Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Alignment	23	38	21	0.00%	Show methods

Class Alignment

Class Alignment	Line # 23	Total Statements 38	Complexity 21	TOTAL Coverage 0.00%
Alignment()   Alignment()	3232	0.00	1.01	-1.0 -1.0 -
Alignment(java.lang.String,java.lang.String[],vamsas.objects.simple.SequenceSet)   Alignment(java.lang.String,java.lang.String[],vamsas.objects.simple.SequenceSet)	3636	3.03	1.01	0.0 0.00%
getGapchar() : java.lang.String   getGapchar() : java.lang.String	4949	1.01	1.01	0.0 0.00%
setGapchar(java.lang.String) : void   setGapchar(java.lang.String) : void	5959	1.01	1.01	0.0 0.00%
getMethod() : java.lang.String[]   getMethod() : java.lang.String[]	6969	1.01	1.01	0.0 0.00%
setMethod(java.lang.String[]) : void   setMethod(java.lang.String[]) : void	7979	1.01	1.01	0.0 0.00%
getSeqs() : vamsas.objects.simple.SequenceSet   getSeqs() : vamsas.objects.simple.SequenceSet	8989	1.01	1.01	0.0 0.00%
setSeqs(vamsas.objects.simple.SequenceSet) : void   setSeqs(vamsas.objects.simple.SequenceSet) : void	9999	1.01	1.01	0.0 0.00%
equals(java.lang.Object) : boolean   equals(java.lang.Object) : boolean	106106	14.014	5.05	0.0 0.00%
hashCode() : int   hashCode() : int	144144	15.015	8.08	0.0 0.00%

 

Contributing tests

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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
		0% Uncovered Elements: 68 (68) Complexity: 21 Complexity Density: 0.55
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
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
32	0	public Alignment()...
33		{
34		}
35
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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
		0% Uncovered Elements: 22 (22) Complexity: 5 Complexity Density: 0.36
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
		0% Uncovered Elements: 27 (27) Complexity: 8 Complexity Density: 0.53
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		}