          Retourne la sequence qui porte ce feature.
 boolean getStrand()
          Strand holding this interval.
 boolean isFramed()
          Return true if this interval is framed.
 java.lang.String seqString()
          String representation for this interval.
 void setFramed(boolean bascule)
           
 java.lang.String toString()
          GFF compliant toString.
 
Methods inherited from class org.blackbox.hypothesis.HAnnotation
compareTo, getAnnotations
 
Methods inherited from class org.blackbox.model.Hypothesis
addObserver, gainFocus, getDomainOrigin, getKnowledge, getKsCreator, loseFocus, notifyObservers, removeObserver, setDomainOrigin, setKnowledge, setKsCreator
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

BBX_Annotation

public BBX_Annotation(HSequence seq,
                      Domain home,
                      KnowledgeSource creator,
                      java.util.Map annotations,
                      boolean strand,
                      int from,
                      int to)
               throws java.lang.RuntimeException
Throws:
java.lang.RuntimeException
Method Detail

featureFrame

public org.biojava.bio.seq.FramedFeature.ReadingFrame featureFrame(int from,
                                                                   int to,
                                                                   boolean strand,
                                                                   HSequence seq)

getStrand

public boolean getStrand()
Description copied from interface: Interval
Strand holding this interval.

Returns:
the frame or 0.

getFrame

public int getFrame()
Description copied from interface: Interval
Frame of this interval.

Returns:
the frame or 0.

getMax

public int getMax()
Description copied from interface: Interval
Retourne la plus grande des deux coordonnees.


getMin

public int getMin()
Description copied from interface: Interval
Retourne la plus petite des deux coordonnees.


getLength

public int getLength()
Description copied from interface: Interval
Retourne la taille de cet intervalle.


setFramed

public void setFramed(boolean bascule)

isFramed

public boolean isFramed()
Description copied from interface: Interval
Return true if this interval is framed.

Returns:
true if this interval is framed.

getSequence

public HSequence getSequence()
Description copied from class: HAnnotation
Retourne la sequence qui porte ce feature.

Specified by:
getSequence in class HAnnotation

seqString

public java.lang.String seqString()
Description copied from interface: Interval
String representation for this interval.

Returns:
the string representation.

toString

public java.lang.String toString()
GFF compliant toString. [attributes] [comments]

Overrides:
toString in class java.lang.Object

asTab

public java.lang.String asTab()

clone

public java.lang.Object clone()
Specified by:
clone in class Hypothesis