public class ReplaceNucleotideSequenceView extends org.biojava3.core.sequence.template.SequenceProxyView<org.biojava3.core.sequence.compound.NucleotideCompound> implements org.biojava3.core.sequence.template.SequenceView<org.biojava3.core.sequence.compound.NucleotideCompound>, CountableSequenceView
Modifier and Type | Field and Description |
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static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
AMBIGUITY_DNA_TO_N_RNA_MAP
Replaces all other ambiguity codes with N and T with U.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
AMBIGUITY_RNA_TO_N_DNA_MAP
Replaces all other ambiguity codes with N and U with T.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
AMBIGUITY_TO_N_MAP
Replaces all other ambiguity codes with N.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
AMBIGUITY_UNKNOWN_DNA_TO_N_RNA_MAP
Replaces all other ambiguity codes and ? with N and T with U.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
AMBIGUITY_UNKNOWN_RNA_TO_N_DNA_MAP
Replaces all other ambiguity codes and ? with N and U with T.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
DNA_TO_RNA_MAP
Replaces T/i> with U.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
RNA_TO_DNA_MAP
Replaces U with T.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
UNKNOWN_DNA_TO_N_RNA_MAP
Replaces ? with N and T with U.
|
static Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
UNKNOWN_RNA_TO_N_DNA_MAP
Replaces ? with N and U with T.
|
Constructor and Description |
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ReplaceNucleotideSequenceView(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound> sequence,
Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap) |
ReplaceNucleotideSequenceView(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound> sequence,
Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap,
Integer bioStart,
Integer bioEnd) |
Modifier and Type | Method and Description |
---|---|
int |
countChangedCompounds() |
org.biojava3.core.sequence.compound.NucleotideCompound |
getCompoundAt(int position) |
countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getBioEnd, getBioStart, getViewedSequence
countCompounds, getAsList, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSubSequence
forEach, iterator, spliterator
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> RNA_TO_DNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> DNA_TO_RNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_TO_N_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_RNA_TO_N_DNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_DNA_TO_N_RNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> UNKNOWN_RNA_TO_N_DNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> UNKNOWN_DNA_TO_N_RNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_UNKNOWN_RNA_TO_N_DNA_MAP
public static final Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_UNKNOWN_DNA_TO_N_RNA_MAP
public ReplaceNucleotideSequenceView(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound> sequence, Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap)
public ReplaceNucleotideSequenceView(org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound> sequence, Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap, Integer bioStart, Integer bioEnd)
public org.biojava3.core.sequence.compound.NucleotideCompound getCompoundAt(int position)
getCompoundAt
in interface org.biojava3.core.sequence.template.Sequence<org.biojava3.core.sequence.compound.NucleotideCompound>
getCompoundAt
in class org.biojava3.core.sequence.template.SequenceProxyView<org.biojava3.core.sequence.compound.NucleotideCompound>
public int countChangedCompounds()
countChangedCompounds
in interface CountableSequenceView