IMPACT_S

Class AlignmentOperations

java.lang.Object

IMPACT_S.AlignmentOperations

public class AlignmentOperations
extends java.lang.Object

Class to handle any kinds of alignment operations.

Author:

Emanuel Maldonado

Constructor Summary

Constructors

Constructor and Description
AlignmentOperations(Utilities utilities) Alignment operations constructor.

Method Summary

Modifier and Type	Method and Description
int[]	filterAlignmentSites(java.util.HashMap<java.lang.String,java.lang.String> codonstable, boolean addGaps, boolean dna) Create a new shorter alignment, in which only selected sites gathered from any significant codons file, are preserved.
void	setFiles(java.lang.String sfilename, java.lang.String sformat, java.lang.String dfilename, java.lang.String dformat) Set files for alignment filtering.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignmentOperations

public AlignmentOperations(Utilities utilities)

Alignment operations constructor.

Parameters:

utilities - object of the class Utilities.

Method Detail

setFiles

public void setFiles(java.lang.String sfilename,
                     java.lang.String sformat,
                     java.lang.String dfilename,
                     java.lang.String dformat)

Set files for alignment filtering.

Parameters:

sfilename - source alignment file.

sformat - source alignment file format.

dfilename - destination alignment file.

dformat - destination alignment file format.

filterAlignmentSites

public int[] filterAlignmentSites(java.util.HashMap<java.lang.String,java.lang.String> codonstable,
                                  boolean addGaps,
                                  boolean dna)

Create a new shorter alignment, in which only selected sites gathered from any significant codons file, are preserved.

Parameters:

codonstable - table from where to get the codons to use.

addGaps - if true, add gaps between non-consecutive sites/columns; false, otherwise.

dna - if true, the source alignment is dna; otherwise, is protein.

Returns:

the array of codons used for selecting sites from alignment (-1 values, mean gap columns); or null if not successful;

See Also:

setFiles(java.lang.String, java.lang.String, java.lang.String, java.lang.String), createNonConsecutiveGaps(int[], int)