Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureMatcherSet	37	87	34	0.3453237434.5%	Show methods

Class FeatureMatcherSet

Class FeatureMatcherSet	Line # 37	Total Statements 87	Complexity 34	TOTAL Coverage 0.3453237434.5%
fromString(String) : FeatureMatcherSet   fromString(String) : FeatureMatcherSet	7676	40.040	11.011	0.0 0.00%
FeatureMatcherSet()   FeatureMatcherSet()	168168	1.01	1.01	1.0 1.0100%
matches(SequenceFeature) : boolean   matches(SequenceFeature) : boolean	173173	11.011	5.05	0.5263158 0.526315852.6%
and(FeatureMatcherI) : void   and(FeatureMatcherI) : void	212212	4.04	3.03	0.6666667 0.666666766.7%
or(FeatureMatcherI) : void   or(FeatureMatcherI) : void	223223	4.04	3.03	0.6666667 0.666666766.7%
isAnded() : boolean   isAnded() : boolean	234234	1.01	1.01	1.0 1.0100%
getMatchers() : Iterable<FeatureMatcherI>   getMatchers() : Iterable<FeatureMatcherI>	240240	1.01	1.01	1.0 1.0100%
toString() : String   toString() : String	251251	12.012	4.04	0.0 0.00%
isEmpty() : boolean   isEmpty() : boolean	279279	1.01	1.01	1.0 1.0100%
toStableString() : String   toStableString() : String	289289	12.012	4.04	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.26618704	jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad	1PASS
	0.1438849	jalview.renderer.seqfeatures.FeatureRendererTest.testIsVisiblejalview.renderer.seqfeatures.FeatureRendererTest.testIsVisible	1PASS
	0.1438849	jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour	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.datamodel.features;
22
23		import java.util.Locale;
24
25		import jalview.datamodel.SequenceFeature;
26		import jalview.util.MessageManager;
27
28		import java.util.ArrayList;
29		import java.util.List;
30
31		/**
32		* A class that models one or more match conditions, which may be combined with
33		* AND or OR (but not a mixture)
34		*
35		* @author gmcarstairs
36		*/
		34.5% Uncovered Elements: 91 (139) Complexity: 34 Complexity Density: 0.39
37		public class FeatureMatcherSet implements FeatureMatcherSetI
38		{
39		private static final String OR = "OR";
40
41		private static final String AND = "AND";
42
43		private static final String SPACE = " ";
44
45		private static final String CLOSE_BRACKET = ")";
46
47		private static final String OPEN_BRACKET = "(";
48
49		private static final String OR_I18N = MessageManager
50		.getString("label.or");
51
52		private static final String AND_18N = MessageManager
53		.getString("label.and");
54
55		List<FeatureMatcherI> matchConditions;
56
57		boolean andConditions;
58
59		/**
60		* A factory constructor that converts a stringified object (as output by
61		* toStableString) to an object instance.
62		*
63		* Format:
64		* <ul>
65		* <li>(condition1) AND (condition2) AND (condition3)</li>
66		* <li>or</li>
67		* <li>(condition1) OR (condition2) OR (condition3)</li>
68		* </ul>
69		* where OR and AND are not case-sensitive, and may not be mixed. Brackets are
70		* optional if there is only one condition.
71		*
72		* @param descriptor
73		* @return
74		* @see FeatureMatcher#fromString(String)
75		*/
		0% Uncovered Elements: 58 (58) Complexity: 11 Complexity Density: 0.28
76	0	public static FeatureMatcherSet fromString(final String descriptor)...
77		{
78	0	String invalid = "Invalid descriptor: " + descriptor;
79	0	boolean firstCondition = true;
80	0	FeatureMatcherSet result = new FeatureMatcherSet();
81
82	0	String leftToParse = descriptor.trim();
83
84	0	while (leftToParse.length() > 0)
85		{
86		/*
87		* inspect AND or OR condition, check not mixed
88		*/
89	0	boolean and = true;
90	0	if (!firstCondition)
91		{
92	0	int spacePos = leftToParse.indexOf(SPACE);
93	0	if (spacePos == -1)
94		{
95		// trailing junk after a match condition
96	0	jalview.bin.Console.errPrintln(invalid);
97	0	return null;
98		}
99	0	String conjunction = leftToParse.substring(0, spacePos);
100	0	leftToParse = leftToParse.substring(spacePos + 1).trim();
101	0	if (conjunction.equalsIgnoreCase(AND))
102		{
103	0	and = true;
104		}
105	0	else if (conjunction.equalsIgnoreCase(OR))
106		{
107	0	and = false;
108		}
109		else
110		{
111		// not an AND or an OR - invalid
112	0	jalview.bin.Console.errPrintln(invalid);
113	0	return null;
114		}
115		}
116
117		/*
118		* now extract the next condition and AND or OR it
119		*/
120	0	String nextCondition = leftToParse;
121	0	if (leftToParse.startsWith(OPEN_BRACKET))
122		{
123	0	int closePos = leftToParse.indexOf(CLOSE_BRACKET);
124	0	if (closePos == -1)
125		{
126	0	jalview.bin.Console.errPrintln(invalid);
127	0	return null;
128		}
129	0	nextCondition = leftToParse.substring(1, closePos);
130	0	leftToParse = leftToParse.substring(closePos + 1).trim();
131		}
132		else
133		{
134	0	leftToParse = "";
135		}
136
137	0	FeatureMatcher fm = FeatureMatcher.fromString(nextCondition);
138	0	if (fm == null)
139		{
140	0	jalview.bin.Console.errPrintln(invalid);
141	0	return null;
142		}
143	0	try
144		{
145	0	if (and)
146		{
147	0	result.and(fm);
148		}
149		else
150		{
151	0	result.or(fm);
152		}
153	0	firstCondition = false;
154		} catch (IllegalStateException e)
155		{
156		// thrown if OR and AND are mixed
157	0	jalview.bin.Console.errPrintln(invalid);
158	0	return null;
159		}
160
161		}
162	0	return result;
163		}
164
165		/**
166		* Constructor
167		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
168	13	public FeatureMatcherSet()...
169		{
170	13	matchConditions = new ArrayList<>();
171		}
172
		52.6% Uncovered Elements: 9 (19) Complexity: 5 Complexity Density: 0.45
173	10	@Override...
174		public boolean matches(SequenceFeature feature)
175		{
176		/*
177		* no conditions matches anything
178		*/
179	10	if (matchConditions.isEmpty())
180		{
181	0	return true;
182		}
183
184		/*
185		* AND until failure
186		*/
187	10	if (andConditions)
188		{
189	10	for (FeatureMatcherI m : matchConditions)
190		{
191	11	if (!m.matches(feature))
192		{
193	7	return false;
194		}
195		}
196	3	return true;
197		}
198
199		/*
200		* OR until match
201		*/
202	0	for (FeatureMatcherI m : matchConditions)
203		{
204	0	if (m.matches(feature))
205		{
206	0	return true;
207		}
208		}
209	0	return false;
210		}
211
		66.7% Uncovered Elements: 2 (6) Complexity: 3 Complexity Density: 0.75
212	13	@Override...
213		public void and(FeatureMatcherI m)
214		{
215	13	if (!andConditions && matchConditions.size() > 1)
216		{
217	0	throw new IllegalStateException("Can't add an AND to OR conditions");
218		}
219	13	matchConditions.add(m);
220	13	andConditions = true;
221		}
222
		66.7% Uncovered Elements: 2 (6) Complexity: 3 Complexity Density: 0.75
223	3	@Override...
224		public void or(FeatureMatcherI m)
225		{
226	3	if (andConditions && matchConditions.size() > 1)
227		{
228	0	throw new IllegalStateException("Can't add an OR to AND conditions");
229		}
230	3	matchConditions.add(m);
231	3	andConditions = false;
232		}
233
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
234	3	@Override...
235		public boolean isAnded()
236		{
237	3	return andConditions;
238		}
239
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
240	3	@Override...
241		public Iterable<FeatureMatcherI> getMatchers()
242		{
243	3	return matchConditions;
244		}
245
246		/**
247		* Answers a string representation of this object suitable for display, and
248		* possibly internationalized. The format is not guaranteed stable and may
249		* change in future.
250		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.33
251	0	@Override...
252		public String toString()
253		{
254	0	StringBuilder sb = new StringBuilder();
255	0	boolean first = true;
256	0	boolean multiple = matchConditions.size() > 1;
257	0	for (FeatureMatcherI matcher : matchConditions)
258		{
259	0	if (!first)
260		{
261	0	String joiner = andConditions ? AND_18N : OR_I18N;
262	0	sb.append(SPACE).append(joiner.toLowerCase(Locale.ROOT))
263		.append(SPACE);
264		}
265	0	first = false;
266	0	if (multiple)
267		{
268	0	sb.append(OPEN_BRACKET).append(matcher.toString())
269		.append(CLOSE_BRACKET);
270		}
271		else
272		{
273	0	sb.append(matcher.toString());
274		}
275		}
276	0	return sb.toString();
277		}
278
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
279	21	@Override...
280		public boolean isEmpty()
281		{
282	21	return matchConditions == null || matchConditions.isEmpty();
283		}
284
285		/**
286		* {@inheritDoc} The output of this method should be parseable by method
287		* <code>fromString<code> to restore the original object.
288		*/
		100% Uncovered Elements: 0 (18) Complexity: 4 Complexity Density: 0.33
289	3	@Override...
290		public String toStableString()
291		{
292	3	StringBuilder sb = new StringBuilder();
293	3	boolean moreThanOne = matchConditions.size() > 1;
294	3	boolean first = true;
295
296	3	for (FeatureMatcherI matcher : matchConditions)
297		{
298	5	if (!first)
299		{
300	2	String joiner = andConditions ? AND : OR;
301	2	sb.append(SPACE).append(joiner).append(SPACE);
302		}
303	5	first = false;
304	5	if (moreThanOne)
305		{
306	4	sb.append(OPEN_BRACKET).append(matcher.toStableString())
307		.append(CLOSE_BRACKET);
308		}
309		else
310		{
311	1	sb.append(matcher.toStableString());
312		}
313		}
314	3	return sb.toString();
315		}
316
317		}