Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TreeBuilder	41	61	23	0.802197880.2%	Show methods

Class TreeBuilder

Class TreeBuilder	Line # 41	Total Statements 61	Complexity 23	TOTAL Coverage 0.802197880.2%
TreeBuilder(AlignmentViewport,ScoreModelI,SimilarityParamsI)   TreeBuilder(AlignmentViewport,ScoreModelI,SimilarityParamsI)	6868	12.012	2.02	0.71428573 0.7142857371.4%
getSequences() : SequenceI[]   getSequences() : SequenceI[]	9696	1.01	1.01	1.0 1.0100%
hasDistances() : boolean   hasDistances() : boolean	105105	1.01	1.01	1.0 1.0100%
hasBootstrap() : boolean   hasBootstrap() : boolean	114114	1.01	1.01	1.0 1.0100%
hasRootDistance() : boolean   hasRootDistance() : boolean	119119	1.01	1.01	1.0 1.0100%
getLabels() : List<String>   getLabels() : List<String>	124124	1.01	1.01	1.0 1.0100%
initAnnotationData() : void   initAnnotationData() : void	132132	3.03	1.01	1.0 1.0100%
computeTree(ScoreModelI,SimilarityParamsI) : void   computeTree(ScoreModelI,SimilarityParamsI) : void	151151	7.07	1.01	1.0 1.0100%
init(AlignmentView,int,int) : void   init(AlignmentView,int,int) : void	167167	14.014	4.04	0.5 0.550%
applyAnnotationsToNode(SequenceNode,int) : void   applyAnnotationsToNode(SequenceNode,int) : void	207207	7.07	6.06	0.7692308 0.769230876.9%
makeLeaves() : void   makeLeaves() : void	224224	12.012	3.03	0.9375 0.937593.8%
getOriginalData() : AlignmentView   getOriginalData() : AlignmentView	250250	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8021978	jalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTreejalview.project.Jalview2xmlTests.testSaveAndLoadAnnotationBasedTree	1PASS

 

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.analysis;
22
23		import jalview.api.analysis.ScoreModelI;
24		import jalview.api.analysis.SimilarityParamsI;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.AlignmentView;
27		import jalview.datamodel.BinaryNode;
28		import jalview.datamodel.CigarArray;
29		import jalview.datamodel.SeqCigar;
30		import jalview.datamodel.SequenceI;
31		import jalview.datamodel.SequenceNode;
32		import jalview.viewmodel.AlignmentViewport;
33
34
35		import java.util.ArrayList;
36		import java.util.BitSet;
37		import java.util.HashMap;
38		import java.util.List;
39		import java.util.Vector;
40
		80.2% Uncovered Elements: 18 (91) Complexity: 23 Complexity Density: 0.38
41		public abstract class TreeBuilder extends TreeEngine
42		{
43		public static final String AVERAGE_DISTANCE = "AV";
44
45		public static final String NEIGHBOUR_JOINING = "NJ";
46
47		protected SequenceI[] sequences;
48
49		protected List<String> labels;
50
51		// Map to store node pos : annotation details
52		// (additional details from annotation property)
53		protected HashMap<Integer, String> annotationDetails;
54
55		ArrayList<AlignmentAnnotation> ssAnnotationForSeqs;
56
57		public AlignmentView seqData;
58
59		private AlignmentView seqStrings;
60
61		/**
62		* Constructor
63		*
64		* @param av
65		* @param sm
66		* @param scoreParameters
67		*/
		71.4% Uncovered Elements: 4 (14) Complexity: 2 Complexity Density: 0.17
68	1	public TreeBuilder(AlignmentViewport av, ScoreModelI sm,...
69		SimilarityParamsI scoreParameters)
70		{
71	1	int start, end;
72	1	boolean selview = av.getSelectionGroup() != null
73		&& av.getSelectionGroup().getSize() >= 1;
74	1	seqStrings = av.getAlignmentView(selview);
75		// FIXME @RENIA - we should check that there are enough annotation tracks to
76		// build a tree!
77	1	if (!selview)// && !sm.isSecondaryStructure())
78		{
79	0	start = 0;
80	0	end = av.getAlignment().getWidth();
81	0	this.sequences = av.getAlignment().getSequencesArray();
82		}
83		else
84		{
85	1	start = av.getSelectionGroup().getStartRes();
86	1	end = av.getSelectionGroup().getEndRes() + 1;
87	1	this.sequences = av.getSelectionGroup()
88		.getSequencesInOrder(av.getAlignment());
89		}
90
91	1	init(seqStrings, start, end);
92
93	1	computeTree(sm, scoreParameters);
94		}
95
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
96	1	public SequenceI[] getSequences()...
97		{
98	1	return sequences;
99		}
100
101		/**
102		*
103		* @return true if tree has real distances
104		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
105	1	public boolean hasDistances()...
106		{
107	1	return true;
108		}
109
110		/**
111		*
112		* @return true if tree has real bootstrap values
113		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
114	1	public boolean hasBootstrap()...
115		{
116	1	return false;
117		}
118
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
119	1	public boolean hasRootDistance()...
120		{
121	1	return true;
122		}
123
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
124	1	public List<String> getLabels(){...
125	1	return this.labels;
126		}
127
128		/**
129		* Initializes the data structures used to hold secondary structure
130		* and metadata during the tree building process.
131		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
132	1	private void initAnnotationData() {...
133	1	this.labels = new ArrayList<>();
134	1	this.annotationDetails = new HashMap<>();
135	1	this.ssAnnotationForSeqs = new ArrayList<>();
136		}
137
138		/**
139		* Calculates the tree using the given score model and parameters, and the
140		* configured tree type
141		* <p>
142		* If the score model computes pairwise distance scores, then these are used
143		* directly to derive the tree
144		* <p>
145		* If the score model computes similarity scores, then the range of the scores
146		* is reversed to give a distance measure, and this is used to derive the tree
147		*
148		* @param sm
149		* @param scoreOptions
150		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
151	1	protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)...
152		{
153	1	initAnnotationData();
154	1	sequences = sm.expandSeqData(sequences, seqData, scoreOptions,
155		labels, ssAnnotationForSeqs, annotationDetails);
156	1	noseqs = sequences.length;
157
158	1	distances = sm.findDistances(seqData, scoreOptions);
159
160	1	makeLeaves();
161
162	1	noClus = clusters.size();
163
164	1	cluster();
165		}
166
		50% Uncovered Elements: 10 (20) Complexity: 4 Complexity Density: 0.29
167	1	protected void init(AlignmentView seqView, int start, int end)...
168		{
169	1	this.node = new Vector<BinaryNode>();
170	1	if (seqView != null)
171		{
172	1	this.seqData = seqView;
173		}
174		else
175		{
176	0	SeqCigar[] seqs = new SeqCigar[sequences.length];
177	0	for (int i = 0; i < sequences.length; i++)
178		{
179	0	seqs[i] = new SeqCigar(sequences[i], start, end);
180		}
181	0	CigarArray sdata = new CigarArray(seqs);
182	0	sdata.addOperation(CigarArray.M, end - start + 1);
183	0	this.seqData = new AlignmentView(sdata, start);
184		}
185
186		/*
187		* count the non-null sequences
188		*/
189	1	noseqs = 0;
190
191	1	done = new BitSet();
192
193	1	for (SequenceI seq : sequences)
194		{
195	15	if (seq != null)
196		{
197	15	noseqs++;
198		}
199		}
200		}
201
202		/**
203		* Attaches annotation and metadata to a specific tree node.
204		* @param sn The SequenceNode (leaf) being processed
205		* @param index The index of the sequence in the alignment
206		*/
		76.9% Uncovered Elements: 3 (13) Complexity: 6 Complexity Density: 0.86
207	18	private void applyAnnotationsToNode(SequenceNode sn, int index) {...
208	18	if (ssAnnotationForSeqs != null && index < ssAnnotationForSeqs.size()) {
209	18	AlignmentAnnotation aa = ssAnnotationForSeqs.get(index);
210	18	if (aa != null) {
211	4	sn.setAlignmentAnnotation(aa);
212
213	4	String detail = annotationDetails.get(index);
214	4	if (detail != null && !detail.isEmpty()) {
215	0	sn.setAnnotationDetails(detail);
216		}
217		}
218		}
219		}
220
221		/**
222		* Start by making a cluster for each individual sequence
223		*/
		93.8% Uncovered Elements: 1 (16) Complexity: 3 Complexity Density: 0.25
224	1	void makeLeaves()...
225		{
226	1	clusters = new Vector<BitSet>();
227
228	19	for (int i = 0; i < noseqs; i++)
229		{
230	18	SequenceNode sn = new SequenceNode();
231
232	18	sn.setElement(sequences[i]);
233
234	18	if (labels.size() == noseqs)
235		{
236	18	sn.setLabel(labels.get(i));
237		}
238
239	18	applyAnnotationsToNode(sn, i);
240
241	18	sn.setName(sequences[i].getName());
242
243	18	node.addElement(sn);
244	18	BitSet bs = new BitSet();
245	18	bs.set(i);
246	18	clusters.addElement(bs);
247		}
248		}
249
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
250	1	public AlignmentView getOriginalData()...
251		{
252	1	return seqStrings;
253		}
254
255		}