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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.datamodel

File SequenceCursor.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
35% of files have more coverage

Code metrics

6
19
5
1
145
55
8
0.42
3.8
5
1.6

Classes

Class Line # Actions
SequenceCursor 27 19 8 12
0.660%
 

Contributing tests

This file is covered by 130 tests. .

Source view

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    */
 
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    */
 
73  25 toggle public SequenceCursor(SequenceI seq, int resPos, int column, int tok)
74    {
75  25 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    */
 
97  189259 toggle public SequenceCursor(SequenceI seq, int resPos, int column, int firstResCol,
98    int lastResCol, int tok)
99    {
100  189259 sequence = seq;
101  189259 residuePosition = resPos;
102  189259 columnPosition = column;
103  189259 firstColumnPosition = firstResCol;
104  189258 lastColumnPosition = lastResCol;
105  189260 token = tok;
106    }
107   
 
108  0 toggle @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    */
 
125  13 toggle @Override
126    public boolean equals(Object obj)
127    {
128  13 if (!(obj instanceof SequenceCursor))
129    {
130  0 return false;
131    }
132  13 SequenceCursor sc = (SequenceCursor) obj;
133  13 return sequence == sc.sequence && residuePosition == sc.residuePosition
134    && columnPosition == sc.columnPosition && token == sc.token;
135    }
136   
 
137  31 toggle @Override
138    public String toString()
139    {
140  31 String name = sequence == null ? "" : sequence.getName();
141  31 return String.format("%s:Pos%d:Col%d:startCol%d:endCol%d:tok%d", name,
142    residuePosition, columnPosition, firstColumnPosition,
143    lastColumnPosition, token);
144    }
145    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.