Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GffHelperFactory	26	18	11	0.00%	Show methods

Class GffHelperFactory

Class GffHelperFactory	Line # 26	Total Statements 18	Complexity 11	TOTAL Coverage 0.00%
getHelper(String[]) : GffHelperI   getHelper(String[]) : GffHelperI	3737	11.011	6.06	0.0 0.00%
looksLikeGff3(String[]) : boolean   looksLikeGff3(String[]) : boolean	7272	7.07	5.05	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		/**
24		* A factory to serve instances of GFF helper classes
25		*/
		0% Uncovered Elements: 32 (32) Complexity: 11 Complexity Density: 0.61
26		public class GffHelperFactory
27		{
28
29		/**
30		* Returns a class to process the GFF line based on inspecting its column
31		* data. This may return a general-purpose GFF2 or GFF3 helper, or a
32		* specialisation for a flavour of GFF generated by a particular tool.
33		*
34		* @param gff
35		* @return
36		*/
		0% Uncovered Elements: 19 (19) Complexity: 6 Complexity Density: 0.55
37	0	public static GffHelperI getHelper(String[] gff)...
38		{
39	0	if (gff == null || gff.length < 6)
40		{
41	0	return null;
42		}
43
44	0	GffHelperI result = null;
45	0	if (ExonerateHelper.recognises(gff))
46		{
47	0	result = new ExonerateHelper();
48		}
49	0	else if (InterProScanHelper.recognises(gff))
50		{
51	0	result = new InterProScanHelper();
52		}
53	0	else if (looksLikeGff3(gff))
54		{
55	0	result = new Gff3Helper();
56		}
57		else
58		{
59	0	result = new Gff2Helper();
60		}
61
62	0	return result;
63		}
64
65		/**
66		* Heuristic rule: if column 9 seems to have Name=Value entries, assume this
67		* is GFF3. GFF3 uses '=' as name-value separator, GFF2 uses space ' '.
68		*
69		* @param gff
70		* @return
71		*/
		0% Uncovered Elements: 11 (11) Complexity: 5 Complexity Density: 0.71
72	0	protected static boolean looksLikeGff3(String[] gff)...
73		{
74	0	if (gff.length >= 9)
75		{
76	0	String attributes = gff[8].trim();
77	0	int pos1 = attributes.indexOf(';');
78	0	int pos2 = attributes.indexOf('=');
79	0	if (pos2 != -1 && (pos1 == -1 || pos2 < pos1))
80		{
81		// there is an '=' before the first ';' (if any)
82		// not foolproof as theoretically GFF2 could be like "Name Value=123;"
83	0	return true;
84		}
85		}
86	0	return false;
87		}
88
89		}