Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HtsContigDb	52	54	28	0.340909134.1%	Show methods

Class HtsContigDb

Class HtsContigDb	Line # 52	Total Statements 54	Complexity 28	TOTAL Coverage 0.340909134.1%
createFastaSequenceIndex(Path,boolean) : void   createFastaSequenceIndex(Path,boolean) : void	6060	3.03	2.02	1.0 1.0100%
HtsContigDb(String,File)   HtsContigDb(String,File)	7272	4.04	2.02	0.8333333 0.833333383.3%
close() : void   close() : void	8282	3.03	3.03	0.8 0.880%
initSource() : void   initSource() : void	9696	4.04	4.04	0.625 0.62562.5%
initSequenceDictionaryFor(File) : ReferenceSequenceFile   initSequenceDictionaryFor(File) : ReferenceSequenceFile	114114	5.05	2.02	0.0 0.00%
getDictionary(File,boolean) : SAMSequenceDictionary   getDictionary(File,boolean) : SAMSequenceDictionary	165165	12.012	4.04	0.0 0.00%
isValid() : boolean   isValid() : boolean	192192	1.01	1.01	1.0 1.0100%
makeSequenceRecord(ReferenceSequence) : SAMSequenceRecord   makeSequenceRecord(ReferenceSequence) : SAMSequenceRecord	200200	6.06	2.02	0.0 0.00%
initCreateSequenceDictionary() : void   initCreateSequenceDictionary() : void	227227	3.03	2.02	0.0 0.00%
md5Hash(byte[]) : String   md5Hash(byte[]) : String	238238	7.07	2.02	0.0 0.00%
getSequenceProxy(String) : SequenceI   getSequenceProxy(String) : SequenceI	260260	5.05	3.03	0.5714286 0.571428657.1%
isIndexed() : boolean   isIndexed() : boolean	273273	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2840909	jalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndexjalview.ext.htsjdk.TestHtsContigDb.testCreateFastaSequenceIndex	1PASS
	0.27272728	jalview.io.vcf.VCFLoaderTest.testLoadVCFContigjalview.io.vcf.VCFLoaderTest.testLoadVCFContig	1PASS
	0.23863636	jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxyjalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy	1PASS
	0.11363637	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 jalview.datamodel.Sequence;
24		import jalview.datamodel.SequenceI;
25
26		import java.io.File;
27		import java.io.IOException;
28		import java.math.BigInteger;
29		import java.nio.file.Path;
30		import java.security.MessageDigest;
31		import java.security.NoSuchAlgorithmException;
32		import java.util.ArrayList;
33		import java.util.HashSet;
34		import java.util.List;
35		import java.util.Set;
36
37		import htsjdk.samtools.SAMException;
38		import htsjdk.samtools.SAMSequenceDictionary;
39		import htsjdk.samtools.SAMSequenceRecord;
40		import htsjdk.samtools.reference.FastaSequenceIndexCreator;
41		import htsjdk.samtools.reference.ReferenceSequence;
42		import htsjdk.samtools.reference.ReferenceSequenceFile;
43		import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
44		import htsjdk.samtools.util.StringUtil;
45
46		/**
47		* a source of sequence data accessed via the HTSJDK
48		*
49		* @author jprocter
50		*
51		*/
		34.1% Uncovered Elements: 58 (88) Complexity: 28 Complexity Density: 0.52
52		public class HtsContigDb
53		{
54		private String name;
55
56		private File dbLocation;
57
58		private htsjdk.samtools.reference.ReferenceSequenceFile refFile = null;
59
		100% Uncovered Elements: 0 (3) Complexity: 2 Complexity Density: 0.67
60	2	public static void createFastaSequenceIndex(Path path, boolean overwrite)...
61		throws IOException
62		{
63	2	try
64		{
65	2	FastaSequenceIndexCreator.create(path, overwrite);
66		} catch (SAMException e)
67		{
68	1	throw new IOException(e.getMessage());
69		}
70		}
71
		83.3% Uncovered Elements: 1 (6) Complexity: 2 Complexity Density: 0.5
72	7	public HtsContigDb(String name, File descriptor)...
73		{
74	7	if (descriptor.isFile())
75		{
76	7	this.name = name;
77	7	dbLocation = descriptor;
78		}
79	7	initSource();
80		}
81
		80% Uncovered Elements: 1 (5) Complexity: 3 Complexity Density: 1
82	5	public void close()...
83		{
84	5	if (refFile != null)
85		{
86	5	try
87		{
88	5	refFile.close();
89		} catch (IOException e)
90		{
91		// ignore
92		}
93		}
94		}
95
		62.5% Uncovered Elements: 3 (8) Complexity: 4 Complexity Density: 1
96	7	private void initSource()...
97		{
98	7	if (refFile != null)
99		{
100	0	return;
101		}
102
103	7	refFile = ReferenceSequenceFileFactory
104		.getReferenceSequenceFile(dbLocation, true);
105	6	if (refFile == null || refFile.getSequenceDictionary() == null)
106		{
107		// refFile = initSequenceDictionaryFor(dbLocation);
108		}
109
110		}
111
112		SAMSequenceDictionary rrefDict = null;
113
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
114	0	private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2)...
115		throws Exception
116		{
117	0	rrefDict = getDictionary(dbLocation2, true);
118	0	if (rrefDict != null)
119		{
120	0	ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory
121		.getReferenceSequenceFile(dbLocation2, true);
122	0	return rrefFile;
123		}
124	0	return null;
125		}
126
127		/**
128		* code below hacked out from picard ----
129		*
130		* picard/src/java/picard/sam/CreateSequenceDictionary.java
131		* https://github.com/
132		* broadinstitute/picard/commit/270580d3e28123496576f0b91b3433179bb5d876
133		*/
134
135		/*
136		* The MIT License
137		*
138		* Copyright (c) 2009 The Broad Institute
139		*
140		* Permission is hereby granted, free of charge, to any person obtaining a
141		* copy of this software and associated documentation files (the "Software"),
142		* to deal in the Software without restriction, including without limitation
143		* the rights to use, copy, modify, merge, publish, distribute, sublicense,
144		* and/or sell copies of the Software, and to permit persons to whom the
145		* Software is furnished to do so, subject to the following conditions:
146		*
147		* The above copyright notice and this permission notice shall be included in
148		* all copies or substantial portions of the Software.
149		*
150		* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
151		* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
152		* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
153		* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
154		* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
155		* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
156		* DEALINGS IN THE SOFTWARE.
157		*/
158		/**
159		*
160		* @param f
161		* @param truncate
162		* @return
163		* @throws Exception
164		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.33
165	0	SAMSequenceDictionary getDictionary(File f, boolean truncate)...
166		throws Exception
167		{
168	0	if (md5 == null)
169		{
170	0	initCreateSequenceDictionary();
171		}
172	0	final ReferenceSequenceFile refSeqFile = ReferenceSequenceFileFactory
173		.getReferenceSequenceFile(f, truncate);
174	0	ReferenceSequence refSeq;
175	0	List<SAMSequenceRecord> ret = new ArrayList<>();
176	0	Set<String> sequenceNames = new HashSet<>();
177	0	for (int numSequences = 0; (refSeq = refSeqFile
178		.nextSequence()) != null; ++numSequences)
179		{
180	0	if (sequenceNames.contains(refSeq.getName()))
181		{
182	0	throw new Exception(
183		"Sequence name appears more than once in reference: "
184		+ refSeq.getName());
185		}
186	0	sequenceNames.add(refSeq.getName());
187	0	ret.add(makeSequenceRecord(refSeq));
188		}
189	0	return new SAMSequenceDictionary(ret);
190		}
191
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
192	8	public boolean isValid()...
193		{
194	8	return dbLocation != null && refFile != null;
195		}
196
197		/**
198		* Create one SAMSequenceRecord from a single fasta sequence
199		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
200	0	private SAMSequenceRecord makeSequenceRecord(...
201		final ReferenceSequence refSeq)
202		{
203
204	0	final SAMSequenceRecord ret = new SAMSequenceRecord(refSeq.getName(),
205		refSeq.length());
206
207		// Compute MD5 of upcased bases
208	0	final byte[] bases = refSeq.getBases();
209	0	for (int i = 0; i < bases.length; ++i)
210		{
211	0	bases[i] = StringUtil.toUpperCase(bases[i]);
212		}
213
214	0	ret.setAttribute(SAMSequenceRecord.MD5_TAG, md5Hash(bases));
215		// if (GENOME_ASSEMBLY != null) {
216		// ret.setAttribute(SAMSequenceRecord.ASSEMBLY_TAG, GENOME_ASSEMBLY);
217		// }
218		// ret.setAttribute(SAMSequenceRecord.URI_TAG, URI);
219		// if (SPECIES != null) {
220		// ret.setAttribute(SAMSequenceRecord.SPECIES_TAG, SPECIES);
221		// }
222	0	return ret;
223		}
224
225		private MessageDigest md5;
226
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
227	0	public void initCreateSequenceDictionary() throws Exception...
228		{
229	0	try
230		{
231	0	md5 = MessageDigest.getInstance("MD5");
232		} catch (NoSuchAlgorithmException e)
233		{
234	0	throw new Exception("MD5 algorithm not found", e);
235		}
236		}
237
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
238	0	private String md5Hash(final byte[] bytes)...
239		{
240	0	md5.reset();
241	0	md5.update(bytes);
242	0	String s = new BigInteger(1, md5.digest()).toString(16);
243	0	if (s.length() != 32)
244		{
245	0	final String zeros = "00000000000000000000000000000000";
246	0	s = zeros.substring(0, 32 - s.length()) + s;
247		}
248	0	return s;
249		}
250
251		// ///// end of hts bits.
252
253		/**
254		* Reads the contig with the given id and returns as a Jalview SequenceI object.
255		* Note the database must be indexed for this operation to succeed.
256		*
257		* @param id
258		* @return
259		*/
		57.1% Uncovered Elements: 3 (7) Complexity: 3 Complexity Density: 0.6
260	5	public SequenceI getSequenceProxy(String id)...
261		{
262	5	if (!isValid() || !refFile.isIndexed())
263		{
264	0	System.err.println(
265		"Cannot read contig as file is invalid or not indexed");
266	0	return null;
267		}
268
269	5	ReferenceSequence sseq = refFile.getSequence(id);
270	5	return new Sequence(sseq.getName(), new String(sseq.getBases()));
271		}
272
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
273	3	public boolean isIndexed()...
274		{
275	3	return refFile != null && refFile.isIndexed();
276		}
277
278		}