public class MSAanalysis
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
aaSymbols |
private int[][] |
Alignment |
private int |
AliNmb |
Constructor and Description |
---|
MSAanalysis(int[][] Align) |
MSAanalysis(java.util.List<java.lang.String> Align) |
Modifier and Type | Method and Description |
---|---|
boolean |
checkIfNonDeletion(int i,
double cutoff)
Check if there is deletion or unknown amino acid frequency higher than the cutoff at the chosen position in MSA.
|
int[][] |
getAlignment()
Get alignment in the integer format.
|
private double |
runEntropyCalc(int i,
boolean ifGaps,
boolean ifNormalized)
Calculate Shannon Entropy.
|
double |
shannonEntropyCalc(int i,
boolean ifGaps)
Calculate Shannon Entropy.
|
double |
shannonEntropyCalc(int i,
boolean ifGaps,
boolean ifNormalized)
Calculate Shannon Entropy.
|
int |
variabilityCalc(int i,
double cutoff,
boolean ifGaps)
Calculate variability for the MSA position - number of different amino acids which occur more frequent than the cutoff value.
|
private int[][] Alignment
private int AliNmb
private int aaSymbols
MSAanalysis(int[][] Align)
Align
- - matrix [sequence number x sequence length] of numbers representing different amino acidsMSAanalysis(java.util.List<java.lang.String> Align)
Align
- - list of sequences written as strings of amino acids symbolspublic int[][] getAlignment()
public boolean checkIfNonDeletion(int i, double cutoff)
i
- - position in the MSA (numbered from 0)cutoff
- - cutoff frequency in percentagepublic double shannonEntropyCalc(int i, boolean ifGaps)
i
- - position in the MSA (numbered from 0)ifGaps
- - true/false - with/without counting gapspublic double shannonEntropyCalc(int i, boolean ifGaps, boolean ifNormalized)
i
- - position in the MSA (numbered from 0)ifGaps
- - true/false - with/without counting gapsifNormalized
- - true if result must be normalizedprivate double runEntropyCalc(int i, boolean ifGaps, boolean ifNormalized)
i
- - position in the MSA (numbered from 0)ifGaps
- - true/false - with/without counting gapsifNormalized
- - true if result must be normalizedpublic int variabilityCalc(int i, double cutoff, boolean ifGaps)
i
- - position in the MSA (numbered from 0)cutoff
- - cutoff frequency in percentageifGaps
- - true/false - with/without counting gaps