1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package vamsas.objects.simple

File Alignment.java

 

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20
38
10
1
177
111
21
0.55
3.8
10
2.1

Classes

Class
Line #
Actions
Alignment 23 38 21
0.00%
 

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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 toggle public Alignment()
33    {
34    }
35   
 
36  0 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle @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 toggle @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    }