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

Constructors
Constructor and Description

Alignment()
Constructs a new Alignment object

Constructors
Constructor and Description
`Alignment()` Constructs a new Alignment object

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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
finalize, 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

Class Alignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Alignment

Method Detail

getSequence

getSequencesAsArrayList

getNumberOfSequences

getMaxSequenceLength

getMinSequenceLength

addSequence

setSequence

removeSequence

removeSequence

removeColumn

isMatchColumn

getCollapsedAlignment

getMatchPositionIndices

getMatchPositionIndexSets

getMatchPositionIndicesAsArrayList

getMostFrequentResidueType

getConsensusSequence

toString

toStringInfo

clone

equals

hashCode