Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceFeaturesI	28	0	0	-1.0 -	Show methods

Class SequenceFeaturesI

Class SequenceFeaturesI	Line # 28	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.datamodel.features;
22
23		import jalview.datamodel.SequenceFeature;
24
25		import java.util.List;
26		import java.util.Set;
27
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
28		public interface SequenceFeaturesI
29		{
30
31		/**
32		* Adds one sequence feature to the store, and returns true, unless the
33		* feature is already contained in the store, in which case this method
34		* returns false. Containment is determined by SequenceFeature.equals()
35		* comparison. Answers false, and does not add the feature, if feature type is
36		* null.
37		*
38		* @param sf
39		*/
40		boolean add(SequenceFeature sf);
41
42		/**
43		* Returns a (possibly empty) list of features, optionally restricted to
44		* specified types, which overlap the given (inclusive) sequence position
45		* range. If types are specified, features are returned in the order of the
46		* types given.
47		*
48		* @param from
49		* @param to
50		* @param type
51		* @return
52		*/
53		List<SequenceFeature> findFeatures(int from, int to, String... type);
54
55		/**
56		* Answers a list of all features stored, in no particular guaranteed order.
57		* Positional features may optionally be restricted to specified types, but
58		* all non-positional features (if any) are always returned.
59		* <p>
60		* To filter non-positional features by type, use
61		* getNonPositionalFeatures(type).
62		*
63		* @param type
64		* @return
65		*/
66		List<SequenceFeature> getAllFeatures(String... type);
67
68		/**
69		* Answers a list of all positional (or non-positional) features which are in
70		* the specified feature group, optionally restricted to features of specified
71		* types.
72		*
73		* @param positional
74		* if true returns positional features, else non-positional features
75		* @param group
76		* the feature group to be matched (which may be null)
77		* @param type
78		* optional feature types to filter by
79		* @return
80		*/
81		List<SequenceFeature> getFeaturesForGroup(boolean positional,
82		String group, String... type);
83
84		/**
85		* Answers a list of all features stored, whose type either matches, or is a
86		* specialisation (in the Sequence Ontology) of, one of the given terms.
87		* Results are returned in no particular order.
88		*
89		* @param ontologyTerm
90		* @return
91		*/
92		List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm);
93
94		/**
95		* Answers the number of (positional or non-positional) features, optionally
96		* restricted to specified feature types. Contact features are counted as 1.
97		*
98		* @param positional
99		* @param type
100		* @return
101		*/
102		int getFeatureCount(boolean positional, String... type);
103
104		/**
105		* Answers the total length of positional features, optionally restricted to
106		* specified feature types. Contact features are counted as length 1.
107		*
108		* @param type
109		* @return
110		*/
111		int getTotalFeatureLength(String... type);
112
113		/**
114		* Answers a list of all positional features, optionally restricted to
115		* specified types, in no particular guaranteed order
116		*
117		* @param type
118		* @return
119		*/
120		List<SequenceFeature> getPositionalFeatures(String... type);
121
122		/**
123		* Answers a list of all contact features, optionally restricted to specified
124		* types, in no particular guaranteed order
125		*
126		* @return
127		*/
128		List<SequenceFeature> getContactFeatures(String... type);
129
130		/**
131		* Answers a list of all non-positional features, optionally restricted to
132		* specified types, in no particular guaranteed order
133		*
134		* @param type
135		* if no type is specified, all are returned
136		* @return
137		*/
138		List<SequenceFeature> getNonPositionalFeatures(String... type);
139
140		/**
141		* Deletes the given feature from the store, returning true if it was found
142		* (and deleted), else false. This method makes no assumption that the feature
143		* is in the 'expected' place in the store, in case it has been modified since
144		* it was added.
145		*
146		* @param sf
147		*/
148		boolean delete(SequenceFeature sf);
149
150		/**
151		* Answers true if this store contains at least one feature, else false
152		*
153		* @return
154		*/
155		boolean hasFeatures();
156
157		/**
158		* Returns a set of the distinct feature groups present in the collection. The
159		* set may include null. The boolean parameter determines whether the groups
160		* for positional or for non-positional features are returned. The optional
161		* type parameter may be used to restrict to groups for specified feature
162		* types.
163		*
164		* @param positionalFeatures
165		* @param type
166		* @return
167		*/
168		Set<String> getFeatureGroups(boolean positionalFeatures, String... type);
169
170		/**
171		* Answers the set of distinct feature types for which there is at least one
172		* feature with one of the given feature group(s). The boolean parameter
173		* determines whether the groups for positional or for non-positional features
174		* are returned.
175		*
176		* @param positionalFeatures
177		* @param groups
178		* @return
179		*/
180		Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
181		String... groups);
182
183		/**
184		* Answers a set of the distinct feature types for which a feature is stored.
185		* The types may optionally be restricted to those which match, or are a
186		* subtype of, given sequence ontology terms
187		*
188		* @return
189		*/
190		Set<String> getFeatureTypes(String... soTerm);
191
192		/**
193		* Answers the minimum score held for positional or non-positional features
194		* for the specified type. This may be Float.NaN if there are no features, or
195		* none has a non-NaN score.
196		*
197		* @param type
198		* @param positional
199		* @return
200		*/
201		float getMinimumScore(String type, boolean positional);
202
203		/**
204		* Answers the maximum score held for positional or non-positional features
205		* for the specified type. This may be Float.NaN if there are no features, or
206		* none has a non-NaN score.
207		*
208		* @param type
209		* @param positional
210		* @return
211		*/
212		float getMaximumScore(String type, boolean positional);
213
214		/**
215		* Adds the shift amount to the start and end of all positional features whose
216		* start position is at or after fromPosition. Returns true if at least one
217		* feature was shifted, else false.
218		*
219		* @param fromPosition
220		* @param shiftBy
221		*/
222		boolean shiftFeatures(int fromPosition, int shiftBy);
223
224		/**
225		* Deletes all positional and non-positional features
226		*/
227		void deleteAll();
228		}