Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HtsContigDb	50	47	25	0.384615438.5%	Show methods

Class HtsContigDb

Class HtsContigDb	Line # 50	Total Statements 47	Complexity 25	TOTAL Coverage 0.384615438.5%
createFastaSequenceIndex(Path,boolean) : void   createFastaSequenceIndex(Path,boolean) : void	5858	3.03	2.02	1.0 1.0100%
HtsContigDb(String,File)   HtsContigDb(String,File)	7070	4.04	2.02	0.8333333 0.833333383.3%
close() : void   close() : void	8080	3.03	3.03	0.8 0.880%
initSource() : void   initSource() : void	9494	4.04	4.04	0.625 0.62562.5%
initSequenceDictionaryFor(File) : ReferenceSequenceFile   initSequenceDictionaryFor(File) : ReferenceSequenceFile	112112	5.05	2.02	0.0 0.00%
getDictionary(File,boolean) : SAMSequenceDictionary   getDictionary(File,boolean) : SAMSequenceDictionary	163163	10.010	3.03	0.0 0.00%
isValid() : boolean   isValid() : boolean	186186	1.01	1.01	1.0 1.0100%
makeSequenceRecord(ReferenceSequence) : SAMSequenceRecord   makeSequenceRecord(ReferenceSequence) : SAMSequenceRecord	194194	6.06	2.02	0.0 0.00%
md5Hash(byte[]) : String   md5Hash(byte[]) : String	219219	5.05	2.02	0.0 0.00%
getSequenceProxy(String) : SequenceI   getSequenceProxy(String) : SequenceI	239239	5.05	3.03	0.5714286 0.571428657.1%
isIndexed() : boolean   isIndexed() : boolean	252252	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.32051283	jalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndexjalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndex	1PASS
	0.30769232	jalview.io.vcf.VCFLoaderTest.testLoadVCFContigjalview.io.vcf.VCFLoaderTest.testLoadVCFContig	1PASS
	0.26923078	jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxyjalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy	1PASS
	0.12820514	jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy_indexedjalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy_indexed	1PASS

 

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.ext.htsjdk;
22
23		import java.io.File;
24		import java.io.IOException;
25		import java.math.BigInteger;
26		import java.nio.file.Path;
27		import java.util.ArrayList;
28		import java.util.HashSet;
29		import java.util.List;
30		import java.util.Set;
31
32		import htsjdk.samtools.SAMException;
33		import htsjdk.samtools.SAMSequenceDictionary;
34		import htsjdk.samtools.SAMSequenceRecord;
35		import htsjdk.samtools.reference.FastaSequenceIndexCreator;
36		import htsjdk.samtools.reference.ReferenceSequence;
37		import htsjdk.samtools.reference.ReferenceSequenceFile;
38		import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
39		import htsjdk.samtools.util.StringUtil;
40		import jalview.datamodel.Sequence;
41		import jalview.datamodel.SequenceI;
42		import jalview.util.DigestUtils;
43
44		/**
45		* a source of sequence data accessed via the HTSJDK
46		*
47		* @author jprocter
48		*
49		*/
		38.5% Uncovered Elements: 48 (78) Complexity: 25 Complexity Density: 0.53
50		public class HtsContigDb
51		{
52		private String name;
53
54		private File dbLocation;
55
56		private htsjdk.samtools.reference.ReferenceSequenceFile refFile = null;
57
		100% Uncovered Elements: 0 (3) Complexity: 2 Complexity Density: 0.67
58	2	public static void createFastaSequenceIndex(Path path, boolean overwrite)...
59		throws IOException
60		{
61	2	try
62		{
63	2	FastaSequenceIndexCreator.create(path, overwrite);
64		} catch (SAMException e)
65		{
66	1	throw new IOException(e.getMessage());
67		}
68		}
69
		83.3% Uncovered Elements: 1 (6) Complexity: 2 Complexity Density: 0.5
70	7	public HtsContigDb(String name, File descriptor)...
71		{
72	7	if (descriptor.isFile())
73		{
74	7	this.name = name;
75	7	dbLocation = descriptor;
76		}
77	7	initSource();
78		}
79
		80% Uncovered Elements: 1 (5) Complexity: 3 Complexity Density: 1
80	5	public void close()...
81		{
82	5	if (refFile != null)
83		{
84	5	try
85		{
86	5	refFile.close();
87		} catch (IOException e)
88		{
89		// ignore
90		}
91		}
92		}
93
		62.5% Uncovered Elements: 3 (8) Complexity: 4 Complexity Density: 1
94	7	private void initSource()...
95		{
96	7	if (refFile != null)
97		{
98	0	return;
99		}
100
101	7	refFile = ReferenceSequenceFileFactory
102		.getReferenceSequenceFile(dbLocation, true);
103	6	if (refFile == null || refFile.getSequenceDictionary() == null)
104		{
105		// refFile = initSequenceDictionaryFor(dbLocation);
106		}
107
108		}
109
110		SAMSequenceDictionary rrefDict = null;
111
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
112	0	private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2)...
113		throws Exception
114		{
115	0	rrefDict = getDictionary(dbLocation2, true);
116	0	if (rrefDict != null)
117		{
118	0	ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory
119		.getReferenceSequenceFile(dbLocation2, true);
120	0	return rrefFile;
121		}
122	0	return null;
123		}
124
125		/**
126		* code below hacked out from picard ----
127		*
128		* picard/src/java/picard/sam/CreateSequenceDictionary.java
129		* https://github.com/
130		* broadinstitute/picard/commit/270580d3e28123496576f0b91b3433179bb5d876
131		*/
132
133		/*
134		* The MIT License
135		*
136		* Copyright (c) 2009 The Broad Institute
137		*
138		* Permission is hereby granted, free of charge, to any person obtaining a
139		* copy of this software and associated documentation files (the "Software"),
140		* to deal in the Software without restriction, including without limitation
141		* the rights to use, copy, modify, merge, publish, distribute, sublicense,
142		* and/or sell copies of the Software, and to permit persons to whom the
143		* Software is furnished to do so, subject to the following conditions:
144		*
145		* The above copyright notice and this permission notice shall be included in
146		* all copies or substantial portions of the Software.
147		*
148		* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
149		* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
150		* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
151		* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
152		* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
153		* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
154		* DEALINGS IN THE SOFTWARE.
155		*/
156		/**
157		*
158		* @param f
159		* @param truncate
160		* @return
161		* @throws Exception
162		*/
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
163	0	SAMSequenceDictionary getDictionary(File f, boolean truncate)...
164		throws Exception
165		{
166	0	final ReferenceSequenceFile refSeqFile = ReferenceSequenceFileFactory
167		.getReferenceSequenceFile(f, truncate);
168	0	ReferenceSequence refSeq;
169	0	List<SAMSequenceRecord> ret = new ArrayList<>();
170	0	Set<String> sequenceNames = new HashSet<>();
171	0	for (int numSequences = 0; (refSeq = refSeqFile
172		.nextSequence()) != null; ++numSequences)
173		{
174	0	if (sequenceNames.contains(refSeq.getName()))
175		{
176	0	throw new Exception(
177		"Sequence name appears more than once in reference: "
178		+ refSeq.getName());
179		}
180	0	sequenceNames.add(refSeq.getName());
181	0	ret.add(makeSequenceRecord(refSeq));
182		}
183	0	return new SAMSequenceDictionary(ret);
184		}
185
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
186	8	public boolean isValid()...
187		{
188	8	return dbLocation != null && refFile != null;
189		}
190
191		/**
192		* Create one SAMSequenceRecord from a single fasta sequence
193		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
194	0	private SAMSequenceRecord makeSequenceRecord(...
195		final ReferenceSequence refSeq)
196		{
197
198	0	final SAMSequenceRecord ret = new SAMSequenceRecord(refSeq.getName(),
199		refSeq.length());
200
201		// Compute MD5 of upcased bases
202	0	final byte[] bases = refSeq.getBases();
203	0	for (int i = 0; i < bases.length; ++i)
204		{
205	0	bases[i] = StringUtil.toUpperCase(bases[i]);
206		}
207
208	0	ret.setAttribute(SAMSequenceRecord.MD5_TAG, md5Hash(bases));
209		// if (GENOME_ASSEMBLY != null) {
210		// ret.setAttribute(SAMSequenceRecord.ASSEMBLY_TAG, GENOME_ASSEMBLY);
211		// }
212		// ret.setAttribute(SAMSequenceRecord.URI_TAG, URI);
213		// if (SPECIES != null) {
214		// ret.setAttribute(SAMSequenceRecord.SPECIES_TAG, SPECIES);
215		// }
216	0	return ret;
217		}
218
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
219	0	private String md5Hash(final byte[] bytes)...
220		{
221	0	String s = new BigInteger(1, DigestUtils.computeMD5(bytes)).toString(16);
222	0	if (s.length() != 32)
223		{
224	0	final String zeros = "00000000000000000000000000000000";
225	0	s = zeros.substring(0, 32 - s.length()) + s;
226		}
227	0	return s;
228		}
229
230		// ///// end of hts bits.
231
232		/**
233		* Reads the contig with the given id and returns as a Jalview SequenceI
234		* object. Note the database must be indexed for this operation to succeed.
235		*
236		* @param id
237		* @return
238		*/
		57.1% Uncovered Elements: 3 (7) Complexity: 3 Complexity Density: 0.6
239	5	public SequenceI getSequenceProxy(String id)...
240		{
241	5	if (!isValid() || !refFile.isIndexed())
242		{
243	0	jalview.bin.Console.errPrintln(
244		"Cannot read contig as file is invalid or not indexed");
245	0	return null;
246		}
247
248	5	ReferenceSequence sseq = refFile.getSequence(id);
249	5	return new Sequence(sseq.getName(), new String(sseq.getBases()));
250		}
251
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
252	3	public boolean isIndexed()...
253		{
254	3	return refFile != null && refFile.isIndexed();
255		}
256
257		}