Interface FeatureI
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- All Known Implementing Classes:
Feature
public interface FeatureI
A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.- Author:
- Hanno Hinsch
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getAttribute(java.lang.String key)
Get the attribute value for this key.java.util.HashMap<java.lang.String,java.lang.String>
getAttributes()
java.lang.String
group()
Get the group id of the feature.boolean
hasAttribute(java.lang.String key)
Check if the feature has a value defined for the specified key.boolean
hasAttribute(java.lang.String key, java.lang.String value)
Check if the feature attributes include the specified key/value pair.Location
location()
Get the location of the feature.java.lang.String
seqname()
Get the sequence name.java.lang.String
toString()
A string representation of the feature.java.lang.String
type()
Get the feature type, for example, "exon", "CDS", etc.java.util.HashMap<java.lang.String,java.lang.String>
userData()
Get HashMap of user data.
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Method Detail
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location
Location location()
Get the location of the feature.- Returns:
- The location.
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group
java.lang.String group()
Get the group id of the feature. The group id is defined in the GFF1 format; features that share a common group id are presumed to be part of some logical group. For example, a gene might be represented by several exon features that all share the same group id.
The exact meaning of a feature's group id, or even its existence, is not guaranteed by this interface. An understanding of a particular file's data format is necessary to properly interpret the group id.- Returns:
- The group id. This may be an empty string.
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type
java.lang.String type()
Get the feature type, for example, "exon", "CDS", etc.- Returns:
- The type.
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seqname
java.lang.String seqname()
Get the sequence name.- Returns:
- Sequence name.
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getAttribute
java.lang.String getAttribute(java.lang.String key)
Get the attribute value for this key.- Parameters:
key
- The key.- Returns:
- The corresponding value. Null if the key has no value defined .
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hasAttribute
boolean hasAttribute(java.lang.String key)
Check if the feature has a value defined for the specified key.- Parameters:
key
- The key.- Returns:
- True if a value is defined for this key.
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hasAttribute
boolean hasAttribute(java.lang.String key, java.lang.String value)
Check if the feature attributes include the specified key/value pair.- Parameters:
key
- The key.value
- The value.- Returns:
- True if the feature's value for this key matches the specified value.
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toString
java.lang.String toString()
A string representation of the feature.- Overrides:
toString
in classjava.lang.Object
- Returns:
- The string.
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userData
java.util.HashMap<java.lang.String,java.lang.String> userData()
Get HashMap of user data.- Returns:
- The user HashMap.
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getAttributes
java.util.HashMap<java.lang.String,java.lang.String> getAttributes()
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