Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
GeneDbSource	34	10	10	20	0.00%	Show methods

Class GeneDbSource

Class GeneDbSource	Line # 34	Total Statements 10	Complexity 10	Uncovered Elements 20	TOTAL Coverage 0.00%
GeneDbSource()   GeneDbSource()	3737	1.01	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	4747	1.01	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	5959	1.01	1.01	1.01	0.0 0.00%
getDbSource() : String   getDbSource() : String	7171	1.01	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	8282	1.01	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	9494	1.01	1.01	1.01	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	108108	1.01	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	118118	1.01	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	124124	1.01	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	130130	1.01	1.01	1.01	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.ws.dbsources;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.datamodel.DBRefSource;
25
26		import com.stevesoft.pat.Regex;
27
28		/**
29		* Test class for accessing GeneDB - not yet finished.
30		*
31		* @author JimP
32		*
33		*/
		0% Uncovered Elements: 20 (20) Complexity: 10 Complexity Density: 1
34		public class GeneDbSource extends EmblXmlSource
35		{
36
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
37	0	public GeneDbSource()...
38		{
39	0	super();
40		}
41
42		/*
43		* (non-Javadoc)
44		*
45		* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
46		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	@Override...
48		public String getAccessionSeparator()
49		{
50		// TODO Auto-generated method stub
51	0	return null;
52		}
53
54		/*
55		* (non-Javadoc)
56		*
57		* @see jalview.ws.DbSourceProxy#getAccessionValidator()
58		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public Regex getAccessionValidator()
61		{
62		// TODO Auto-generated method stub
63	0	return null;
64		}
65
66		/*
67		* (non-Javadoc)
68		*
69		* @see jalview.ws.DbSourceProxy#getDbSource()
70		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	@Override...
72		public String getDbSource()
73		{
74	0	return DBRefSource.GENEDB;
75		}
76
77		/*
78		* (non-Javadoc)
79		*
80		* @see jalview.ws.DbSourceProxy#getDbVersion()
81		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	@Override...
83		public String getDbVersion()
84		{
85		// TODO Auto-generated method stub
86	0	return "0";
87		}
88
89		/*
90		* (non-Javadoc)
91		*
92		* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
93		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
94	0	@Override...
95		public AlignmentI getSequenceRecords(String queries) throws Exception
96		{
97		// query of form
98		// http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
99		//
100	0	return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
101		}
102
103		/*
104		* (non-Javadoc)
105		*
106		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
107		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
108	0	@Override...
109		public boolean isValidReference(String accession)
110		{
111		// TODO Auto-generated method stub
112	0	return false;
113		}
114
115		/**
116		* return T.Brucei Mannosyl-Transferase TbPIG-M
117		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	@Override...
119		public String getTestQuery()
120		{
121	0	return "Tb927.6.3300";
122		}
123
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
124	0	@Override...
125		public String getDbName()
126		{
127	0	return "GeneDB"; // getDbSource();
128		}
129
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	@Override...
131		public int getTier()
132		{
133	0	return 0;
134		}
135		}