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java.lang.Objectorg.biojava3.core.sequence.MultipleSequenceAlignment<S,C>
public class MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound>
Implements a minimal data structure for reading and writing a sequence alignment. The full Profile
data
structure in the alignment module provides additional functionality.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojava3.core.sequence.template.LightweightProfile |
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LightweightProfile.StringFormat |
Constructor Summary | |
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MultipleSequenceAlignment()
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Method Summary | |
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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 |
List<S> |
getAlignedSequences()
Get the list of sequences |
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 |
String |
toString()
String representation of the MSA |
String |
toString(int width)
Get a string representation of the MSA with a fixed width |
String |
toString(LightweightProfile.StringFormat format)
Support for different MSA formats |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public MultipleSequenceAlignment()
Method Detail |
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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 List<S> getAlignedSequences()
getAlignedSequences
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
public 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()
getLength
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
public int getSize()
getSize
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
public String toString(int width)
toString
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
width
-
public String toString(LightweightProfile.StringFormat format)
toString
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
format
-
public String toString()
toString
in interface LightweightProfile<S extends Sequence<C>,C extends Compound>
toString
in class Object
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