Classes

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

Class SequenceCollectionI

Class SequenceCollectionI	Line # 26	Total Statements 0	Complexity 0	Uncovered Elements 0	TOTAL Coverage -1.0 -

 

Contributing tests

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;
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		List<SequenceI> getSequences();
29
30		List<SequenceI> getSequences(
31		Map<SequenceI, SequenceCollectionI> hiddenReps);
32
33		int getWidth();
34
35		/**
36		*
37		* @return true if getSeqrep doesn't return null
38		*/
39		boolean hasSeqrep();
40
41		/**
42		* get the reference or representative sequence within this collection
43		*
44		* @return null or the current reference sequence
45		*/
46		SequenceI getSeqrep();
47
48		/**
49		* set the reference or representative sequence for this collection. Reference
50		* is assumed to be present within the collection.
51		*
52		* @return
53		*/
54		void setSeqrep(SequenceI refseq);
55
56		/**
57		* @return the first column included in this collection. Runs from 0<=i<N_cols
58		*/
59		int getStartRes();
60
61		/**
62		*
63		* @return the last column in this collection. Runs from 0<=i<N_cols
64		*/
65		int getEndRes();
66
67		/**
68		* Answers true if sequence data is nucleotide (according to some heuristic)
69		*
70		* @return
71		*/
72		boolean isNucleotide();
73		}