Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModelI	30	2	2	0.550%	Show methods

Class ScoreModelI

Class ScoreModelI	Line # 30	Total Statements 2	Complexity 2	TOTAL Coverage 0.550%
isSecondaryStructure() : boolean   isSecondaryStructure() : boolean	6868	1.01	1.01	1.0 1.0100%
expandSeqData(SequenceI[],AlignmentView,SimilarityParamsI,List<String>) : SequenceI[]   expandSeqData(SequenceI[],AlignmentView,SimilarityParamsI,List<String>) : SequenceI[]	129129	1.01	1.01	0.0 0.00%

 

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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 java.util.List;
24
25		import jalview.api.AlignmentViewPanel;
26		import jalview.datamodel.AlignmentView;
27		import jalview.datamodel.SequenceI;
28		import jalview.math.MatrixI;
29
		50% Uncovered Elements: 2 (4) Complexity: 2 Complexity Density: 1
30		public interface ScoreModelI
31		{
32		/**
33		* Answers a name for the score model, suitable for display in menus. Names
34		* should be unique across score models in use.
35		*
36		* @return
37		* @see jalview.analysis.scoremodels.ScoreModels#forName(String)
38		*/
39		String getName();
40
41		/**
42		* Answers an informative description of the model, suitable for use in
43		* tooltips. Descriptions may be internationalised, and need not be unique
44		* (but should be).
45		*
46		* @return
47		*/
48		String getDescription();
49
50		/**
51		* Answers true if this model is applicable for nucleotide data (so should be
52		* shown in menus in that context)
53		*
54		* @return
55		*/
56		boolean isDNA();
57
58		/**
59		* Answers true if this model is applicable for peptide data (so should be
60		* shown in menus in that context)
61		*
62		* @return
63		*/
64		boolean isProtein();
65
66		// TODO getName, isDNA, isProtein can be static methods in Java 8
67
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
68	25	default public boolean isSecondaryStructure()...
69		{
70	25	return false;
71		}
72
73		/**
74		* Answers false by default Answers true if the data has secondary structure
75		* (so should be shown in menus in that context)
76		*
77		* @return
78		*/
79
80		/**
81		* Returns a distance score for the given sequence regions, that is, a matrix
82		* whose value [i][j] is the distance of sequence i from sequence j by some
83		* measure. The options parameter provides configuration choices for how the
84		* similarity score is calculated.
85		*
86		* @param seqData
87		* @param options
88		* @return
89		*/
90
91		MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
92
93		/**
94		* Returns a similarity score for the given sequence regions, that is, a
95		* matrix whose value [i][j] is the similarity of sequence i to sequence j by
96		* some measure. The options parameter provides configuration choices for how
97		* the similarity score is calculated.
98		*
99		* @param seqData
100		* @param options
101		* @return
102		*/
103		MatrixI findSimilarities(AlignmentView seqData,
104		SimilarityParamsI options);
105
106		/**
107		* Returns a score model object configured for the given alignment view.
108		* Depending on the score model, this may just be a singleton instance, or a
109		* new instance configured with data from the view.
110		*
111		* @param avp
112		* @return
113		*/
114		ScoreModelI getInstance(AlignmentViewPanel avp);
115
116		/**
117		* Score models may create multiple leaves for a single sequence - implement
118		* this method if you do
119		*
120		* @param sequences
121		* - sequences to be filtered/expanded set of leaves
122		* @param seqData
123		* - origin
124		* @param labels
125		* - strings to show instead of the SequenceI.getName() for each
126		* element of sequences attached to leaves
127		* @return filtered/expanded set of leaves to be analysed
128		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
129	0	default SequenceI[] expandSeqData(SequenceI[] sequences,...
130		AlignmentView seqData, SimilarityParamsI scoreParams,
131		List<String> labels)
132		{
133	0	return sequences;
134		};
135		}