Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotatedCollectionI	23	0	0	-1.0 -	Show methods

Class AnnotatedCollectionI

Class AnnotatedCollectionI	Line # 23	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;
22
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
23		public interface AnnotatedCollectionI
24		extends SequenceCollectionI, ContactMapHolderI
25		{
26
27		/**
28		* TODO: decide if null is a valid response if there is no annotation on the
29		* object
30		*
31		* @return null
32		*/
33		AlignmentAnnotation[] getAlignmentAnnotation();
34
35		/**
36		* Returns a list of annotations matching the given calc id, or an empty list
37		* if calcId is null
38		*
39		* @param calcId
40		* @return
41		*/
42		Iterable<AlignmentAnnotation> findAnnotation(String calcId);
43
44		/**
45		* Returns an iterable collection of any annotations that match on given
46		* sequence ref, calcId and label (ignoring null values).
47		*
48		* @param seq
49		* null or reference sequence to select annotation for
50		* @param calcId
51		* null or the calcId to select annotation for
52		* @param label
53		* null or the label to select annotation for
54		*/
55		Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
56		String calcId, String label);
57
58		/**
59		* context for this annotated collection
60		*
61		* @return null or the collection upon which this collection is defined (e.g.
62		* alignment, parent group).
63		*/
64		AnnotatedCollectionI getContext();
65
66		/**
67		*
68		* @return true if there are sequence associated secondary structure
69		* annotations to use for tree calculations/etc
70		*/
71		boolean isSecondaryStructurePresent();
72		}