Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationJob	19	58	20	0.00%	Show methods

Class AnnotationJob

Class AnnotationJob	Line # 19	Total Statements 58	Complexity 20	TOTAL Coverage 0.00%
AnnotationJob(List<SequenceI>,boolean[],Map<String, SequenceI>,int,int,int)   AnnotationJob(List<SequenceI>,boolean[],Map<String, SequenceI>,int,int,int)	2929	6.06	1.01	0.0 0.00%
isInputValid() : boolean   isInputValid() : boolean	4040	5.05	2.02	0.0 0.00%
create(SequenceCollectionI,boolean,boolean,boolean,boolean,int) : AnnotationJob   create(SequenceCollectionI,boolean,boolean,boolean,boolean,int) : AnnotationJob	5050	31.031	9.09	0.0 0.00%
replaceNonStandardResidues(char[],char,boolean) : void   replaceNonStandardResidues(char[],char,boolean) : void	108108	4.04	4.04	0.0 0.00%
updateResidueMap(BitSet,SequenceI) : void   updateResidueMap(BitSet,SequenceI) : void	132132	3.03	1.01	0.0 0.00%
adjustColumns(List<SequenceI>,BitSet,boolean) : void   adjustColumns(List<SequenceI>,BitSet,boolean) : void	151151	9.09	3.03	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.actions.annotation;
2
3		import java.util.ArrayList;
4		import java.util.Arrays;
5		import java.util.BitSet;
6		import java.util.HashMap;
7		import java.util.List;
8		import java.util.Map;
9
10		import jalview.analysis.AlignSeq;
11		import jalview.analysis.SeqsetUtils;
12		import jalview.datamodel.Sequence;
13		import jalview.datamodel.SequenceCollectionI;
14		import jalview.datamodel.SequenceI;
15		import jalview.schemes.ResidueProperties;
16		import jalview.util.Comparison;
17		import jalview.ws2.actions.BaseJob;
18
		0% Uncovered Elements: 90 (90) Complexity: 20 Complexity Density: 0.34
19		public class AnnotationJob extends BaseJob
20		{
21		final boolean[] gapMap;
22
23		final Map<String, SequenceI> seqNames;
24
25		final int regionStart, regionEnd;
26
27		final int minSize;
28
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
29	0	public AnnotationJob(List<SequenceI> inputSeqs, boolean[] gapMap,...
30		Map<String, SequenceI> seqNames, int start, int end, int minSize)
31		{
32	0	super(inputSeqs);
33	0	this.gapMap = gapMap;
34	0	this.seqNames = seqNames;
35	0	this.regionStart = start;
36	0	this.regionEnd = end;
37	0	this.minSize = minSize;
38		}
39
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
40	0	@Override...
41		public boolean isInputValid()
42		{
43	0	int nvalid = 0;
44	0	for (SequenceI sq : getInputSequences())
45	0	if (sq.getStart() <= sq.getEnd())
46	0	nvalid++;
47	0	return nvalid >= minSize;
48		}
49
		0% Uncovered Elements: 47 (47) Complexity: 9 Complexity Density: 0.29
50	0	public static AnnotationJob create(SequenceCollectionI inputSeqs,...
51		boolean bySequence, boolean submitGaps, boolean requireAligned,
52		boolean filterNonStandardResidues, int minSize)
53		{
54	0	List<SequenceI> sequences = new ArrayList<>();
55	0	int minlen = 10;
56	0	int width = 0;
57	0	Map<String, SequenceI> namesMap = bySequence ? new HashMap<>() : null;
58	0	BitSet residueMap = new BitSet();
59	0	int start = inputSeqs.getStartRes();
60	0	int end = inputSeqs.getEndRes();
61		// TODO: URGENT! unify with JPred / MSA code to handle hidden regions
62		// correctly
63		// TODO: push attributes into WsJob instance (so they can be safely
64		// persisted/restored
65	0	for (SequenceI sq : inputSeqs.getSequences())
66		{
67	0	int sqLen = (bySequence)
68		? sq.findPosition(end + 1) - sq.findPosition(start + 1)
69		: sq.getEnd() - sq.getStart();
70	0	if (sqLen < minlen)
71	0	continue;
72	0	width = Math.max(width, sq.getLength());
73	0	String newName = SeqsetUtils.unique_name(sequences.size() + 1);
74	0	if (namesMap != null)
75	0	namesMap.put(newName, sq);
76	0	char[] seqChars = sq.getSequence(start, end + 1);
77	0	if (filterNonStandardResidues)
78	0	replaceNonStandardResidues(seqChars, Comparison.GAP_DASH,
79		sq.isProtein());
80	0	Sequence seq;
81	0	if (submitGaps)
82		{
83	0	seq = new Sequence(newName, seqChars);
84	0	updateResidueMap(residueMap, seq);
85		} else
86		{
87		// TODO: add ability to exclude hidden regions
88	0	seq = new Sequence(newName,
89		AlignSeq.extractGaps(Comparison.GapChars, new String(seqChars)));
90		// for annotation need to also record map to sequence start/end
91		// position in range
92		// then transfer back to original sequence on return.
93		}
94	0	sequences.add(seq);
95		}
96	0	boolean[] gapMapArray = null;
97	0	if (submitGaps)
98		{
99	0	adjustColumns(sequences, residueMap, requireAligned);
100	0	gapMapArray = new boolean[width];
101	0	for (int i = 0; i < width; i++)
102	0	gapMapArray[i] = residueMap.get(i);
103		}
104	0	return new AnnotationJob(sequences, gapMapArray, namesMap, start, end,
105		minSize);
106		}
107
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 1
108	0	static void replaceNonStandardResidues(char[] seq, char replacement,...
109		boolean isProtein)
110		{
111	0	for (int i = 0; i < seq.length; i++)
112		{
113	0	char chr = seq[i];
114	0	if (isProtein ? ResidueProperties.aaIndex[chr] >= 20
115		: ResidueProperties.nucleotideIndex[chr] >= 5)
116		{
117	0	seq[i] = replacement;
118		}
119		}
120		}
121
122		/**
123		* Add residue positions of the given sequence to the residues map. Perform an
124		* "or" operation between the given residue map and the inverse of the gap map
125		* of the given sequence.
126		*
127		* @param residueMap
128		* mapping to be updated in-place
129		* @param seq
130		* the sequence whose residue positions are added to the map
131		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
132	0	static void updateResidueMap(BitSet residueMap, SequenceI seq)...
133		{
134	0	var gaps = seq.gapBitset();
135	0	gaps.flip(0, seq.getLength());
136	0	residueMap.or(gaps);
137		}
138
139		/**
140		* Remove columns not included in the mask from the sequences in-place. If
141		* {@code padToLength} is set, the shorter sequences are padded with gaps at
142		* the end.
143		*
144		* @param sequences
145		* list of sequences to be modified
146		* @param mask
147		* mask of columns that will remain
148		* @param padToLength
149		* if gaps should be added to the end of shorter sequences
150		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
151	0	static void adjustColumns(List<SequenceI> sequences, BitSet mask,...
152		boolean padToLength)
153		{
154	0	int width = mask.cardinality();
155	0	for (SequenceI seq : sequences)
156		{
157	0	char[] chars = SeqsetUtils.filterSequence(seq.getSequence(), mask);
158	0	if (padToLength && chars.length < width)
159		{
160	0	int limit = chars.length;
161	0	chars = Arrays.copyOf(chars, width);
162	0	Arrays.fill(chars, limit, chars.length, Comparison.GAP_DASH);
163		}
164	0	seq.setEnd(seq.getStart());
165	0	seq.setSequence(chars);
166		}
167		}
168		}