Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceCursor	27	19	8	0.00%	Show methods

Class SequenceCursor

Class SequenceCursor	Line # 27	Total Statements 19	Complexity 8	TOTAL Coverage 0.00%
SequenceCursor(SequenceI,int,int,int)   SequenceCursor(SequenceI,int,int,int)	7373	1.01	1.01	0.0 0.00%
SequenceCursor(SequenceI,int,int,int,int,int)   SequenceCursor(SequenceI,int,int,int,int,int)	9797	6.06	1.01	0.0 0.00%
hashCode() : int   hashCode() : int	108108	6.06	2.02	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	125125	4.04	2.02	0.0 0.00%
toString() : String   toString() : String	137137	2.02	2.02	0.0 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 jalview.datamodel;
22
23		/**
24		* An immutable object representing one or more residue and corresponding
25		* alignment column positions for a sequence
26		*/
		0% Uncovered Elements: 30 (30) Complexity: 8 Complexity Density: 0.42
27		public class SequenceCursor
28		{
29		/**
30		* the aligned sequence this cursor applies to
31		*/
32		public final SequenceI sequence;
33
34		/**
35		* residue position in sequence (start...), 0 if undefined
36		*/
37		public final int residuePosition;
38
39		/**
40		* column position (1...) corresponding to residuePosition, or 0 if undefined
41		*/
42		public final int columnPosition;
43
44		/**
45		* column position (1...) of first residue in the sequence, or 0 if undefined
46		*/
47		public final int firstColumnPosition;
48
49		/**
50		* column position (1...) of last residue in the sequence, or 0 if undefined
51		*/
52		public final int lastColumnPosition;
53
54		/**
55		* a token which may be used to check whether this cursor is still valid for
56		* its sequence (allowing it to be ignored if the sequence has changed)
57		*/
58		public final int token;
59
60		/**
61		* Constructor
62		*
63		* @param seq
64		* sequence this cursor applies to
65		* @param resPos
66		* residue position in sequence (start..)
67		* @param column
68		* column position in alignment (1..)
69		* @param tok
70		* a token that may be validated by the sequence to check the cursor
71		* is not stale
72		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	public SequenceCursor(SequenceI seq, int resPos, int column, int tok)...
74		{
75	0	this(seq, resPos, column, 0, 0, tok);
76		}
77
78		/**
79		* Constructor
80		*
81		* @param seq
82		* sequence this cursor applies to
83		* @param resPos
84		* residue position in sequence (start..)
85		* @param column
86		* column position in alignment (1..)
87		* @param firstResCol
88		* column position of the first residue in the sequence (1..), or 0
89		* if not known
90		* @param lastResCol
91		* column position of the last residue in the sequence (1..), or 0 if
92		* not known
93		* @param tok
94		* a token that may be validated by the sequence to check the cursor
95		* is not stale
96		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
97	0	public SequenceCursor(SequenceI seq, int resPos, int column,...
98		int firstResCol, int lastResCol, int tok)
99		{
100	0	sequence = seq;
101	0	residuePosition = resPos;
102	0	columnPosition = column;
103	0	firstColumnPosition = firstResCol;
104	0	lastColumnPosition = lastResCol;
105	0	token = tok;
106		}
107
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
108	0	@Override...
109		public int hashCode()
110		{
111	0	int hash = 31 * residuePosition;
112	0	hash = 31 * hash + columnPosition;
113	0	hash = 31 * hash + token;
114	0	if (sequence != null)
115		{
116	0	hash += sequence.hashCode();
117		}
118	0	return hash;
119		}
120
121		/**
122		* Two cursors are equal if they refer to the same sequence object and have
123		* the same residue position, column position and token value
124		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
125	0	@Override...
126		public boolean equals(Object obj)
127		{
128	0	if (!(obj instanceof SequenceCursor))
129		{
130	0	return false;
131		}
132	0	SequenceCursor sc = (SequenceCursor) obj;
133	0	return sequence == sc.sequence && residuePosition == sc.residuePosition
134		&& columnPosition == sc.columnPosition && token == sc.token;
135		}
136
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
137	0	@Override...
138		public String toString()
139		{
140	0	String name = sequence == null ? "" : sequence.getName();
141	0	return String.format("%s:Pos%d:Col%d:startCol%d:endCol%d:tok%d", name,
142		residuePosition, columnPosition, firstColumnPosition,
143		lastColumnPosition, token);
144		}
145		}