Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModelI	27	1	1	1.0100%	Show methods

Class ScoreModelI

Class ScoreModelI	Line # 27	Total Statements 1	Complexity 1	TOTAL Coverage 1.0100%
isSecondaryStructure() : boolean   isSecondaryStructure() : boolean	6565	1.01	1.01	1.0 1.0100%

 

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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.api.analysis;
22
23		import jalview.api.AlignmentViewPanel;
24		import jalview.datamodel.AlignmentView;
25		import jalview.math.MatrixI;
26
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 1
27		public interface ScoreModelI
28		{
29		/**
30		* Answers a name for the score model, suitable for display in menus. Names
31		* should be unique across score models in use.
32		*
33		* @return
34		* @see jalview.analysis.scoremodels.ScoreModels#forName(String)
35		*/
36		String getName();
37
38		/**
39		* Answers an informative description of the model, suitable for use in
40		* tooltips. Descriptions may be internationalised, and need not be unique
41		* (but should be).
42		*
43		* @return
44		*/
45		String getDescription();
46
47		/**
48		* Answers true if this model is applicable for nucleotide data (so should be
49		* shown in menus in that context)
50		*
51		* @return
52		*/
53		boolean isDNA();
54
55		/**
56		* Answers true if this model is applicable for peptide data (so should be
57		* shown in menus in that context)
58		*
59		* @return
60		*/
61		boolean isProtein();
62
63		// TODO getName, isDNA, isProtein can be static methods in Java 8
64
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
65	25	default public boolean isSecondaryStructure()...
66		{
67	25	return false;
68		}
69
70		/**
71		* Answers false by default Answers true if the data has secondary structure
72		* (so should be shown in menus in that context)
73		*
74		* @return
75		*/
76
77		/**
78		* Returns a distance score for the given sequence regions, that is, a matrix
79		* whose value [i][j] is the distance of sequence i from sequence j by some
80		* measure. The options parameter provides configuration choices for how the
81		* similarity score is calculated.
82		*
83		* @param seqData
84		* @param options
85		* @return
86		*/
87
88		MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
89
90		/**
91		* Returns a similarity score for the given sequence regions, that is, a
92		* matrix whose value [i][j] is the similarity of sequence i to sequence j by
93		* some measure. The options parameter provides configuration choices for how
94		* the similarity score is calculated.
95		*
96		* @param seqData
97		* @param options
98		* @return
99		*/
100		MatrixI findSimilarities(AlignmentView seqData,
101		SimilarityParamsI options);
102
103		/**
104		* Returns a score model object configured for the given alignment view.
105		* Depending on the score model, this may just be a singleton instance, or a
106		* new instance configured with data from the view.
107		*
108		* @param avp
109		* @return
110		*/
111		ScoreModelI getInstance(AlignmentViewPanel avp);
112		}