jgromacs.data
Class Alignment

java.lang.Object
  jgromacs.data.Alignment

All Implemented Interfaces:

java.lang.Cloneable

public class Alignment
extends java.lang.Object
implements java.lang.Cloneable

Objects of this class represent a sequence alignment

Constructor Summary

Alignment()
Constructs a new Alignment object

Method Summary

void	addSequence(Sequence seq) Adds a new sequence to the alignment
java.lang.Object	clone() Returns an identical Alignment object
boolean	equals(java.lang.Object other) Returns true if the two alignments are identical
Alignment	getCollapsedAlignment() Returns the collapsed alignment in which only the match columns are included (i.e.
Sequence	getConsensusSequence() Returns the (majority) consensus sequence of the alignment
IndexSetList	getMatchPositionIndexSets() Returns the list of match position index sets (i.e.
IndexSet	getMatchPositionIndices(int i) Returns the set of position indices in sequence #i that are included in the match columns of alignment
java.util.ArrayList<java.lang.Integer>	getMatchPositionIndicesAsArrayList(int i) Returns the list of match position indices in sequence #i as an ArrayList object
int	getMaxSequenceLength() Returns the length of the longest sequence in the alignment
int	getMinSequenceLength() Returns the length of the shortest sequence in the alignment
ResidueType	getMostFrequentResidueType(int i) Returns the most frequent residue type in column #i of the alignment
int	getNumberOfSequences() Returns the number of sequences in the alignment
Sequence	getSequence(int i) Returns sequence #i of the alignment
java.util.ArrayList<Sequence>	getSequencesAsArrayList() Returns sequences of the alignment as an ArrayList object
int	hashCode() Returns hash code
boolean	isMatchColumn(int i) Returns true if column #i is a match column (i.e.
void	removeColumn(int i) Removes column #i from the alignment
void	removeSequence(int i) Removes sequence #i from the alignment
void	removeSequence(Sequence seq) Removes the given sequence from the alignment
void	setSequence(int i, Sequence seq) Replaces sequence #i of the alignment with a new sequence
java.lang.String	toString() Returns the String representation of alignment
java.lang.String	toStringInfo() Returns summary information about the alignment

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Alignment

public Alignment()

Constructs a new Alignment object

Method Detail

getSequence

public Sequence getSequence(int i)

Returns sequence #i of the alignment

Returns:

sequence #i

getSequencesAsArrayList

public java.util.ArrayList<Sequence> getSequencesAsArrayList()

Returns sequences of the alignment as an ArrayList object

Returns:

list of sequences as an ArrayList

getNumberOfSequences

public int getNumberOfSequences()

Returns the number of sequences in the alignment

Returns:

number of sequences

getMaxSequenceLength

public int getMaxSequenceLength()

Returns the length of the longest sequence in the alignment

Returns:

length of longest sequence

getMinSequenceLength

public int getMinSequenceLength()

Returns the length of the shortest sequence in the alignment

Returns:

length of shortest sequence

addSequence

public void addSequence(Sequence seq)

Adds a new sequence to the alignment

Parameters:

seq - new sequence

setSequence

public void setSequence(int i,
                        Sequence seq)

Replaces sequence #i of the alignment with a new sequence

Parameters:

seq - new sequence

removeSequence

public void removeSequence(int i)

Removes sequence #i from the alignment

removeSequence

public void removeSequence(Sequence seq)

Removes the given sequence from the alignment

Parameters:

seq - the sequence to be removed

removeColumn

public void removeColumn(int i)

Removes column #i from the alignment

isMatchColumn

public boolean isMatchColumn(int i)

Returns true if column #i is a match column (i.e. there is no gap in column #i of the alignment)

getCollapsedAlignment

public Alignment getCollapsedAlignment()

Returns the collapsed alignment in which only the match columns are included (i.e. the columns without gaps)

Returns:

collapsed alignment

getMatchPositionIndices

public IndexSet getMatchPositionIndices(int i)

Returns the set of position indices in sequence #i that are included in the match columns of alignment

Returns:

index set of match positions

getMatchPositionIndexSets

public IndexSetList getMatchPositionIndexSets()

Returns the list of match position index sets (i.e. match position index group of each sequence in the alignment)

Returns:

list of match positions index set

getMatchPositionIndicesAsArrayList

public java.util.ArrayList<java.lang.Integer> getMatchPositionIndicesAsArrayList(int i)

Returns the list of match position indices in sequence #i as an ArrayList object

Returns:

ArrayList of match positions

getMostFrequentResidueType

public ResidueType getMostFrequentResidueType(int i)

Returns the most frequent residue type in column #i of the alignment

Returns:

most frequent residue type

getConsensusSequence

public Sequence getConsensusSequence()

Returns the (majority) consensus sequence of the alignment

Returns:

consensus sequence

toString

public java.lang.String toString()

Returns the String representation of alignment

Overrides:

toString in class java.lang.Object

Returns:

String representation

toStringInfo

public java.lang.String toStringInfo()

Returns summary information about the alignment

Returns:

summary information

clone

public java.lang.Object clone()

Returns an identical Alignment object

Overrides:

clone in class java.lang.Object

Returns:

clone of the alignment

equals

public boolean equals(java.lang.Object other)

Returns true if the two alignments are identical

Overrides:

equals in class java.lang.Object

Parameters:

other - the other alignment

hashCode

public int hashCode()

Returns hash code

Overrides:

hashCode in class java.lang.Object