org.biojava3.core.sequence
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 and Description |
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MultipleSequenceAlignment() |
Modifier and Type | Method and Description |
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void |
addAlignedSequence(S sequence)
A sequence that has been aligned to other sequences will have inserts.
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S |
getAlignedSequence(int listIndex)
Uses bioIndex starting at 1 instead of 0
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java.util.List<S> |
getAlignedSequences()
Get the list of sequences
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java.util.List<C> |
getCompoundsAt(int alignmentIndex)
Get a list of compounds at a sequence position
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CompoundSet<C> |
getCompoundSet()
Get the Compounds defined in the first sequence
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int |
getLength()
Get the length of the MSA where it is assumed that
all sequence position
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int |
getSize()
Get the number of sequences in the MSA
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boolean |
removeAlignedSequence(S sequence)
Remove a sequence
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java.lang.String |
toString()
String representation of the MSA
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java.lang.String |
toString(int width)
Get a string representation of the MSA with a fixed width
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java.lang.String |
toString(LightweightProfile.StringFormat format)
Support for different MSA formats
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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)