| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/ |
| H A D | FuncotatorUtilsUnitTest.java | 7 import htsjdk.tribble.annotation.Strand;
141 Strand.decode(strand), in helpCreateDataForTestGetBasesInWindowAroundReferenceAllele()
331 Strand.NONE in provideReferenceAndExonListForGatkExceptions()
1214 Strand.POSITIVE, in provideDataForGetTranscriptAlleleStartPosition()
1220 Strand.NEGATIVE, in provideDataForGetTranscriptAlleleStartPosition()
1226 Strand.POSITIVE, in provideDataForGetTranscriptAlleleStartPosition()
1232 Strand.NEGATIVE, in provideDataForGetTranscriptAlleleStartPosition()
1238 Strand.POSITIVE, in provideDataForGetTranscriptAlleleStartPosition()
1244 Strand.NEGATIVE, in provideDataForGetTranscriptAlleleStartPosition()
1271 Strand.POSITIVE, in provideDataForGetTranscriptAlleleStartPosition()
[all …]
|
| H A D | ProteinChangeInfoUnitTest.java | 5 import htsjdk.tribble.annotation.Strand;
60 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
70 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
82 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
93 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
103 Strand.NEGATIVE, false, in provideForTestCreateProteinChangeInfo()
113 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
122 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
134 Strand.POSITIVE, false, in provideForTestCreateProteinChangeInfo()
245 Strand.POSITIVE, true, in provideForTestCreateProteinChangeInfo()
[all …]
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/sequence/ |
| H A D | Strand_ESTest.java | 53 Strand strand0 = new Strand(bases0, 1); in test01()
96 Strand strand0 = new Strand(bases0, 120); in test05()
124 Strand strand0 = new Strand(bases0, 3); in test08()
134 Strand strand0 = new Strand(bases0, 1); in test09()
161 Strand strand0 = new Strand(bases0, 120); in test11()
248 Strand strand0 = new Strand(bases0, 1); in test16()
283 Strand strand0 = new Strand(bases0, 1); in test18()
436 Strand strand0 = new Strand(bases0, 1); in test27()
570 Strand strand0 = new Strand(bases0, 0); in test37()
579 Strand strand0 = new Strand(bases0, 1); in test38()
[all …]
|
| H A D | MarkerChangeEvent_ESTest.java | 21 import uk.ac.sanger.artemis.sequence.Strand;
33 MarkerChangeEvent markerChangeEvent0 = new MarkerChangeEvent(marker0, (Strand) null, 5); in test0()
34 Strand strand0 = markerChangeEvent0.getStrand(); in test0()
42 Strand strand0 = new Strand(bases0, (-52)); in test1()
45 Strand strand1 = markerChangeEvent0.getStrand(); in test1()
46 assertEquals(1, Strand.FORWARD); in test1()
53 markerChangeEvent0 = new MarkerChangeEvent((Marker) null, (Strand) null, 0); in test2()
71 MarkerChangeEvent markerChangeEvent0 = new MarkerChangeEvent(marker0, (Strand) null, 5); in test3()
79 Strand strand0 = bases0.getForwardStrand(); in test4()
82 Strand strand1 = markerChangeEvent0.getStrand(); in test4()
|
| /dports/www/squid/squid-4.15/src/ipc/ |
| H A D | Strand.cc | 37 CBDATA_NAMESPACED_CLASS_INIT(Ipc, Strand);
39 Ipc::Strand::Strand(): in Strand() function in Ipc::Strand
45 void Ipc::Strand::start() in start()
51 void Ipc::Strand::registerSelf() in registerSelf()
63 void Ipc::Strand::receive(const TypedMsgHdr &message) in receive()
122 void Ipc::Strand::handleRegistrationResponse(const HereIamMessage &msg) in handleRegistrationResponse()
135 void Ipc::Strand::handleCacheMgrRequest(const Mgr::Request& request) in handleCacheMgrRequest()
142 void Ipc::Strand::handleCacheMgrResponse(const Mgr::Response& response) in handleCacheMgrResponse()
148 void Ipc::Strand::handleSnmpRequest(const Snmp::Request& request) in handleSnmpRequest()
154 void Ipc::Strand::handleSnmpResponse(const Snmp::Response& response) in handleSnmpResponse()
[all …]
|
| H A D | Strand.h | 27 class Strand: public Port
29 CBDATA_CLASS(Strand);
32 Strand();
54 Strand(const Strand&); // not implemented
55 Strand& operator =(const Strand&); // not implemented
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | Strand.java | 16 @DefaultSerializer(Strand.Serializer.class)
17 public enum Strand { enum
25 Strand(final char ce) { in Strand() method in Strand
29 public static Strand decode(final String ce) { in decode()
35 … ce, Stream.of(values()).map(Strand::encodeAsString).collect(Collectors.joining(", ")))); in decode()
38 public static Strand decode(final char ce) { in decode()
57 public static final class Serializer extends com.esotericsoftware.kryo.Serializer<Strand> {
60 public void write(final Kryo kryo, final Output output, final Strand strand) { in write()
65 public Strand read(final Kryo kryo, final Input input, final Class<Strand> kclass) { in read()
66 return Strand.values()[input.readInt()]; in read()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/plot/ |
| H A D | GCDeviationAlgorithm_ESTest.java | 20 import uk.ac.sanger.artemis.sequence.Strand;
30 Strand strand0 = bases0.getReverseStrand(); in test00()
48 Strand strand0 = bases0.getReverseStrand(); in test01()
56 Strand strand0 = bases0.getReverseStrand(); in test02()
91 Strand strand0 = bases0.getReverseStrand(); in test04()
100 Strand strand0 = bases0.getForwardStrand(); in test05()
108 Strand strand0 = bases0.getReverseStrand(); in test06()
117 Strand strand0 = bases0.getReverseStrand(); in test07()
126 Strand strand0 = bases0.getForwardStrand(); in test08()
134 Strand strand0 = bases0.getReverseStrand(); in test09()
[all …]
|
| H A D | GCWindowAlgorithm_ESTest.java | 21 import uk.ac.sanger.artemis.sequence.Strand;
29 Strand strand0 = bases0.getReverseStrand(); in test00()
40 Strand strand0 = bases0.getForwardStrand(); in test01()
52 Strand strand0 = bases0.getReverseStrand(); in test02()
62 Strand strand0 = bases0.getReverseStrand(); in test03()
73 Strand strand0 = bases0.getReverseStrand(); in test04()
92 Strand strand0 = bases0.getReverseStrand(); in test05()
113 Strand strand0 = bases0.getForwardStrand(); in test06()
131 Strand strand0 = bases0.getForwardStrand(); in test07()
165 Strand strand0 = bases0.getReverseStrand(); in test09()
[all …]
|
| H A D | AGWindowAlgorithm_ESTest.java | 21 import uk.ac.sanger.artemis.sequence.Strand;
80 assertEquals(2, Strand.REVERSE); in test00()
81 assertEquals(1, Strand.FORWARD); in test00()
108 assertEquals(2, Strand.REVERSE); in test00()
109 assertEquals(1, Strand.FORWARD); in test00()
137 assertEquals(2, Strand.REVERSE); in test00()
138 assertEquals(1, Strand.FORWARD); in test00()
184 assertEquals(1, Strand.FORWARD); in test01()
185 assertEquals(2, Strand.REVERSE); in test01()
211 assertEquals(1, Strand.FORWARD); in test01()
[all …]
|
| H A D | KarlinSigAlgorithm_ESTest.java | 18 import uk.ac.sanger.artemis.sequence.Strand;
27 Strand strand0 = bases0.getReverseStrand(); in test00()
38 Strand strand0 = bases0.getReverseStrand(); in test01()
58 Strand strand0 = bases0.getReverseStrand(); in test02()
70 Strand strand0 = bases0.getReverseStrand(); in test03()
105 Strand strand0 = bases0.getReverseStrand(); in test05()
117 Strand strand0 = bases0.getReverseStrand(); in test06()
129 Strand strand0 = bases0.getReverseStrand(); in test07()
140 Strand strand0 = bases0.getReverseStrand(); in test08()
152 Strand strand0 = bases0.getReverseStrand(); in test09()
[all …]
|
| H A D | ATDeviationAlgorithm_ESTest.java | 19 import uk.ac.sanger.artemis.sequence.Strand;
60 assertEquals(2, Strand.REVERSE); in test00()
61 assertEquals(1, Strand.FORWARD); in test00()
80 assertEquals(2, Strand.REVERSE); in test00()
81 assertEquals(1, Strand.FORWARD); in test00()
108 assertEquals(2, Strand.REVERSE); in test00()
109 assertEquals(1, Strand.FORWARD); in test00()
148 assertEquals(1, Strand.FORWARD); in test01()
149 assertEquals(2, Strand.REVERSE); in test01()
160 assertEquals(1, Strand.FORWARD); in test01()
[all …]
|
| H A D | CumulativeGCSkewAlgorithm_ESTest.java | 64 assertEquals(1, Strand.FORWARD); in test00()
65 assertEquals(2, Strand.REVERSE); in test00()
84 assertEquals(1, Strand.FORWARD); in test00()
85 assertEquals(2, Strand.REVERSE); in test00()
113 assertEquals(1, Strand.FORWARD); in test00()
114 assertEquals(2, Strand.REVERSE); in test00()
155 assertEquals(1, Strand.FORWARD); in test01()
156 assertEquals(2, Strand.REVERSE); in test01()
167 assertEquals(1, Strand.FORWARD); in test01()
168 assertEquals(2, Strand.REVERSE); in test01()
[all …]
|
| H A D | Codon12CorrelationAlgorithm_ESTest.java | 21 import uk.ac.sanger.artemis.sequence.Strand;
30 Strand strand0 = bases0.getForwardStrand(); in test00()
42 Strand strand0 = bases0.getReverseStrand(); in test01()
55 Strand strand0 = bases0.getForwardStrand(); in test02()
75 Strand strand0 = bases0.getForwardStrand(); in test03()
109 Strand strand0 = bases0.getReverseStrand(); in test05()
122 Strand strand0 = bases0.getReverseStrand(); in test06()
134 Strand strand0 = bases0.getForwardStrand(); in test07()
147 Strand strand0 = bases0.getForwardStrand(); in test08()
160 Strand strand0 = bases0.getReverseStrand(); in test09()
[all …]
|
| H A D | GCFrameAlgorithm_ESTest.java | 25 import uk.ac.sanger.artemis.sequence.Strand;
34 Strand strand0 = bases0.getForwardStrand(); in test00()
48 Strand strand0 = bases0.getReverseStrand(); in test01()
62 Strand strand0 = bases0.getReverseStrand(); in test02()
74 Strand strand0 = bases0.getReverseStrand(); in test03()
87 Strand strand0 = bases0.getReverseStrand(); in test04()
105 Strand strand0 = bases0.getReverseStrand(); in test05()
140 Strand strand0 = bases0.getReverseStrand(); in test07()
152 Strand strand0 = bases0.getForwardStrand(); in test08()
166 Strand strand0 = bases0.getReverseStrand(); in test09()
[all …]
|
| H A D | CSCSAlgorithm_ESTest.java | 22 import uk.ac.sanger.artemis.sequence.Strand;
30 Strand strand0 = bases0.getReverseStrand(); in test00()
49 Strand strand0 = bases0.getForwardStrand(); in test01()
83 Strand strand0 = bases0.getForwardStrand(); in test03()
95 Strand strand0 = bases0.getForwardStrand(); in test04()
106 Strand strand0 = bases0.getForwardStrand(); in test05()
121 Strand strand0 = bases0.getForwardStrand(); in test06()
133 Strand strand0 = bases0.getForwardStrand(); in test07()
146 Strand strand0 = bases0.getForwardStrand(); in test08()
160 Strand strand0 = bases0.getForwardStrand(); in test09()
[all …]
|
| H A D | EntropyAlgorithm_ESTest.java | 21 import uk.ac.sanger.artemis.sequence.Strand;
30 Strand strand0 = bases0.getForwardStrand(); in test00()
40 Strand strand0 = bases0.getReverseStrand(); in test01()
59 Strand strand0 = bases0.getForwardStrand(); in test02()
92 Strand strand0 = bases0.getReverseStrand(); in test04()
105 Strand strand0 = bases0.getForwardStrand(); in test05()
117 Strand strand0 = bases0.getForwardStrand(); in test06()
130 Strand strand0 = bases0.getForwardStrand(); in test07()
143 Strand strand0 = bases0.getForwardStrand(); in test08()
158 Strand strand0 = bases0.getReverseStrand(); in test09()
[all …]
|
| /dports/devel/omniORB/omniORB-4.2.4/include/omniORB4/ |
| H A D | omniTransport.h | 59 class Strand; variable
123 friend class Strand; variable
136 class Strand : public RopeLink, public StrandList {
139 Strand() {} in Strand() function
140 virtual ~Strand() {} in ~Strand()
143 Strand(const Strand&);
144 Strand& operator=(const Strand&);
|
| /dports/biology/seqan1/seqan-1.3.1/demos/ |
| H A D | ecoln.out | 57 Strand = Plus / Plus
78 Strand = Plus / Plus
94 Strand = Plus / Plus
110 Strand = Plus / Plus
126 Strand = Plus / Plus
164 Strand = Plus / Plus
177 Strand = Plus / Plus
255 Strand = Plus / Plus
268 Strand = Plus / Plus
282 Strand = Plus / Plus
[all …]
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/unassigned_or_unused/ |
| H A D | ecoln.out | 57 Strand = Plus / Plus
78 Strand = Plus / Plus
94 Strand = Plus / Plus
110 Strand = Plus / Plus
126 Strand = Plus / Plus
164 Strand = Plus / Plus
177 Strand = Plus / Plus
255 Strand = Plus / Plus
268 Strand = Plus / Plus
282 Strand = Plus / Plus
[all …]
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/funcotator/ |
| H A D | StrandCorrectedAllele.java | 3 import htsjdk.tribble.annotation.Strand;
15 private final Strand strand;
17 private StrandCorrectedAllele(final String allele, final boolean isRef, final Strand strand) { in StrandCorrectedAllele()
31 return new StrandCorrectedAllele(bases, false, Strand.POSITIVE); in create()
41 public static StrandCorrectedAllele create(final String bases, final Strand strand) { in create()
53 return new StrandCorrectedAllele(bases, isRef, Strand.POSITIVE); in create()
64 …static StrandCorrectedAllele create(final String bases, final boolean isRef, final Strand strand) { in create()
71 public Strand getStrand() { in getStrand()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/uk/ac/sanger/artemis/sequence/ |
| H A D | BasesTest.java | 151 assertEquals(4, bases.getRawPosition(4, Strand.FORWARD)); in testGetRawPosition()
152 assertEquals(0, bases.getRawPosition(0, Strand.FORWARD)); in testGetRawPosition()
249 int [] stopCodons = bases.getStopCodons(range, Strand.FORWARD); in testGetStopCodons()
299 String seq1 = bases.getSubSequence (range1, Strand.FORWARD); in testGetSubSequence()
306 String seq2 = bases.getSubSequence (range2, Strand.REVERSE); in testGetSubSequence()
313 String seq3 = bases.getSubSequence (range3, Strand.FORWARD); in testGetSubSequence()
329 char [] seq1 = bases.getSubSequenceC(range1, Strand.FORWARD); in testGetSubSequenceC()
336 char [] seq2 = bases.getSubSequenceC(range2, Strand.REVERSE); in testGetSubSequenceC()
343 char [] seq3 = bases.getSubSequenceC(range3, Strand.FORWARD); in testGetSubSequenceC()
438 bases.addBases(20, Strand.FORWARD, basesToAdd); in testAddBases()
[all …]
|
| /dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/ |
| H A D | frac_problems2.blast | 27 Strand = Plus / Plus
73 Strand = Plus / Plus
119 Strand = Plus / Plus
140 Strand = Plus / Plus
161 Strand = Plus / Plus
182 Strand = Plus / Plus
203 Strand = Plus / Plus
224 Strand = Plus / Plus
245 Strand = Plus / Plus
261 Strand = Plus / Plus
[all …]
|
| H A D | a_thaliana.blastn | 59 Strand = Plus / Plus
73 Strand = Plus / Plus
90 Strand = Plus / Plus
116 Strand = Plus / Plus
129 Strand = Plus / Plus
168 Strand = Plus / Plus
182 Strand = Plus / Plus
208 Strand = Plus / Plus
222 Strand = Plus / Plus
236 Strand = Plus / Plus
[all …]
|
| H A D | multiresult_blastn+.bls | 43 Strand=Plus/Plus
55 Strand=Plus/Minus
68 Strand=Plus/Plus
80 Strand=Plus/Plus
92 Strand=Plus/Plus
104 Strand=Plus/Plus
117 Strand=Plus/Minus
129 Strand=Plus/Plus
141 Strand=Plus/Minus
189 Strand=Plus/Plus
[all …]
|