Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DbSourceProxyImpl	36	19	15	0.00%	Show methods

Class DbSourceProxyImpl

Class DbSourceProxyImpl	Line # 36	Total Statements 19	Complexity 15	TOTAL Coverage 0.00%
DbSourceProxyImpl()   DbSourceProxyImpl()	4343	0.00	1.01	-1.0 -1.0 -
getRawRecords() : StringBuffer   getRawRecords() : StringBuffer	5252	1.01	1.01	0.0 0.00%
queryInProgress() : boolean   queryInProgress() : boolean	6363	1.01	1.01	0.0 0.00%
startQuery() : void   startQuery() : void	7373	1.01	1.01	0.0 0.00%
stopQuery() : void   stopQuery() : void	8282	1.01	1.01	0.0 0.00%
parseResult(String) : AlignmentI   parseResult(String) : AlignmentI	9494	5.05	2.02	0.0 0.00%
getAccessionIdFromQuery(String) : String   getAccessionIdFromQuery(String) : String	111111	5.05	3.03	0.0 0.00%
getMaximumQueryCount() : int   getMaximumQueryCount() : int	126126	1.01	1.01	0.0 0.00%
isDnaCoding() : boolean   isDnaCoding() : boolean	135135	1.01	1.01	0.0 0.00%
isAlignmentSource() : boolean   isAlignmentSource() : boolean	144144	1.01	1.01	0.0 0.00%
getDescription() : String   getDescription() : String	150150	1.01	1.01	0.0 0.00%
getFeatureColourScheme() : FeatureSettingsModelI   getFeatureColourScheme() : FeatureSettingsModelI	156156	1.01	1.01	0.0 0.00%

 

Contributing tests

Source view

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.seqfetcher;
22
23		import jalview.api.FeatureSettingsModelI;
24		import jalview.datamodel.AlignmentI;
25		import jalview.io.DataSourceType;
26		import jalview.io.FileFormatI;
27		import jalview.io.FormatAdapter;
28		import jalview.io.IdentifyFile;
29
30		/**
31		* common methods for implementations of the DbSourceProxy interface.
32		*
33		* @author JimP
34		*
35		*/
		0% Uncovered Elements: 37 (37) Complexity: 15 Complexity Density: 0.79
36		public abstract class DbSourceProxyImpl implements DbSourceProxy
37		{
38
39		boolean queryInProgress = false;
40
41		protected StringBuffer results = null;
42
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
43	0	public DbSourceProxyImpl()...
44		{
45		}
46
47		/*
48		* (non-Javadoc)
49		*
50		* @see jalview.ws.DbSourceProxy#getRawRecords()
51		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	@Override...
53		public StringBuffer getRawRecords()
54		{
55	0	return results;
56		}
57
58		/*
59		* (non-Javadoc)
60		*
61		* @see jalview.ws.DbSourceProxy#queryInProgress()
62		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
63	0	@Override...
64		public boolean queryInProgress()
65		{
66	0	return queryInProgress;
67		}
68
69		/**
70		* call to set the queryInProgress flag
71		*
72		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	protected void startQuery()...
74		{
75	0	queryInProgress = true;
76		}
77
78		/**
79		* call to clear the queryInProgress flag
80		*
81		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
82	0	protected void stopQuery()...
83		{
84	0	queryInProgress = false;
85		}
86
87		/**
88		* create an alignment from raw text file...
89		*
90		* @param result
91		* @return null or a valid alignment
92		* @throws Exception
93		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
94	0	protected AlignmentI parseResult(String result) throws Exception...
95		{
96	0	AlignmentI sequences = null;
97	0	FileFormatI format = new IdentifyFile().identify(result,
98		DataSourceType.PASTE);
99	0	if (format != null)
100		{
101	0	sequences = new FormatAdapter().readFile(result.toString(),
102		DataSourceType.PASTE, format);
103		}
104	0	return sequences;
105		}
106
107		/**
108		* Returns the first accession id in the query (up to the first accession id
109		* separator), or the whole query if there is no separator or it is not found
110		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
111	0	@Override...
112		public String getAccessionIdFromQuery(String query)
113		{
114	0	String sep = getAccessionSeparator();
115	0	if (sep == null)
116		{
117	0	return query;
118		}
119	0	int sepPos = query.indexOf(sep);
120	0	return sepPos == -1 ? query : query.substring(0, sepPos);
121		}
122
123		/**
124		* Default is only one accession id per query - override if more are allowed.
125		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
126	0	@Override...
127		public int getMaximumQueryCount()
128		{
129	0	return 1;
130		}
131
132		/**
133		* Returns false - override to return true for DNA coding data sources
134		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	@Override...
136		public boolean isDnaCoding()
137		{
138	0	return false;
139		}
140
141		/**
142		* Answers false - override as required in subclasses
143		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
144	0	@Override...
145		public boolean isAlignmentSource()
146		{
147	0	return false;
148		}
149
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
150	0	@Override...
151		public String getDescription()
152		{
153	0	return "";
154		}
155
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
156	0	@Override...
157		public FeatureSettingsModelI getFeatureColourScheme()
158		{
159	0	return null;
160		}
161		}