Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Gff2Helper	31	5	3	0.00%	Show methods

Class Gff2Helper

Class Gff2Helper	Line # 31	Total Statements 5	Complexity 3	TOTAL Coverage 0.00%
parseNameValuePairs(String) : Map<String, List<String>>   parseNameValuePairs(String) : Map<String, List<String>>	3939	1.01	1.01	0.0 0.00%
processGff(SequenceI,String[],AlignmentI,List<SequenceI>,boolean) : SequenceFeature   processGff(SequenceI,String[],AlignmentI,List<SequenceI>,boolean) : SequenceFeature	4848	4.04	2.02	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
27		import java.io.IOException;
28		import java.util.List;
29		import java.util.Map;
30
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
31		public class Gff2Helper extends GffHelperBase
32		{
33		/**
34		* GFF2 uses space character to delimit name/value pairs on column 9
35		*
36		* @param text
37		* @return
38		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
39	0	public static Map<String, List<String>> parseNameValuePairs(String text)...
40		{
41	0	return parseNameValuePairs(text, ";", ' ', ",");
42		}
43
44		/**
45		* Default processing if not overridden is just to construct a sequence
46		* feature
47		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
48	0	@Override...
49		public SequenceFeature processGff(SequenceI seq, String[] gff,
50		AlignmentI align, List<SequenceI> newseqs,
51		boolean relaxedIdMatching) throws IOException
52		{
53	0	Map<String, List<String>> attributes = null;
54	0	if (gff.length > ATTRIBUTES_COL)
55		{
56	0	attributes = parseNameValuePairs(gff[ATTRIBUTES_COL]);
57		}
58	0	return buildSequenceFeature(gff, attributes);
59		}
60
61		}