public class UnalignedSequenceView<C extends org.biojava3.core.sequence.template.Compound> extends RemoveSequenceView<C> implements org.biojava3.core.sequence.template.SequenceView<C>
SequenceView
interface which provides access
to an aligned sequence (with gaps) as if it would be unaligned (without
gaps).Constructor and Description |
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UnalignedSequenceView(org.biojava3.core.sequence.template.Sequence<C> sequence,
org.biojava3.core.sequence.template.CompoundSet<C> nonGapCompoundSet)
Creates a new instance of this class.
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UnalignedSequenceView(org.biojava3.core.sequence.template.Sequence<C> sequence,
org.biojava3.core.sequence.template.CompoundSet<C> nonGapCompoundSet,
java.lang.Integer bioStart,
java.lang.Integer bioEnd)
Creates a new instance of this class.
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Modifier and Type | Method and Description |
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org.biojava3.core.sequence.template.CompoundSet<C> |
getNonGapCompoundSet()
Returns the set of compounds representing non-gap positions in the underlying sequence.
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protected boolean |
keepPosition(int viewedPos) |
getCompoundAt, getLength, getRemainingPositions
countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getSequenceAsString, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getBioEnd, getBioStart, getViewedSequence
public UnalignedSequenceView(org.biojava3.core.sequence.template.Sequence<C> sequence, org.biojava3.core.sequence.template.CompoundSet<C> nonGapCompoundSet, java.lang.Integer bioStart, java.lang.Integer bioEnd)
sequence
- the underlying aligned sequencenonGapCompoundSet
- the set of compounds representing non-gap positions in sequence
bioStart
- start index, cannot be less than 1bioEnd
- end index, cannot be greater than the sequence lengthpublic UnalignedSequenceView(org.biojava3.core.sequence.template.Sequence<C> sequence, org.biojava3.core.sequence.template.CompoundSet<C> nonGapCompoundSet)
sequence
- the underlying aligned sequencenonGapCompoundSet
- the set of compounds representing non-gap positions in sequence
protected boolean keepPosition(int viewedPos)
keepPosition
in class RemoveSequenceView<C extends org.biojava3.core.sequence.template.Compound>
public org.biojava3.core.sequence.template.CompoundSet<C> getNonGapCompoundSet()