org.biojava.bio.seq
Interface StrandedFeature
- public interface StrandedFeature
- extends Feature
Adds the concept of 'strand' to features.
Strandedness only applies to some types of sequence, such as DNA. Any
implementation should blow chunks to avoid being added to a sequence for
which strand is a foreign concept.
- Author:
- Matthew Pocock
POSITIVE
public static final StrandedFeature.Strand POSITIVE
- flag to indicate that a feature is on the positive strand.
NEGATIVE
public static final StrandedFeature.Strand NEGATIVE
- flag to indicate that a feature is on the negative strand.
UNKNOWN
public static final StrandedFeature.Strand UNKNOWN
- flag to indicate that a feature has an unknown strand.
getStrand
public StrandedFeature.Strand getStrand()
- Retrieve the strand that this feature lies upon.
This will be one of StrandedFeature.POSITIVE or NEGATIVE.
- Returns:
- one of the Strand constants
getSymbols
public SymbolList getSymbols()
- Return a list of symbols that are contained in this feature.
The symbols may not be contiguous in the original sequence, but they
will be concatinated together in the resulting SymbolList.
The order of the Symbols within the resulting symbol list will be
according to the concept of ordering within the location object.
If the feature is on the negative strand then the SymbolList will be
reversecomplemented as apropreate.
- Specified by:
- getSymbols in interface Feature
- Returns:
- a SymbolList containing each symbol of the parent sequence contained
within this feature in the order they appear in the parent