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java.lang.Objectorg.blackbox.model.Hypothesis
org.blackbox.hypothesis.HAnnotation
org.blackbox.shell.BBX_Annotation
public class BBX_Annotation
Field Summary |
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Fields inherited from class org.blackbox.model.Hypothesis |
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curEvent |
Constructor Summary | |
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BBX_Annotation(HSequence seq,
Domain home,
KnowledgeSource creator,
java.util.Map annotations,
boolean strand,
int from,
int to)
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Method Summary | |
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java.lang.String |
asTab()
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java.lang.Object |
clone()
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org.biojava.bio.seq.FramedFeature.ReadingFrame |
featureFrame(int from,
int to,
boolean strand,
HSequence seq)
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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)
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java.lang.String |
toString()
GFF compliant toString. |
Methods inherited from class org.blackbox.hypothesis.HAnnotation |
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compareTo, getAnnotations |
Methods inherited from class org.blackbox.model.Hypothesis |
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addObserver, gainFocus, getDomainOrigin, getKnowledge, getKsCreator, loseFocus, notifyObservers, removeObserver, setDomainOrigin, setKnowledge, setKsCreator |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public BBX_Annotation(HSequence seq, Domain home, KnowledgeSource creator, java.util.Map annotations, boolean strand, int from, int to) throws java.lang.RuntimeException
java.lang.RuntimeException
Method Detail |
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public org.biojava.bio.seq.FramedFeature.ReadingFrame featureFrame(int from, int to, boolean strand, HSequence seq)
public boolean getStrand()
Interval
public int getFrame()
Interval
public int getMax()
Interval
public int getMin()
Interval
public int getLength()
Interval
public void setFramed(boolean bascule)
public boolean isFramed()
Interval
public HSequence getSequence()
HAnnotation
getSequence
in class HAnnotation
public java.lang.String seqString()
Interval
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String asTab()
public java.lang.Object clone()
clone
in class Hypothesis
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