org.biojava3.genome.parsers.gff
Constructor and Description |
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Feature(Feature feature)
Make a copy of the specified feature.
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Feature(java.lang.String seqname,
java.lang.String source,
java.lang.String type,
Location location,
java.lang.Double score,
int frame,
java.lang.String attributes)
Construct a new Feature from raw data (usually a GFF row).
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Modifier and Type | Method and Description |
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java.lang.String |
attributes()
Get the string of key/value attributes.
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int |
frame()
Get frame (aka phase).
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java.lang.String |
getAttribute(java.lang.String key)
Get value of specified attribute key.
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java.lang.String |
getAttributeOld(java.lang.String key) |
java.lang.String |
group()
Get the first item (everything before first semicolon, if it has one)
in the attribute field, which is assumed to
be a group identifer.
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boolean |
hasAttribute(java.lang.String key)
Check if the feature has a value defined for the specified key.
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boolean |
hasAttribute(java.lang.String key,
java.lang.String value)
Check if the feature attributes include the specified key/value pair.
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Location |
location()
Get location of feature.
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static void |
main(java.lang.String[] args)
Deprecated.
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double |
score()
Get score.
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java.lang.String |
seqname()
Get the sequence name.
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java.lang.String |
source()
Get source (aka method).
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java.lang.String |
toString()
A string representation of the feature.
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java.lang.String |
type()
Get feature type, such as "exon" or "CDS".
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java.util.HashMap<java.lang.String,java.lang.Object> |
userData()
Get HashMap of user data.
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public Feature(Feature feature)
feature
- Feature to clone.public Feature(java.lang.String seqname, java.lang.String source, java.lang.String type, Location location, java.lang.Double score, int frame, java.lang.String attributes)
seqname
- The sequence name field (field 1).source
- The source or method field (field 2).type
- The type of feature field (field 3).location
- The location of the feature. (calculated from GFF start, end and strand fields).score
- The score field (field 7).frame
- The frame or phase field (field 8).attributes
- A string of key/value pairs separated by semicolons (field 9).public java.lang.String seqname()
public java.lang.String source()
public java.lang.String type()
public Location location()
public double score()
public int frame()
public java.lang.String attributes()
public java.util.HashMap<java.lang.String,java.lang.Object> userData()
public java.lang.String getAttribute(java.lang.String key)
getAttribute
in interface FeatureI
key
- The key.public java.lang.String getAttributeOld(java.lang.String key)
public boolean hasAttribute(java.lang.String key)
FeatureI
hasAttribute
in interface FeatureI
key
- The key.public boolean hasAttribute(java.lang.String key, java.lang.String value)
FeatureI
hasAttribute
in interface FeatureI
key
- The key.value
- The value.public java.lang.String group()
public java.lang.String toString()
FeatureI
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception