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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
DNA_TO_RNA_MAP
Replaces T/i> with U.
|
static java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> |
RNA_TO_DNA_MAP
Replaces U with T.
|
static java.util.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 java.util.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,
java.util.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,
java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap,
java.lang.Integer bioStart,
java.lang.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
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> RNA_TO_DNA_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> DNA_TO_RNA_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_TO_N_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_RNA_TO_N_DNA_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_DNA_TO_N_RNA_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> UNKNOWN_RNA_TO_N_DNA_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> UNKNOWN_DNA_TO_N_RNA_MAP
public static final java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> AMBIGUITY_UNKNOWN_RNA_TO_N_DNA_MAP
public static final java.util.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, java.util.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, java.util.Map<org.biojava3.core.sequence.compound.NucleotideCompound,org.biojava3.core.sequence.compound.NucleotideCompound> replacementMap, java.lang.Integer bioStart, java.lang.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