Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceCollectionI	26	0	0	-1.0 -	Show methods

Class SequenceCollectionI

Class SequenceCollectionI	Line # 26	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
23		import java.util.List;
24		import java.util.Map;
25
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
26		public interface SequenceCollectionI
27		{
28		/**
29		*
30		* @return (visible) sequences in this collection. This may be a direct
31		* reference to the collection so not thread safe
32		*/
33		List<SequenceI> getSequences();
34
35		/**
36		* FIXME: AlignmentI.getSequences(hiddenReps) doesn't actually obey this
37		* contract!
38		*
39		* @param hiddenReps
40		* @return the full set of sequences in this collection, including any
41		* sequences represented by sequences in the collection.
42		*/
43		List<SequenceI> getSequences(
44		Map<SequenceI, SequenceCollectionI> hiddenReps);
45
46		int getWidth();
47
48		/**
49		*
50		* @return true if getSeqrep doesn't return null
51		*/
52		boolean hasSeqrep();
53
54		/**
55		* get the reference or representative sequence within this collection
56		*
57		* @return null or the current reference sequence
58		*/
59		SequenceI getSeqrep();
60
61		/**
62		* set the reference or representative sequence for this collection. Reference
63		* is assumed to be present within the collection.
64		*
65		* @return
66		*/
67		void setSeqrep(SequenceI refseq);
68
69		/**
70		* @return the first column included in this collection. Runs from 0<=i<N_cols
71		*/
72		int getStartRes();
73
74		/**
75		*
76		* @return the last column in this collection. Runs from 0<=i<N_cols
77		*/
78		int getEndRes();
79
80		/**
81		* Answers true if sequence data is nucleotide (according to some heuristic)
82		*
83		* @return
84		*/
85		boolean isNucleotide();
86
87		/**
88		* Returns the (possibly empty) list of HMM consensus sequences in the
89		* collection
90		*
91		* @return
92		*/
93		List<SequenceI> getHmmSequences();
94		}