LightweightProfile<S,C>
public class MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> extends java.lang.Object implements LightweightProfile<S,C>
Profile
data
structure in the alignment module provides additional functionality.LightweightProfile.StringFormat
Constructor | Description |
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MultipleSequenceAlignment() |
Modifier and Type | Method | Description |
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void |
addAlignedSequence(S sequence) |
A sequence that has been aligned to other sequences will have inserts.
|
S |
getAlignedSequence(int listIndex) |
Uses bioIndex starting at 1 instead of 0
|
java.util.List<S> |
getAlignedSequences() |
Get the list of sequences
|
java.util.List<C> |
getCompoundsAt(int alignmentIndex) |
Get a list of compounds at a sequence position
|
CompoundSet<C> |
getCompoundSet() |
Get the Compounds defined in the first sequence
|
int |
getLength() |
Get the length of the MSA where it is assumed that
all sequence position
|
int |
getSize() |
Get the number of sequences in the MSA
|
boolean |
removeAlignedSequence(S sequence) |
Remove a sequence
|
java.lang.String |
toString() |
String representation of the MSA
|
java.lang.String |
toString(int width) |
Get a string representation of the MSA with a fixed width
|
java.lang.String |
toString(LightweightProfile.StringFormat format) |
Support for different MSA formats
|
public void addAlignedSequence(S sequence)
sequence
- public boolean removeAlignedSequence(S sequence)
sequence
- public S getAlignedSequence(int listIndex)
getAlignedSequence
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
listIndex
- public java.util.List<S> getAlignedSequences()
getAlignedSequences
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
public java.util.List<C> getCompoundsAt(int alignmentIndex)
getCompoundsAt
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
alignmentIndex
- public CompoundSet<C> getCompoundSet()
getCompoundSet
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
public int getLength()
public int getSize()
public java.lang.String toString(int width)
public java.lang.String toString(LightweightProfile.StringFormat format)