C
- public class ConcatenatedSequenceView<C extends org.biojava3.core.sequence.template.Compound> extends java.lang.Object implements org.biojava3.core.sequence.template.SequenceView<C>
Modifier and Type | Class and Description |
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class |
ConcatenatedSequenceView.ViewedSequence |
Constructor and Description |
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ConcatenatedSequenceView() |
ConcatenatedSequenceView(java.util.Collection<org.biojava3.core.sequence.template.Sequence<C>> sequences) |
ConcatenatedSequenceView(org.biojava3.core.sequence.template.Sequence<C> sequence) |
ConcatenatedSequenceView(org.biojava3.core.sequence.template.Sequence<C>[] sequences) |
Modifier and Type | Method and Description |
---|---|
int |
countCompounds(C... compounds) |
org.biojava3.core.sequence.AccessionID |
getAccession()
Returns the accession ID of the first viewed sequence.
|
java.util.List<C> |
getAsList() |
java.lang.Integer |
getBioEnd() |
java.lang.Integer |
getBioStart() |
C |
getCompoundAt(int position) |
org.biojava3.core.sequence.template.CompoundSet<C> |
getCompoundSet() |
int |
getIndexOf(C compound) |
org.biojava3.core.sequence.template.SequenceView<C> |
getInverse() |
int |
getLastIndexOf(C compound) |
int |
getLength() |
java.lang.String |
getSequenceAsString() |
org.biojava3.core.sequence.template.SequenceView<C> |
getSubSequence(java.lang.Integer bioStart,
java.lang.Integer bioEnd) |
org.biojava3.core.sequence.template.Sequence<C> |
getViewedSequence()
Returns the first viewed sequence.
|
ConcatenatedSequenceView.ViewedSequence |
getViewedSequenceByPosition(int position) |
int |
getViewedSequenceCount() |
java.util.Iterator<C> |
iterator() |
java.util.List<org.biojava3.core.sequence.template.Sequence<C>> |
sequencesAsList()
Returns a list implementation that allows to edit the underlying list of viewed sequences.
|
public ConcatenatedSequenceView()
public ConcatenatedSequenceView(java.util.Collection<org.biojava3.core.sequence.template.Sequence<C>> sequences)
public ConcatenatedSequenceView(org.biojava3.core.sequence.template.Sequence<C>[] sequences)
public ConcatenatedSequenceView(org.biojava3.core.sequence.template.Sequence<C> sequence)
public int getViewedSequenceCount()
public org.biojava3.core.sequence.template.Sequence<C> getViewedSequence()
getViewedSequence
in interface org.biojava3.core.sequence.template.SequenceView<C extends org.biojava3.core.sequence.template.Compound>
SequenceView.getViewedSequence()
public java.util.Iterator<C> iterator()
iterator
in interface java.lang.Iterable<C extends org.biojava3.core.sequence.template.Compound>
public ConcatenatedSequenceView.ViewedSequence getViewedSequenceByPosition(int position)
public C getCompoundAt(int position)
getCompoundAt
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public int getLength()
getLength
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public int countCompounds(C... compounds)
countCompounds
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public java.util.List<C> getAsList()
getAsList
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public org.biojava3.core.sequence.template.CompoundSet<C> getCompoundSet()
getCompoundSet
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public int getIndexOf(C compound)
getIndexOf
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public org.biojava3.core.sequence.template.SequenceView<C> getInverse()
getInverse
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public int getLastIndexOf(C compound)
getLastIndexOf
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public java.lang.String getSequenceAsString()
getSequenceAsString
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public org.biojava3.core.sequence.template.SequenceView<C> getSubSequence(java.lang.Integer bioStart, java.lang.Integer bioEnd)
getSubSequence
in interface org.biojava3.core.sequence.template.Sequence<C extends org.biojava3.core.sequence.template.Compound>
public org.biojava3.core.sequence.AccessionID getAccession()
getAccession
in interface org.biojava3.core.sequence.template.Accessioned
Accessioned.getAccession()
public java.lang.Integer getBioEnd()
getBioEnd
in interface org.biojava3.core.sequence.template.SequenceView<C extends org.biojava3.core.sequence.template.Compound>
public java.lang.Integer getBioStart()
getBioStart
in interface org.biojava3.core.sequence.template.SequenceView<C extends org.biojava3.core.sequence.template.Compound>
public java.util.List<org.biojava3.core.sequence.template.Sequence<C>> sequencesAsList()