Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreModelI	33	2	2	0.550%	Show methods

Class ScoreModelI

Class ScoreModelI	Line # 33	Total Statements 2	Complexity 2	TOTAL Coverage 0.550%
isSecondaryStructure() : boolean   isSecondaryStructure() : boolean	7171	1.01	1.01	1.0 1.0100%
expandSeqData(SequenceI[],AlignmentView,SimilarityParamsI,List<String>,ArrayList<AlignmentAnnotation>,HashMap<Integer, String>) : SequenceI[]   expandSeqData(SequenceI[],AlignmentView,SimilarityParamsI,List<String>,ArrayList<AlignmentAnnotation>,HashMap<Integer, String>) : SequenceI[]	139139	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.HashMap;
25		import java.util.List;
26
27		import jalview.api.AlignmentViewPanel;
28		import jalview.datamodel.AlignmentAnnotation;
29		import jalview.datamodel.AlignmentView;
30		import jalview.datamodel.SequenceI;
31		import jalview.math.MatrixI;
32
		50% Uncovered Elements: 2 (4) Complexity: 2 Complexity Density: 1
33		public interface ScoreModelI
34		{
35		/**
36		* Answers a name for the score model, suitable for display in menus. Names
37		* should be unique across score models in use.
38		*
39		* @return
40		* @see jalview.analysis.scoremodels.ScoreModels#forName(String)
41		*/
42		String getName();
43
44		/**
45		* Answers an informative description of the model, suitable for use in
46		* tooltips. Descriptions may be internationalised, and need not be unique
47		* (but should be).
48		*
49		* @return
50		*/
51		String getDescription();
52
53		/**
54		* Answers true if this model is applicable for nucleotide data (so should be
55		* shown in menus in that context)
56		*
57		* @return
58		*/
59		boolean isDNA();
60
61		/**
62		* Answers true if this model is applicable for peptide data (so should be
63		* shown in menus in that context)
64		*
65		* @return
66		*/
67		boolean isProtein();
68
69		// TODO getName, isDNA, isProtein can be static methods in Java 8
70
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
71	25	default public boolean isSecondaryStructure()...
72		{
73	25	return false;
74		}
75
76		/**
77		* Answers false by default Answers true if the data has secondary structure
78		* (so should be shown in menus in that context)
79		*
80		* @return
81		*/
82
83		/**
84		* Returns a distance score for the given sequence regions, that is, a matrix
85		* whose value [i][j] is the distance of sequence i from sequence j by some
86		* measure. The options parameter provides configuration choices for how the
87		* similarity score is calculated.
88		*
89		* @param seqData
90		* @param options
91		* @return
92		*/
93
94		MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
95
96		/**
97		* Returns a similarity score for the given sequence regions, that is, a
98		* matrix whose value [i][j] is the similarity of sequence i to sequence j by
99		* some measure. The options parameter provides configuration choices for how
100		* the similarity score is calculated.
101		*
102		* @param seqData
103		* @param options
104		* @return
105		*/
106		MatrixI findSimilarities(AlignmentView seqData,
107		SimilarityParamsI options);
108
109		/**
110		* Returns a score model object configured for the given alignment view.
111		* Depending on the score model, this may just be a singleton instance, or a
112		* new instance configured with data from the view.
113		*
114		* @param avp
115		* @return
116		*/
117		ScoreModelI getInstance(AlignmentViewPanel avp);
118
119		/**
120		* Score models may create multiple leaves for a single sequence - implement
121		* this method if you do
122		*
123		* @param sequences
124		* - sequences to be filtered/expanded set of leaves
125		* @param seqData
126		* - origin
127		* @param scoreParams
128		* - Parameters used by the similarity scoring model.
129		* @param labels
130		* - strings to show instead of the SequenceI.getName() for each
131		* element of sequences attached to leaves
132		* @param ssAnnotationForSeqs
133		* - Secondary structure annotations associated with the sequences.
134		* @param annotationDetails
135		* - Additional metadata about annotations (e.g., PDB ID, chain ID).
136		*
137		* @return filtered/expanded set of leaves to be analysed
138		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
139	0	default SequenceI[] expandSeqData(SequenceI[] sequences,...
140		AlignmentView seqData, SimilarityParamsI scoreParams,
141		List<String> labels, ArrayList<AlignmentAnnotation> ssAnnotationForSeqs,
142		HashMap<Integer, String> annotationDetails)
143		{
144	0	return sequences;
145		};
146		}