owltools.gaf.rules
Class AnnotationRuleViolation

java.lang.Object
  extended by owltools.gaf.rules.AnnotationRuleViolation

public class AnnotationRuleViolation
extends Object

Data associated with a rule violation


Nested Class Summary
static class AnnotationRuleViolation.ViolationType
           
 
Constructor Summary
AnnotationRuleViolation(String ruleId, String msg)
          Create a simple violation from with a given message.
AnnotationRuleViolation(String ruleId, String message, GeneAnnotation sourceAnnotation)
          Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String ruleId, String message, GeneAnnotation sourceAnnotation, AnnotationRuleViolation.ViolationType type)
          Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String ruleId, String message, String annotationRow)
          Create a violation object with a message and a the corresponding annotation row.
AnnotationRuleViolation(String ruleId, String message, String annotationRow, AnnotationRuleViolation.ViolationType type)
          Create a violation object with a message and a the corresponding annotation row and AnnotationRuleViolation.ViolationType.
 
Method Summary
 String getAnnotationRow()
           
 String getGafDocument()
           
 int getLineNumber()
           
 String getMessage()
           
 String getRuleId()
           
 GeneAnnotation getSourceAnnotation()
           
 Set<GeneAnnotation> getSuggestedReplacements()
           
 AnnotationRuleViolation.ViolationType getType()
           
 void setAnnotationRow(String annotationRow)
           
 void setGafDoument(String gafDoument)
           
 void setLineNumber(int lineNumber)
           
 void setSourceAnnotation(GeneAnnotation sourceAnnotation)
           
 void setSuggestedReplacements(Set<GeneAnnotation> suggestedReplacements)
           
 void setType(AnnotationRuleViolation.ViolationType type)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

AnnotationRuleViolation

public AnnotationRuleViolation(String ruleId,
                               String msg)
Create a simple violation from with a given message.

Parameters:
ruleId -
msg -

AnnotationRuleViolation

public AnnotationRuleViolation(String ruleId,
                               String message,
                               GeneAnnotation sourceAnnotation)
Create a violation object with a message and a the corresponding source annotation.

Parameters:
ruleId -
message -
sourceAnnotation -

AnnotationRuleViolation

public AnnotationRuleViolation(String ruleId,
                               String message,
                               GeneAnnotation sourceAnnotation,
                               AnnotationRuleViolation.ViolationType type)
Create a violation object with a message and a the corresponding source annotation.

Parameters:
ruleId -
message -
sourceAnnotation -
type -

AnnotationRuleViolation

public AnnotationRuleViolation(String ruleId,
                               String message,
                               String annotationRow)
Create a violation object with a message and a the corresponding annotation row.

Parameters:
ruleId -
message -
annotationRow -

AnnotationRuleViolation

public AnnotationRuleViolation(String ruleId,
                               String message,
                               String annotationRow,
                               AnnotationRuleViolation.ViolationType type)
Create a violation object with a message and a the corresponding annotation row and AnnotationRuleViolation.ViolationType.

Parameters:
ruleId -
message -
annotationRow -
type -
Method Detail

getRuleId

public String getRuleId()

getMessage

public String getMessage()

getSuggestedReplacements

public Set<GeneAnnotation> getSuggestedReplacements()

setSuggestedReplacements

public void setSuggestedReplacements(Set<GeneAnnotation> suggestedReplacements)

getSourceAnnotation

public GeneAnnotation getSourceAnnotation()

setSourceAnnotation

public void setSourceAnnotation(GeneAnnotation sourceAnnotation)

getAnnotationRow

public String getAnnotationRow()

setAnnotationRow

public void setAnnotationRow(String annotationRow)

getLineNumber

public int getLineNumber()

setLineNumber

public void setLineNumber(int lineNumber)

getGafDocument

public String getGafDocument()

setGafDoument

public void setGafDoument(String gafDoument)

getType

public AnnotationRuleViolation.ViolationType getType()
Returns:
the type

setType

public void setType(AnnotationRuleViolation.ViolationType type)
Parameters:
type - the type to set

toString

public String toString()
Overrides:
toString in class Object


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