2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2014 Christian M. Zmasek
6 // Copyright (C) 2014 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
25 package org.forester.msa_compactor;
27 import org.forester.msa.Msa;
28 import org.forester.msa.MsaMethods;
30 public final class MsaProperties {
32 final private double _average_identity_ratio;
33 final private double _gap_ratio;
34 final private int _length;
35 final private int _number_of_sequences;
36 final private String _removed_seq;
38 public MsaProperties( final int number_of_sequences,
40 final double gap_ratio,
41 final double average_identity_ratio,
42 final String removed_seq ) {
43 _number_of_sequences = number_of_sequences;
45 _gap_ratio = gap_ratio;
46 _average_identity_ratio = average_identity_ratio;
47 _removed_seq = removed_seq;
50 public MsaProperties( final Msa msa, final String removed_seq, final boolean calculate_aln_mean_identity ) {
51 _number_of_sequences = msa.getNumberOfSequences();
52 _length = msa.getLength();
53 _gap_ratio = MsaMethods.calcGapRatio( msa );
54 _removed_seq = removed_seq;
55 if ( calculate_aln_mean_identity ) {
56 _average_identity_ratio = MsaMethods.calculateIdentityRatio( 0, msa.getLength() - 1, msa ).arithmeticMean();
59 _average_identity_ratio = -1;
63 public final double getAverageIdentityRatio() {
64 return _average_identity_ratio;
67 public final double getGapRatio() {
71 public final int getLength() {
75 public final int getNumberOfSequences() {
76 return _number_of_sequences;
79 public final String getRemovedSeq() {