Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
InterProScanHelper	35	18	11	0.00%	Show methods

Class InterProScanHelper

Class InterProScanHelper	Line # 35	Total Statements 18	Complexity 11	TOTAL Coverage 0.00%
processGff(SequenceI,String[],AlignmentI,List<SequenceI>,boolean) : SequenceFeature   processGff(SequenceI,String[],AlignmentI,List<SequenceI>,boolean) : SequenceFeature	5959	3.03	2.02	0.0 0.00%
buildSequenceFeature(String[],Map<String, List<String>>) : SequenceFeature   buildSequenceFeature(String[],Map<String, List<String>>) : SequenceFeature	8484	6.06	2.02	0.0 0.00%
recognises(String[]) : boolean   recognises(String[]) : boolean	110110	5.05	4.04	0.0 0.00%
findTargetId(String,Map<String, List<String>>) : String   findTargetId(String,Map<String, List<String>>) : String	127127	4.04	3.03	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.io.gff;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.datamodel.SequenceFeature;
25		import jalview.datamodel.SequenceI;
26		import jalview.util.StringUtils;
27
28		import java.io.IOException;
29		import java.util.List;
30		import java.util.Map;
31
32		/**
33		* A handler to parse GFF in the format generated by InterProScan
34		*/
		0% Uncovered Elements: 30 (30) Complexity: 11 Complexity Density: 0.61
35		public class InterProScanHelper extends Gff3Helper
36		{
37		private static final String INTER_PRO_SCAN = "InterProScan";
38
39		private static final String SIGNATURE_DESC = "signature_desc";
40
41		/**
42		* Process one GFF feature line (as modelled by SequenceFeature)
43		*
44		* @param seq
45		* the sequence with which this feature is associated
46		* @param gff
47		* the gff column data
48		* @param align
49		* the alignment we are adding GFF to
50		* @param newseqs
51		* any new sequences referenced by the GFF
52		* @param relaxedIdMatching
53		* if true, match word tokens in sequence names
54		* @return a sequence feature if one should be added to the sequence, else
55		* null (i.e. it has been processed in another way e.g. to generate a
56		* mapping)
57		* @throws IOException
58		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
59	0	@Override...
60		public SequenceFeature processGff(SequenceI seq, String[] gff,
61		AlignmentI align, List<SequenceI> newseqs,
62		boolean relaxedIdMatching) throws IOException
63		{
64		/*
65		* ignore the 'polypeptide' match of the whole sequence
66		*/
67	0	if (".".equals(gff[SOURCE_COL]))
68		{
69	0	return null;
70		}
71
72	0	return super.processGff(seq, gff, align, newseqs, relaxedIdMatching);
73		}
74
75		/**
76		* An override that
77		* <ul>
78		* <li>uses Source (column 2) as feature type instead of the default column
79		* 3</li>
80		* <li>sets "InterProScan" as the feature group</li>
81		* <li>extracts "signature_desc" attribute as the feature description</li>
82		* </ul>
83		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
84	0	@Override...
85		protected SequenceFeature buildSequenceFeature(String[] gff,
86		Map<String, List<String>> attributes)
87		{
88	0	SequenceFeature sf = super.buildSequenceFeature(gff, SOURCE_COL,
89		INTER_PRO_SCAN, attributes);
90
91		/*
92		* signature_desc is a more informative source of description
93		*/
94	0	List<String> desc = attributes.get(SIGNATURE_DESC);
95	0	String description = StringUtils.listToDelimitedString(desc, ", ");
96	0	if (description.length() > 0)
97		{
98	0	sf.setDescription(description);
99		}
100
101	0	return sf;
102		}
103
104		/**
105		* Tests whether the GFF data looks like it was generated by InterProScan
106		*
107		* @param columns
108		* @return
109		*/
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 0.8
110	0	public static boolean recognises(String[] columns)...
111		{
112	0	SequenceOntologyI so = SequenceOntologyFactory.getInstance();
113	0	String type = columns[TYPE_COL];
114	0	if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
115		|| (".".equals(columns[SOURCE_COL])
116		&& so.isA(type, SequenceOntologyI.POLYPEPTIDE)))
117		{
118	0	return true;
119		}
120	0	return false;
121		}
122
123		/**
124		* Overriden method, because InterProScan GFF has the target sequence id in
125		* GFF field 'ID' rather than the usual 'Target' :-O
126		*/
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
127	0	@Override...
128		protected String findTargetId(String target,
129		Map<String, List<String>> set)
130		{
131	0	List<String> ids = set.get(ID);
132	0	if (ids == null || ids.size() != 1)
133		{
134	0	return null;
135		}
136	0	return ids.get(0);
137		}
138
139		}