Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SparseCount	35	26	18	0.00%	Show methods

Class SparseCount

Class SparseCount	Line # 35	Total Statements 26	Complexity 18	TOTAL Coverage 0.00%
SparseCount(int)   SparseCount(int)	5858	1.01	1.01	0.0 0.00%
SparseCount()   SparseCount()	6767	1.01	1.01	0.0 0.00%
add(int,int) : int   add(int,int) : int	7979	8.08	3.03	0.0 0.00%
handleOverflow() : void   handleOverflow() : void	103103	8.08	2.02	0.0 0.00%
size() : int   size() : int	122122	1.01	2.02	0.0 0.00%
get(int) : int   get(int) : int	133133	1.01	2.02	0.0 0.00%
put(int,int) : void   put(int,int) : void	144144	3.03	2.02	0.0 0.00%
keyAt(int) : int   keyAt(int) : int	156156	1.01	2.02	0.0 0.00%
valueAt(int) : int   valueAt(int) : int	161161	1.01	2.02	0.0 0.00%
isUsingInt() : boolean   isUsingInt() : boolean	172172	1.01	1.01	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.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		*/
		0% Uncovered Elements: 50 (50) Complexity: 18 Complexity Density: 0.69
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	public SparseCount(int profileSize)...
59		{
60	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	public SparseCount()...
68		{
69	0	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		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
79	0	public int add(int key, int value)...
80		{
81	0	int newValue = 0;
82	0	if (useInts)
83		{
84	0	newValue = intProfile.add(key, value);
85		}
86		else
87		{
88	0	try
89		{
90	0	newValue = shortProfile.add(key, value);
91		} catch (ArithmeticException e)
92		{
93	0	handleOverflow();
94	0	newValue = intProfile.add(key, value);
95		}
96		}
97	0	return newValue;
98		}
99
100		/**
101		* Switch from counting shorts to counting ints
102		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
103	0	synchronized void handleOverflow()...
104		{
105	0	int size = shortProfile.size();
106	0	intProfile = new SparseIntArray(size);
107	0	for (int i = 0; i < size; i++)
108		{
109	0	short key = shortProfile.keyAt(i);
110	0	short value = shortProfile.valueAt(i);
111	0	intProfile.put(key, value);
112		}
113	0	shortProfile = null;
114	0	useInts = true;
115		}
116
117		/**
118		* Returns the size of the profile (number of distinct items counted)
119		*
120		* @return
121		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
122	0	public int size()...
123		{
124	0	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		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
133	0	public int get(int key)...
134		{
135	0	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		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
144	0	public void put(int key, int value)...
145		{
146	0	if (useInts)
147		{
148	0	intProfile.put(key, value);
149		}
150		else
151		{
152	0	shortProfile.put(key, value);
153		}
154		}
155
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
156	0	public int keyAt(int k)...
157		{
158	0	return useInts ? intProfile.keyAt(k) : shortProfile.keyAt(k);
159		}
160
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
161	0	public int valueAt(int k)...
162		{
163	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
172	0	boolean isUsingInt()...
173		{
174	0	return useInts;
175		}
176		}