Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModelI	32	2	2	0.550%	Show methods

Class ScoreModelI

Class ScoreModelI	Line # 32	Total Statements 2	Complexity 2	TOTAL Coverage 0.550%
isSecondaryStructure() : boolean   isSecondaryStructure() : boolean	7070	1.01	1.01	1.0 1.0100%
expandSeqData(SequenceI[],AlignmentView,SimilarityParamsI,List<String>,ArrayList<AlignmentAnnotation>) : SequenceI[]   expandSeqData(SequenceI[],AlignmentView,SimilarityParamsI,List<String>,ArrayList<AlignmentAnnotation>) : SequenceI[]	131131	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.ArrayList;
24		import java.util.List;
25
26		import jalview.api.AlignmentViewPanel;
27		import jalview.datamodel.AlignmentAnnotation;
28		import jalview.datamodel.AlignmentView;
29		import jalview.datamodel.SequenceI;
30		import jalview.math.MatrixI;
31
		50% Uncovered Elements: 2 (4) Complexity: 2 Complexity Density: 1
32		public interface ScoreModelI
33		{
34		/**
35		* Answers a name for the score model, suitable for display in menus. Names
36		* should be unique across score models in use.
37		*
38		* @return
39		* @see jalview.analysis.scoremodels.ScoreModels#forName(String)
40		*/
41		String getName();
42
43		/**
44		* Answers an informative description of the model, suitable for use in
45		* tooltips. Descriptions may be internationalised, and need not be unique
46		* (but should be).
47		*
48		* @return
49		*/
50		String getDescription();
51
52		/**
53		* Answers true if this model is applicable for nucleotide data (so should be
54		* shown in menus in that context)
55		*
56		* @return
57		*/
58		boolean isDNA();
59
60		/**
61		* Answers true if this model is applicable for peptide data (so should be
62		* shown in menus in that context)
63		*
64		* @return
65		*/
66		boolean isProtein();
67
68		// TODO getName, isDNA, isProtein can be static methods in Java 8
69
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
70	25	default public boolean isSecondaryStructure()...
71		{
72	25	return false;
73		}
74
75		/**
76		* Answers false by default Answers true if the data has secondary structure
77		* (so should be shown in menus in that context)
78		*
79		* @return
80		*/
81
82		/**
83		* Returns a distance score for the given sequence regions, that is, a matrix
84		* whose value [i][j] is the distance of sequence i from sequence j by some
85		* measure. The options parameter provides configuration choices for how the
86		* similarity score is calculated.
87		*
88		* @param seqData
89		* @param options
90		* @return
91		*/
92
93		MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
94
95		/**
96		* Returns a similarity score for the given sequence regions, that is, a
97		* matrix whose value [i][j] is the similarity of sequence i to sequence j by
98		* some measure. The options parameter provides configuration choices for how
99		* the similarity score is calculated.
100		*
101		* @param seqData
102		* @param options
103		* @return
104		*/
105		MatrixI findSimilarities(AlignmentView seqData,
106		SimilarityParamsI options);
107
108		/**
109		* Returns a score model object configured for the given alignment view.
110		* Depending on the score model, this may just be a singleton instance, or a
111		* new instance configured with data from the view.
112		*
113		* @param avp
114		* @return
115		*/
116		ScoreModelI getInstance(AlignmentViewPanel avp);
117
118		/**
119		* Score models may create multiple leaves for a single sequence - implement
120		* this method if you do
121		*
122		* @param sequences
123		* - sequences to be filtered/expanded set of leaves
124		* @param seqData
125		* - origin
126		* @param labels
127		* - strings to show instead of the SequenceI.getName() for each
128		* element of sequences attached to leaves
129		* @return filtered/expanded set of leaves to be analysed
130		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	default SequenceI[] expandSeqData(SequenceI[] sequences,...
132		AlignmentView seqData, SimilarityParamsI scoreParams,
133		List<String> labels, ArrayList<AlignmentAnnotation> ssAnnotationForSeqs)
134		{
135	0	return sequences;
136		};
137		}