Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SparseDoubleArray	70	119	45	0.4945652249.5%	Show methods

Class SparseDoubleArray

Class SparseDoubleArray	Line # 70	Total Statements 119	Complexity 45	TOTAL Coverage 0.4945652249.5%
SparseDoubleArray()   SparseDoubleArray()	8181	1.01	1.01	1.0 1.0100%
SparseDoubleArray(int)   SparseDoubleArray(int)	9393	7.07	2.02	0.6666667 0.666666766.7%
SparseDoubleArray(double[])   SparseDoubleArray(double[])	114114	4.04	3.03	0.0 0.00%
clone() : SparseDoubleArray   clone() : SparseDoubleArray	126126	6.06	2.02	0.0 0.00%
get(int) : double   get(int) : double	146146	1.01	1.01	1.0 1.0100%
get(int,double) : double   get(int,double) : double	155155	4.04	2.02	1.0 1.0100%
delete(int) : void   delete(int) : void	171171	3.03	2.02	1.0 1.0100%
removeAt(int) : void   removeAt(int) : void	183183	3.03	1.01	1.0 1.0100%
put(int,double) : void   put(int,double) : void	195195	18.018	4.04	0.6666667 0.666666766.7%
size() : int   size() : int	232232	1.01	1.01	1.0 1.0100%
keyAt(int) : int   keyAt(int) : int	248248	1.01	1.01	1.0 1.0100%
valueAt(int) : double   valueAt(int) : double	266266	1.01	1.01	1.0 1.0100%
indexOfKey(int) : int   indexOfKey(int) : int	275275	1.01	1.01	0.0 0.00%
indexOfValue(double) : int   indexOfValue(double) : int	286286	4.04	3.03	0.0 0.00%
clear() : void   clear() : void	301301	1.01	1.01	0.0 0.00%
append(int,double) : void   append(int,double) : void	310310	15.015	4.04	0.0 0.00%
idealDoubleArraySize(int) : int   idealDoubleArraySize(int) : int	341341	1.01	1.01	1.0 1.0100%
idealByteArraySize(int) : int   idealByteArraySize(int) : int	352352	4.04	3.03	0.75 0.7575%
toString() : String   toString() : String	371371	14.014	4.04	0.0 0.00%
add(int,double) : double   add(int,double) : double	405405	21.021	4.04	0.7037037 0.703703770.4%
divide(int,double) : double   divide(int,double) : double	448448	8.08	3.03	0.8333333 0.833333383.3%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.46195653	jalview.math.SparseMatrixTest.testTred_reproduciblejalview.math.SparseMatrixTest.testTred_reproducible	1PASS
	0.46195653	jalview.math.SparseMatrixTest.testTred_matchesMatrixjalview.math.SparseMatrixTest.testTred_matchesMatrix	1PASS
	0.46195653	jalview.math.SparseMatrixTest.testTqli_matchesMatrixjalview.math.SparseMatrixTest.testTqli_matchesMatrix	1PASS
	0.24456522	jalview.math.SparseMatrixTest.testTransposejalview.math.SparseMatrixTest.testTranspose	1PASS
	0.24456522	jalview.math.SparseMatrixTest.testPreMultiply_sparseProductjalview.math.SparseMatrixTest.testPreMultiply_sparseProduct	1PASS
	0.23369566	jalview.math.SparseMatrixTest.testPreMultiplyjalview.math.SparseMatrixTest.testPreMultiply	1PASS
	0.23369566	jalview.math.SparseMatrixTest.testPostMultiplyjalview.math.SparseMatrixTest.testPostMultiply	1PASS
	0.21195652	jalview.math.SparseMatrixTest.testConstructorjalview.math.SparseMatrixTest.testConstructor	1PASS
	0.17391305	jalview.math.SparseMatrixTest.testFillRatiojalview.math.SparseMatrixTest.testFillRatio	1PASS
	0.16304348	jalview.math.SparseMatrixTest.testPreMultiply_tooFewColumnsjalview.math.SparseMatrixTest.testPreMultiply_tooFewColumns	1PASS
	0.16304348	jalview.math.SparseMatrixTest.testPreMultiply_tooManyColumnsjalview.math.SparseMatrixTest.testPreMultiply_tooManyColumns	1PASS

 

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.ext.android;
22
23		/*
24		* Copyright (C) 2006 The Android Open Source Project
25		*
26		* Licensed under the Apache License, Version 2.0 (the "License");
27		* you may not use this file except in compliance with the License.
28		* You may obtain a copy of the License at
29		*
30		* http://www.apache.org/licenses/LICENSE-2.0
31		*
32		* Unless required by applicable law or agreed to in writing, software
33		* distributed under the License is distributed on an "AS IS" BASIS,
34		* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
35		* See the License for the specific language governing permissions and
36		* limitations under the License.
37		*/
38		/**
39		* SparseDoubleArray map integers to doubles. Unlike a normal array of integers,
40		* there can be gaps in the indices. It is intended to be more memory efficient
41		* than using a HashMap to map Integer to Double, both because it avoids
42		* auto-boxing keys and values and its data structure doesn't rely on an extra
43		* entry object for each mapping.
44		*
45		* <p>
46		* Note that this container keeps its mappings in an array data structure, using
47		* a binary search to find keys. The implementation is not intended to be
48		* appropriate for data structures that may contain large numbers of items. It
49		* is generally slower than a traditional HashMap, since lookups require a
50		* binary search and adds and removes require inserting and deleting entries in
51		* the array. For containers holding up to hundreds of items, the performance
52		* difference is not significant, less than 50%.
53		* </p>
54		*
55		* <p>
56		* It is possible to iterate over the items in this container using
57		* {@link #keyAt(int)} and {@link #valueAt(int)}. Iterating over the keys using
58		* <code>keyAt(int)</code> with ascending values of the index will return the
59		* keys in ascending order, or the values corresponding to the keys in ascending
60		* order in the case of <code>valueAt(int)<code>.
61		* </p>
62		*/
63
64		/*
65		* Change log:
66		* Jan 2017 cloned from SparseIntArray for Jalview to support SparseMatrix
67		* - SparseDoubleArray(double[]) constructor added
68		* - multiply() added for more efficient multiply (or divide) of a value
69		*/
		49.5% Uncovered Elements: 93 (184) Complexity: 45 Complexity Density: 0.38
70		public class SparseDoubleArray implements Cloneable
71		{
72		private int[] mKeys;
73
74		private double[] mValues;
75
76		private int mSize;
77
78		/**
79		* Creates a new SparseDoubleArray containing no mappings.
80		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
81	85	public SparseDoubleArray()...
82		{
83	85	this(10);
84		}
85
86		/**
87		* Creates a new SparseDoubleArray containing no mappings that will not
88		* require any additional memory allocation to store the specified number of
89		* mappings. If you supply an initial capacity of 0, the sparse array will be
90		* initialized with a light-weight representation not requiring any additional
91		* array allocations.
92		*/
		66.7% Uncovered Elements: 3 (9) Complexity: 2 Complexity Density: 0.29
93	85	public SparseDoubleArray(int initialCapacity)...
94		{
95	85	if (initialCapacity == 0)
96		{
97	0	mKeys = ContainerHelpers.EMPTY_INTS;
98	0	mValues = ContainerHelpers.EMPTY_DOUBLES;
99		}
100		else
101		{
102	85	initialCapacity = idealDoubleArraySize(initialCapacity);
103	85	mKeys = new int[initialCapacity];
104	85	mValues = new double[initialCapacity];
105		}
106	85	mSize = 0;
107		}
108
109		/**
110		* Constructor given an array of double values; stores the non-zero values
111		*
112		* @param row
113		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
114	0	public SparseDoubleArray(double[] row)...
115		{
116	0	this();
117	0	for (int i = 0; i < row.length; i++)
118		{
119	0	if (row[i] != 0d)
120		{
121	0	put(i, row[i]);
122		}
123		}
124		}
125
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
126	0	@Override...
127		public SparseDoubleArray clone()
128		{
129	0	SparseDoubleArray clone = null;
130	0	try
131		{
132	0	clone = (SparseDoubleArray) super.clone();
133	0	clone.mKeys = mKeys.clone();
134	0	clone.mValues = mValues.clone();
135		} catch (CloneNotSupportedException cnse)
136		{
137		/* ignore */
138		}
139	0	return clone;
140		}
141
142		/**
143		* Gets the value mapped from the specified key, or <code>0</code> if no such
144		* mapping has been made.
145		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
146	7019	public double get(int key)...
147		{
148	7019	return get(key, 0d);
149		}
150
151		/**
152		* Gets the int mapped from the specified key, or the specified value if no
153		* such mapping has been made.
154		*/
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.5
155	7019	public double get(int key, double valueIfKeyNotFound)...
156		{
157	7019	int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
158	7019	if (i < 0)
159		{
160	1443	return valueIfKeyNotFound;
161		}
162		else
163		{
164	5576	return mValues[i];
165		}
166		}
167
168		/**
169		* Removes the mapping from the specified key, if there was any.
170		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
171	385	public void delete(int key)...
172		{
173	385	int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
174	385	if (i >= 0)
175		{
176	267	removeAt(i);
177		}
178		}
179
180		/**
181		* Removes the mapping at the given index.
182		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
183	267	public void removeAt(int index)...
184		{
185	267	System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
186	267	System.arraycopy(mValues, index + 1, mValues, index,
187		mSize - (index + 1));
188	267	mSize--;
189		}
190
191		/**
192		* Adds a mapping from the specified key to the specified value, replacing the
193		* previous mapping from the specified key if there was one.
194		*/
		66.7% Uncovered Elements: 8 (24) Complexity: 4 Complexity Density: 0.22
195	669	public void put(int key, double value)...
196		{
197	669	int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
198	669	if (i >= 0)
199		{
200	398	mValues[i] = value;
201		}
202		else
203		{
204	271	i = ~i;
205	271	if (mSize >= mKeys.length)
206		{
207	0	int n = idealDoubleArraySize(mSize + 1);
208	0	int[] nkeys = new int[n];
209	0	double[] nvalues = new double[n];
210		// Log.e("SparseDoubleArray", "grow " + mKeys.length + " to " + n);
211	0	System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
212	0	System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
213	0	mKeys = nkeys;
214	0	mValues = nvalues;
215		}
216	271	if (mSize - i != 0)
217		{
218		// Log.e("SparseDoubleArray", "move " + (mSize - i));
219	73	System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
220	73	System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
221		}
222	271	mKeys[i] = key;
223	271	mValues[i] = value;
224	271	mSize++;
225		}
226		}
227
228		/**
229		* Returns the number of key-value mappings that this SparseDoubleArray
230		* currently stores.
231		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
232	173	public int size()...
233		{
234	173	return mSize;
235		}
236
237		/**
238		* Given an index in the range <code>0...size()-1</code>, returns the key from
239		* the <code>index</code>th key-value mapping that this SparseDoubleArray
240		* stores.
241		*
242		* <p>
243		* The keys corresponding to indices in ascending order are guaranteed to be
244		* in ascending order, e.g., <code>keyAt(0)</code> will return the smallest
245		* key and <code>keyAt(size()-1)</code> will return the largest key.
246		* </p>
247		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
248	91	public int keyAt(int index)...
249		{
250	91	return mKeys[index];
251		}
252
253		/**
254		* Given an index in the range <code>0...size()-1</code>, returns the value
255		* from the <code>index</code>th key-value mapping that this SparseDoubleArray
256		* stores.
257		*
258		* <p>
259		* The values corresponding to indices in ascending order are guaranteed to be
260		* associated with keys in ascending order, e.g., <code>valueAt(0)</code> will
261		* return the value associated with the smallest key and
262		* <code>valueAt(size()-1)</code> will return the value associated with the
263		* largest key.
264		* </p>
265		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
266	91	public double valueAt(int index)...
267		{
268	91	return mValues[index];
269		}
270
271		/**
272		* Returns the index for which {@link #keyAt} would return the specified key,
273		* or a negative number if the specified key is not mapped.
274		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
275	0	public int indexOfKey(int key)...
276		{
277	0	return ContainerHelpers.binarySearch(mKeys, mSize, key);
278		}
279
280		/**
281		* Returns an index for which {@link #valueAt} would return the specified key,
282		* or a negative number if no keys map to the specified value. Beware that
283		* this is a linear search, unlike lookups by key, and that multiple keys can
284		* map to the same value and this will find only one of them.
285		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
286	0	public int indexOfValue(double value)...
287		{
288	0	for (int i = 0; i < mSize; i++)
289		{
290	0	if (mValues[i] == value)
291		{
292	0	return i;
293		}
294		}
295	0	return -1;
296		}
297
298		/**
299		* Removes all key-value mappings from this SparseDoubleArray.
300		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
301	0	public void clear()...
302		{
303	0	mSize = 0;
304		}
305
306		/**
307		* Puts a key/value pair into the array, optimizing for the case where the key
308		* is greater than all existing keys in the array.
309		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.27
310	0	public void append(int key, double value)...
311		{
312	0	if (mSize != 0 && key <= mKeys[mSize - 1])
313		{
314	0	put(key, value);
315	0	return;
316		}
317	0	int pos = mSize;
318	0	if (pos >= mKeys.length)
319		{
320	0	int n = idealDoubleArraySize(pos + 1);
321	0	int[] nkeys = new int[n];
322	0	double[] nvalues = new double[n];
323		// Log.e("SparseDoubleArray", "grow " + mKeys.length + " to " + n);
324	0	System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
325	0	System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
326	0	mKeys = nkeys;
327	0	mValues = nvalues;
328		}
329	0	mKeys[pos] = key;
330	0	mValues[pos] = value;
331	0	mSize = pos + 1;
332		}
333
334		/**
335		* Created by analogy with
336		* com.android.internal.util.ArrayUtils#idealLongArraySize
337		*
338		* @param i
339		* @return
340		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
341	85	public static int idealDoubleArraySize(int need)...
342		{
343	85	return idealByteArraySize(need * 8) / 8;
344		}
345
346		/**
347		* Inlined here by copying from com.android.internal.util.ArrayUtils
348		*
349		* @param i
350		* @return
351		*/
		75% Uncovered Elements: 2 (8) Complexity: 3 Complexity Density: 0.75
352	85	public static int idealByteArraySize(int need)...
353		{
354	340	for (int i = 4; i < 32; i++)
355		{
356	340	if (need <= (1 << i) - 12)
357		{
358	85	return (1 << i) - 12;
359		}
360		}
361
362	0	return need;
363		}
364
365		/**
366		* {@inheritDoc}
367		*
368		* <p>
369		* This implementation composes a string by iterating over its mappings.
370		*/
		0% Uncovered Elements: 20 (20) Complexity: 4 Complexity Density: 0.29
371	0	@Override...
372		public String toString()
373		{
374	0	if (size() <= 0)
375		{
376	0	return "{}";
377		}
378	0	StringBuilder buffer = new StringBuilder(mSize * 28);
379	0	buffer.append('{');
380	0	for (int i = 0; i < mSize; i++)
381		{
382	0	if (i > 0)
383		{
384	0	buffer.append(", ");
385		}
386	0	int key = keyAt(i);
387	0	buffer.append(key);
388	0	buffer.append('=');
389	0	double value = valueAt(i);
390	0	buffer.append(value);
391		}
392	0	buffer.append('}');
393	0	return buffer.toString();
394		}
395
396		/**
397		* Method (copied from put) added for Jalview to efficiently increment a key's
398		* value if present, else add it with the given value. This avoids a double
399		* binary search (once to get the value, again to put the updated value).
400		*
401		* @param key
402		* @oparam toAdd
403		* @return the new value for the key
404		*/
		70.4% Uncovered Elements: 8 (27) Complexity: 4 Complexity Density: 0.19
405	1432	public double add(int key, double toAdd)...
406		{
407	1432	double newValue = toAdd;
408	1432	int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
409	1432	if (i >= 0)
410		{
411	1094	mValues[i] += toAdd;
412	1094	newValue = mValues[i];
413		}
414		else
415		{
416	338	i = ~i;
417	338	if (mSize >= mKeys.length)
418		{
419	0	int n = idealDoubleArraySize(mSize + 1);
420	0	int[] nkeys = new int[n];
421	0	double[] nvalues = new double[n];
422	0	System.arraycopy(mKeys, 0, nkeys, 0, mKeys.length);
423	0	System.arraycopy(mValues, 0, nvalues, 0, mValues.length);
424	0	mKeys = nkeys;
425	0	mValues = nvalues;
426		}
427	338	if (mSize - i != 0)
428		{
429	275	System.arraycopy(mKeys, i, mKeys, i + 1, mSize - i);
430	275	System.arraycopy(mValues, i, mValues, i + 1, mSize - i);
431		}
432	338	mKeys[i] = key;
433	338	mValues[i] = toAdd;
434	338	mSize++;
435		}
436	1432	return newValue;
437		}
438
439		/**
440		* Method added for Jalview to efficiently multiply a key's value if present,
441		* else do nothing. This avoids a double binary search (once to get the value,
442		* again to put the updated value).
443		*
444		* @param key
445		* @oparam toAdd
446		* @return the new value for the key
447		*/
		83.3% Uncovered Elements: 2 (12) Complexity: 3 Complexity Density: 0.38
448	146	public double divide(int key, double divisor)...
449		{
450	146	double newValue = 0d;
451	146	if (divisor == 0d)
452		{
453	0	return newValue;
454		}
455	146	int i = ContainerHelpers.binarySearch(mKeys, mSize, key);
456	146	if (i >= 0)
457		{
458	125	mValues[i] /= divisor;
459	125	newValue = mValues[i];
460		}
461	146	return newValue;
462		}
463		}