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java.lang.Objectprocope.evaluation.complexquality.go.GOAnnotations
public class GOAnnotations
Represents a set of gene-product to GO-term annotations which are normally read from a file.
Constructor Summary | |
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GOAnnotations()
Create new empty GO annotations object. |
Method Summary | |
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void |
addAnnotation(int protein,
String term)
Adds the annotation of a given protein to a GO term. |
int |
getAnnotationCount(String term)
Returns the number of gene products annotated to a given GO term |
Set<String> |
getGOTerms(int protein)
Returns a set of identifiers of GO terms which are annotated to a given protein. |
Set<Integer> |
getProteins()
Returns the proteins which are used in this annotation set. |
boolean |
isAnnotated(int protein,
String term)
Checks whether a protein is annotated to a GO term. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public GOAnnotations()
Method Detail |
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public void addAnnotation(int protein, String term)
protein
- protein for which the term is annotatedterm
- identifier of the annotated GO termpublic int getAnnotationCount(String term)
term
- identifier of the GO term
public Set<String> getGOTerms(int protein)
protein
- protein for which the GO terms will be retrieved
public boolean isAnnotated(int protein, String term)
protein
- protein for which an annotation is checkedterm
- identifier of the GO term
public Set<Integer> getProteins()
getProteins
in interface ProteinSet
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