Class |
Line # |
Actions |
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Alignment | 23 | 38 | 21 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package vamsas.objects.simple; | |
22 | ||
23 | public class Alignment extends vamsas.objects.simple.Object | |
24 | implements java.io.Serializable | |
25 | { | |
26 | private java.lang.String gapchar; | |
27 | ||
28 | private java.lang.String[] method; | |
29 | ||
30 | private vamsas.objects.simple.SequenceSet seqs; | |
31 | ||
32 | 0 | public Alignment() |
33 | { | |
34 | } | |
35 | ||
36 | 0 | public Alignment(java.lang.String gapchar, java.lang.String[] method, |
37 | vamsas.objects.simple.SequenceSet seqs) | |
38 | { | |
39 | 0 | this.gapchar = gapchar; |
40 | 0 | this.method = method; |
41 | 0 | this.seqs = seqs; |
42 | } | |
43 | ||
44 | /** | |
45 | * Gets the gapchar value for this Alignment. | |
46 | * | |
47 | * @return gapchar | |
48 | */ | |
49 | 0 | public java.lang.String getGapchar() |
50 | { | |
51 | 0 | return gapchar; |
52 | } | |
53 | ||
54 | /** | |
55 | * Sets the gapchar value for this Alignment. | |
56 | * | |
57 | * @param gapchar | |
58 | */ | |
59 | 0 | public void setGapchar(java.lang.String gapchar) |
60 | { | |
61 | 0 | this.gapchar = gapchar; |
62 | } | |
63 | ||
64 | /** | |
65 | * Gets the method value for this Alignment. | |
66 | * | |
67 | * @return method | |
68 | */ | |
69 | 0 | public java.lang.String[] getMethod() |
70 | { | |
71 | 0 | return method; |
72 | } | |
73 | ||
74 | /** | |
75 | * Sets the method value for this Alignment. | |
76 | * | |
77 | * @param method | |
78 | */ | |
79 | 0 | public void setMethod(java.lang.String[] method) |
80 | { | |
81 | 0 | this.method = method; |
82 | } | |
83 | ||
84 | /** | |
85 | * Gets the seqs value for this Alignment. | |
86 | * | |
87 | * @return seqs | |
88 | */ | |
89 | 0 | public vamsas.objects.simple.SequenceSet getSeqs() |
90 | { | |
91 | 0 | return seqs; |
92 | } | |
93 | ||
94 | /** | |
95 | * Sets the seqs value for this Alignment. | |
96 | * | |
97 | * @param seqs | |
98 | */ | |
99 | 0 | public void setSeqs(vamsas.objects.simple.SequenceSet seqs) |
100 | { | |
101 | 0 | this.seqs = seqs; |
102 | } | |
103 | ||
104 | private java.lang.Object __equalsCalc = null; | |
105 | ||
106 | 0 | @Override |
107 | public synchronized boolean equals(java.lang.Object obj) | |
108 | { | |
109 | 0 | if (obj == null) |
110 | { | |
111 | 0 | return false; |
112 | } | |
113 | 0 | if (!(obj instanceof Alignment)) |
114 | { | |
115 | 0 | return false; |
116 | } | |
117 | 0 | Alignment other = (Alignment) obj; |
118 | 0 | if (this == obj) |
119 | { | |
120 | 0 | return true; |
121 | } | |
122 | 0 | if (__equalsCalc != null) |
123 | { | |
124 | 0 | return (__equalsCalc == obj); |
125 | } | |
126 | 0 | __equalsCalc = obj; |
127 | 0 | boolean _equals; |
128 | 0 | _equals = super.equals(obj) |
129 | && ((this.gapchar == null && other.getGapchar() == null) | |
130 | || (this.gapchar != null | |
131 | && this.gapchar.equals(other.getGapchar()))) | |
132 | && ((this.method == null && other.getMethod() == null) | |
133 | || (this.method != null && java.util.Arrays | |
134 | .equals(this.method, other.getMethod()))) | |
135 | && ((this.seqs == null && other.getSeqs() == null) | |
136 | || (this.seqs != null | |
137 | && this.seqs.equals(other.getSeqs()))); | |
138 | 0 | __equalsCalc = null; |
139 | 0 | return _equals; |
140 | } | |
141 | ||
142 | private boolean __hashCodeCalc = false; | |
143 | ||
144 | 0 | @Override |
145 | public synchronized int hashCode() | |
146 | { | |
147 | 0 | if (__hashCodeCalc) |
148 | { | |
149 | 0 | return 0; |
150 | } | |
151 | 0 | __hashCodeCalc = true; |
152 | 0 | int _hashCode = super.hashCode(); |
153 | 0 | if (getGapchar() != null) |
154 | { | |
155 | 0 | _hashCode += getGapchar().hashCode(); |
156 | } | |
157 | 0 | if (getMethod() != null) |
158 | { | |
159 | 0 | for (int i = 0; i < java.lang.reflect.Array |
160 | .getLength(getMethod()); i++) | |
161 | { | |
162 | 0 | java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i); |
163 | 0 | if (obj != null && !obj.getClass().isArray()) |
164 | { | |
165 | 0 | _hashCode += obj.hashCode(); |
166 | } | |
167 | } | |
168 | } | |
169 | 0 | if (getSeqs() != null) |
170 | { | |
171 | 0 | _hashCode += getSeqs().hashCode(); |
172 | } | |
173 | 0 | __hashCodeCalc = false; |
174 | 0 | return _hashCode; |
175 | } | |
176 | ||
177 | } |