Clover icon

Coverage Report

  1. Project Clover database Wed Jan 7 2026 02:49:01 GMT
  2. Package jalview.util

File SparseCount.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

14
26
10
1
176
82
18
0.69
2.6
10
1.8

Classes

Class Line # Actions
SparseCount 35 26 18
0.8484%
 

Contributing tests

This file is covered by 43 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.util;
22   
23    import jalview.ext.android.SparseIntArray;
24    import jalview.ext.android.SparseShortArray;
25   
26    /**
27    * A class to count occurrences of characters with minimal memory footprint.
28    * Sparse arrays of short values are used to hold the counts, with automatic
29    * promotion to arrays of int if any count exceeds the maximum value for a
30    * short.
31    *
32    * @author gmcarstairs
33    *
34    */
 
35    public class SparseCount
36    {
37    private static final int DEFAULT_PROFILE_SIZE = 2;
38   
39    /*
40    * array of keys (chars) and values (counts)
41    * held either as shorts or (if shorts overflow) as ints
42    */
43    private SparseShortArray shortProfile;
44   
45    private SparseIntArray intProfile;
46   
47    /*
48    * flag is set true after short overflow occurs
49    */
50    private boolean useInts;
51   
52    /**
53    * Constructor which initially creates a new sparse array of short values to
54    * hold counts.
55    *
56    * @param profileSize
57    */
 
58  498 toggle public SparseCount(int profileSize)
59    {
60  498 this.shortProfile = new SparseShortArray(profileSize);
61    }
62   
63    /**
64    * Constructor which allocates an initial count array for only two distinct
65    * values (the array will grow if needed)
66    */
 
67  493 toggle public SparseCount()
68    {
69  493 this(DEFAULT_PROFILE_SIZE);
70    }
71   
72    /**
73    * Adds the given value for the given key (or sets the initial value), and
74    * returns the new value
75    *
76    * @param key
77    * @param value
78    */
 
79  9414 toggle public int add(int key, int value)
80    {
81  9414 int newValue = 0;
82  9414 if (useInts)
83    {
84  0 newValue = intProfile.add(key, value);
85    }
86    else
87    {
88  9414 try
89    {
90  9414 newValue = shortProfile.add(key, value);
91    } catch (ArithmeticException e)
92    {
93  2 handleOverflow();
94  2 newValue = intProfile.add(key, value);
95    }
96    }
97  9414 return newValue;
98    }
99   
100    /**
101    * Switch from counting shorts to counting ints
102    */
 
103  2 toggle synchronized void handleOverflow()
104    {
105  2 int size = shortProfile.size();
106  2 intProfile = new SparseIntArray(size);
107  4 for (int i = 0; i < size; i++)
108    {
109  2 short key = shortProfile.keyAt(i);
110  2 short value = shortProfile.valueAt(i);
111  2 intProfile.put(key, value);
112    }
113  2 shortProfile = null;
114  2 useInts = true;
115    }
116   
117    /**
118    * Returns the size of the profile (number of distinct items counted)
119    *
120    * @return
121    */
 
122  1257 toggle public int size()
123    {
124  1257 return useInts ? intProfile.size() : shortProfile.size();
125    }
126   
127    /**
128    * Returns the value for the key (zero if no such key)
129    *
130    * @param key
131    * @return
132    */
 
133  11 toggle public int get(int key)
134    {
135  11 return useInts ? intProfile.get(key) : shortProfile.get(key);
136    }
137   
138    /**
139    * Sets the value for the given key
140    *
141    * @param key
142    * @param value
143    */
 
144  12 toggle public void put(int key, int value)
145    {
146  12 if (useInts)
147    {
148  0 intProfile.put(key, value);
149    }
150    else
151    {
152  12 shortProfile.put(key, value);
153    }
154    }
155   
 
156  385 toggle public int keyAt(int k)
157    {
158  385 return useInts ? intProfile.keyAt(k) : shortProfile.keyAt(k);
159    }
160   
 
161  671 toggle public int valueAt(int k)
162    {
163  671 return useInts ? intProfile.valueAt(k) : shortProfile.valueAt(k);
164    }
165   
166    /**
167    * Answers true if this object wraps arrays of int values, false if using
168    * short values
169    *
170    * @return
171    */
 
172  4 toggle boolean isUsingInt()
173    {
174  4 return useInts;
175    }
176    }
  • Report generated by OpenClover v 4.4.1 on Wed Jan 7 2026 02:56:53 GMT using coverage data from Wed Jan 7 2026 02:56:43 GMT.
  • OpenClover is free and open-source software.