| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/io/ |
| H A D | ChadoCanonicalGene_ESTest.java | 35 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test00()
44 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test01()
51 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test02()
67 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test03()
83 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test04()
99 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test05()
117 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test06()
133 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test07()
149 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test08()
165 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test09()
[all …]
|
| H A D | DatabaseInferredFeature_ESTest.java | 21 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
41 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test0()
62 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test1()
97 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test3()
117 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test4()
141 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test6()
153 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test7()
172 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test8()
192 … = new DatabaseInferredFeature(key0, location0, (QualifierVector) null, (ChadoCanonicalGene) null); in test9()
|
| H A D | ValidateFeature_ESTest.java | 21 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
239 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test13()
294 …ature0 = new DatabaseInferredFeature(key0, location0, qualifierVector0, (ChadoCanonicalGene) null); in test17()
306 …ature0 = new DatabaseInferredFeature(key0, location0, qualifierVector0, (ChadoCanonicalGene) null); in test18()
317 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test19()
337 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test21()
357 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test23()
|
| H A D | ReadAndWriteEntry_ESTest.java | 28 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
155 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test03()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/components/genebuilder/ |
| H A D | GeneUtils_ESTest.java | 126 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test06()
217 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test12()
282 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test16()
349 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test20()
365 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test21()
417 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test25()
473 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test31()
560 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test39()
599 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test43()
615 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test44()
[all …]
|
| H A D | ProteinMapPanel_ESTest.java | 34 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
51 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test00()
73 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test01()
97 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test02()
123 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test03()
148 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test04()
174 …ProteinMapPanel proteinMapPanel0 = new ProteinMapPanel((Feature) null, (ChadoCanonicalGene) null, … in test05()
199 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test06()
|
| H A D | GeneComponentTree_ESTest.java | 18 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
25 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test0()
|
| H A D | BasicProteinMapPanel_ESTest.java | 24 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
32 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test0()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/ |
| H A D | GeneUtils.java | 58 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
593 final Vector<ChadoCanonicalGene> duplicatedGenes = new Vector<ChadoCanonicalGene>(); in duplicateGeneModel()
594 final Vector<ChadoCanonicalGene> newGenes = new Vector<ChadoCanonicalGene>(); in duplicateGeneModel()
611 final ChadoCanonicalGene newchadoGene = new ChadoCanonicalGene(); in duplicateGeneModel()
659 final ChadoCanonicalGene chadoGene) in duplicateFeatures()
726 final ChadoCanonicalGene chadoGene = new ChadoCanonicalGene(); in createGeneModel()
955 final ChadoCanonicalGene chado_gene) throws ReadOnlyException in deleteAllFeature()
1119 final ChadoCanonicalGene chado_gene) in checkTranscriptBoundary()
1160 final ChadoCanonicalGene chado_gene, in checkTranscriptBoundary()
1259 final ChadoCanonicalGene gene = feature.getChadoGene(); in propagateId()
[all …]
|
| H A D | MapPanel.java | 37 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
44 protected ChadoCanonicalGene chado_gene;
|
| H A D | GeneComponentTree.java | 28 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
51 private ChadoCanonicalGene chado_gene;
56 public GeneComponentTree(final ChadoCanonicalGene chado_gene, in GeneComponentTree()
128 final ChadoCanonicalGene chado_gene) in createNodes()
|
| H A D | BasicProteinMapPanel.java | 35 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
47 final ChadoCanonicalGene chado_gene, in BasicProteinMapPanel()
|
| H A D | GeneBuilderFrame.java | 75 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
95 private ChadoCanonicalGene chado_gene;
281 … final ChadoCanonicalGene chadoGene = ((GFFStreamFeature)feature.getEmblFeature()).getChadoGene(); in getProteinFeature()
388 final ChadoCanonicalGene chado_gene) in buildCheckBoxes()
631 private void addListeners(final ChadoCanonicalGene chado_gene) in addListeners()
|
| H A D | GeneViewerPanel.java | 52 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
123 public GeneViewerPanel(final ChadoCanonicalGene chado_gene, in GeneViewerPanel()
580 ChadoCanonicalGene chado_gene) in deleteFeatures()
604 createTranscript(final ChadoCanonicalGene chadoGene, in createTranscript()
611 createTranscript(final ChadoCanonicalGene chadoGene, in createTranscript()
950 ChadoCanonicalGene chado_gene, in drawTranscriptOnLine()
1358 final ChadoCanonicalGene chado_gene, in addFeature()
1464 addProteinFeature(final ChadoCanonicalGene chadoGene, in addProteinFeature()
1504 final ChadoCanonicalGene chadoGene, in addExonFeature()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/components/ |
| H A D | FeaturePlotGroup_ESTest.java | 17 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
48 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test1()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/chado/ |
| H A D | ChadoTransaction_ESTest.java | 21 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
54 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test01()
72 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test02()
280 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test22()
331 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test26()
|
| H A D | ArtemisUtils_ESTest.java | 28 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
73 ChadoCanonicalGene chadoCanonicalGene0 = new ChadoCanonicalGene(); in test01()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/components/genebuilder/gff/ |
| H A D | BasicPropertiesPanel_ESTest.java | 16 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
25 …basicPropertiesPanel0 = new BasicPropertiesPanel((ChadoCanonicalGene) null, (BasicGeneBuilderFrame… in test0()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/ |
| H A D | IndexedGFFDocumentEntry.java | 456 HashMap<String, ChadoCanonicalGene> chado_gene = new HashMap<String, ChadoCanonicalGene>(); in combineGeneFeatures()
475 ChadoCanonicalGene gene = new ChadoCanonicalGene(); in combineGeneFeatures()
484 …HashMap<String, ChadoCanonicalGene> transcripts_lookup = new HashMap<String, ChadoCanonicalGene>(); in combineGeneFeatures()
499 ChadoCanonicalGene gene = (ChadoCanonicalGene)chado_gene.get(parent); in combineGeneFeatures()
548 final ChadoCanonicalGene gene = (ChadoCanonicalGene)transcripts_lookup.get(parent); in combineGeneFeatures()
571 ChadoCanonicalGene gene = chado_gene.get(enum_genes.next()); in combineGeneFeatures()
588 private void combineChadoExons(ChadoCanonicalGene gene, FeatureVector features) in combineChadoExons()
|
| H A D | GFFDocumentEntry.java | 199 ChadoCanonicalGene gene = new ChadoCanonicalGene(); in combineGeneFeatures()
227 ChadoCanonicalGene gene = (ChadoCanonicalGene)chado_gene.get(parent); in combineGeneFeatures()
272 final ChadoCanonicalGene gene = (ChadoCanonicalGene)transcripts_lookup.get(parent); in combineGeneFeatures()
322 ChadoCanonicalGene gene = (ChadoCanonicalGene)enum_genes.nextElement(); in combineGeneFeatures()
530 ChadoCanonicalGene chadoGene = ((GFFStreamFeature)queryFeature).getChadoGene(); in addDomain()
597 private void combineChadoExons(ChadoCanonicalGene gene) in combineChadoExons()
|
| H A D | ValidateFeature.java | 444 final ChadoCanonicalGene gene = gffFeature.getChadoGene(); in isCompleteGeneModelOK()
457 final ChadoCanonicalGene gene = gffFeature.getChadoGene(); in isBoundaryOK()
466 final ChadoCanonicalGene gene = gffFeature.getChadoGene(); in isStrandOK()
481 final ChadoCanonicalGene gene = gffFeature.getChadoGene(); in isPartialConsistent()
523 final ChadoCanonicalGene gene, in isPartialChildren()
574 final ChadoCanonicalGene gene = gffFeature.getChadoGene(); in isIdPrefixConsistent()
714 final ChadoCanonicalGene chadoGene = gffF.getChadoGene(); in getCodingFeaturePredicate()
|
| H A D | PublicDBDocumentEntry.java | 217 ChadoCanonicalGene chadoGene = ((GFFStreamFeature)feature).getChadoGene(); in mapGffToNativeFeature()
266 ChadoCanonicalGene chadoGene = ((GFFStreamFeature)feature).getChadoGene(); in mapGffToNativeFeature()
347 ChadoCanonicalGene gene = ((GFFStreamFeature)feature).getChadoGene(); in joinUtrs()
544 ChadoCanonicalGene chadoGene) in handleTranscripts()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/gff/ |
| H A D | BasicPropertiesPanel.java | 35 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
49 public BasicPropertiesPanel(final ChadoCanonicalGene chadoGene, in BasicPropertiesPanel()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/ |
| H A D | EditMenu.java | 36 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
867 final ChadoCanonicalGene g = f.getChadoGene(); in addGeneModelFeaturesToSelection()
1384 ChadoCanonicalGene chadoGene = null; in gffMergeFeatures()
1385 ChadoCanonicalGene chadoGene2 = null; in gffMergeFeatures()
1409 chadoGene = new ChadoCanonicalGene(); in gffMergeFeatures()
1454 final ChadoCanonicalGene thisChadoGene = (ChadoCanonicalGene)geneModels.get(i); in gffMergeFeatures()
1477 chadoGene = (ChadoCanonicalGene)geneModels.get(0); in gffMergeFeatures()
1579 final java.util.List<ChadoCanonicalGene> geneModels = new Vector<ChadoCanonicalGene>(); in getGeneModels()
1716 ChadoCanonicalGene chado_gene = duplicateGenes.get(0); in unmergeFeature()
1749 final ChadoCanonicalGene orig_chado_gene = orig_feature.getChadoGene(); in unmergeFeature()
[all …]
|
| H A D | ValidateViewer.java | 46 import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
268 final ChadoCanonicalGene gene = gffFeature.getChadoGene(); in fixBoundary()
|