/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/uk/ac/sanger/artemis/components/variant/ |
H A D | WriteVariantSitesTest.java | 40 EntryGroup entryGroup = vcfView.getEntryGroup(); in testSNPSites() local 44 entryGroup.getAllFeatures(), in testSNPSites() 45 entryGroup.getSequenceEntry().getBases()); in testSNPSites() 69 EntryGroup entryGroup = vcfView.getEntryGroup(); in testInsertionSites() local 73 entryGroup.getAllFeatures(), in testInsertionSites() 74 entryGroup.getSequenceEntry().getBases()); in testInsertionSites() 98 EntryGroup entryGroup = vcfView.getEntryGroup(); in testMultiAlleleSites() local 102 entryGroup.getAllFeatures(), in testMultiAlleleSites() 103 entryGroup.getSequenceEntry().getBases()); in testMultiAlleleSites() 132 entryGroup.getAllFeatures(), in testDeletionSites() [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/uk/ac/sanger/artemis/components/ |
H A D | TransferAnnotationToolTest.java | 65 private EntryGroup entryGroup; field in TransferAnnotationToolTest 75 entryGroup = readFile(); in setup() 76 originatingFeature = getFeature("gene", "O", "CDS", entryGroup); in setup() 119 testTransferResult(entryGroup, 2, productStr); in testAppend() 143 testTransferResult(entryGroup, 1, productStr); in testOverwrite() 152 private void testTransferResult(final EntryGroup entryGroup, in testTransferResult() argument 156 final Feature featureN = getFeature("gene", "N", "CDS", entryGroup); in testTransferResult() 198 entryGroup.add(entry); in readFile() 199 return entryGroup; in readFile() 228 final EntryGroup entryGroup) in getFeature() argument [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/digest/ |
H A D | CircularGenomeController.java | 113 entries.add(entryGroup); in setup() 118 EntryGroup entryGroup = getEntryGroupFromFile(null); in setup() local 119 File sequenceFile = new File(((File) entryGroup.getSequenceEntry() in setup() 121 + File.separator + entryGroup.getSequenceEntry().getName()); in setup() 126 entries.add(entryGroup); in setup() 385 final EntryEdit entryEdit = new EntryEdit(entryGroup); in addMouseListener() 500 final EntryGroup entryGroup; in getEntryGroupFromFile() local 507 entryGroup = new SimpleEntryGroup(entry.getBases()); in getEntryGroupFromFile() 509 entryGroup = new SimpleEntryGroup(); in getEntryGroupFromFile() 510 entryGroup.add(entry); in getEntryGroupFromFile() [all …]
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H A D | Utils.java | 90 final ReportDetails rd, final EntryGroup entryGroup) in createDNADrawFromReportDetails() argument 93 dna.setArtemisEntryGroup(entryGroup); in createDNADrawFromReportDetails() 135 Track fileTrack = new Track(0.8, "CDS", true, true, entryGroup in createDNADrawFromReportDetails()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/ |
H A D | IOUtils.java | 185 final EntryGroup entryGroup = vcfView.getEntryGroup(); in exportVariantFasta() local 200 entryGroup.getSequenceLength(), in exportVariantFasta() 201 entryGroup.getAllFeatures(), in exportVariantFasta() 202 entryGroup.getBases()); in exportVariantFasta() 558 EntryGroup entryGroup = vcfView.getEntryGroup(); in exportFastaByRange() local 593 Bases bases = entryGroup.getSequenceEntry().getBases(); in exportFastaByRange() 1306 final FeatureEnumeration feature_enum = entryGroup.features (); in getFeatures() 1322 final EntryGroup entryGroup) in createFeatures() argument 1324 final Entry newEntry = entryGroup.createEntry("VCF"); in createFeatures() 1327 int send = entryGroup.getSequenceLength(); in createFeatures() [all …]
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H A D | VCFview.java | 148 private EntryGroup entryGroup; field in VCFview 237 this.entryGroup = feature_display.getEntryGroup(); in VCFview() 239 this.entryGroup = getReference(reference); in VCFview() 240 if(entryGroup != null) in VCFview() 924 EntryGroup entryGroup = new SimpleEntryGroup(); in getReference() local 939 if (entryGroup.getSequenceEntry() != null) in getReference() 948 entryGroup.add(entry); in getReference() 962 return entryGroup; in getReference() 1324 if(entryGroup == null) in getCDSFeaturesInRange() 1805 if(entryGroup == null) in highlightRange() [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/ |
H A D | Wizard.java | 263 final EntryGroup entryGroup = new SimpleEntryGroup(); in loadTemplate() local 312 entry = getEntry(fileName, entryGroup); in loadTemplate() 336 dna.setArtemisEntryGroup(entryGroup); in loadTemplate() 530 if(entryGroup.getSequenceEntry() != null) in getEntry() 531 bases = entryGroup.getSequenceEntry().getBases(); in getEntry() 537 entryGroup.add(entry); in getEntry() 665 final EntryGroup entryGroup = new SimpleEntryGroup(); in getDNADrawFromFile() local 670 entryGroup.add(entry); in getDNADrawFromFile() 671 return getDNADrawFromArtemisEntry(dna_current, entryGroup, entry); in getDNADrawFromFile() 705 dna_current.setArtemisEntryGroup(entryGroup); in getDNADrawFromArtemisEntry() [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/ |
H A D | MappedReads.java | 390 private EntryGroup entryGroup; field in MappedReads.CalculateNewFeatures 406 entryGroup = feature_display.getEntryGroup(); in CalculateNewFeatures() 497 fwdStart, j+k, r, excluseKeys, fwdMarkers, entryGroup, i); in construct() 502 revStart, j+k, r, excluseKeys, revMarkers, entryGroup, i); in construct() 512 final Entry newEntry = entryGroup.createEntry ( in construct() 618 final EntryGroup entryGroup, in findFeatures() argument 627 entryGroup.getFeaturesInRange(range); in findFeatures() 649 final FeatureVector features = entryGroup.getFeaturesInRange(range); in findFeatures() 674 FeatureVector features = entryGroup.getFeaturesInRange(range); in findFeatures()
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H A D | BamView.java | 3540 private Entry getEntry(final String entryFileName, final EntryGroup entryGroup) in getEntry() argument 3559 if(entryGroup.getSequenceEntry() != null) in getEntry() 3560 bases = entryGroup.getSequenceEntry().getBases(); in getEntry() 3570 entryGroup.add(entry); in getEntry()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/ |
H A D | BasePlot.java | 137 private EntryGroup entryGroup; field in BasePlot 175 final EntryGroup entryGroup) in BasePlot() argument 182 this.entryGroup = entryGroup; in BasePlot() 379 if(GeneUtils.isDatabaseEntry(entryGroup)) in calculateFeatures() 384 Entry entry = entryGroup.getDefaultEntry(); in calculateFeatures() 437 entryGroup.createEntry ("CDS_" + minFeatureSize + "_" + in calculateFeatures() 729 entryGroup.getSequenceEntry(), getStart(), getEnd()); in drawMultiValueGraph()
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H A D | TransferAnnotationTool.java | 128 final EntryGroup entryGroup, in TransferAnnotationTool() argument 155 framePanel, entryGroup); in TransferAnnotationTool() 402 final EntryGroup entryGroup) in addBottomButtons() argument 440 geneNameCheckBoxes, qP.getFeature(), entryGroup, in addBottomButtons() 523 final EntryGroup entryGroup, in transferAnnotation() argument 593 final FeatureVector features = entryGroup.getAllFeatures(); in transferAnnotation() 596 entryGroup.getActionController().startAction(); in transferAnnotation() 598 GeneUtils.isDatabaseEntry(entryGroup), geneNames, genesUpdated); in transferAnnotation() 599 entryGroup.getActionController().endAction(); in transferAnnotation()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/ |
H A D | IndexedGFFDocumentEntry.java | 69 private EntryGroup entryGroup; field in IndexedGFFDocumentEntry 1157 public void setEntryGroup(EntryGroup entryGroup) in setEntryGroup() argument 1159 this.entryGroup = entryGroup; in setEntryGroup() 1164 Entry entry = entryGroup.getSequenceEntry().getEMBLEntry(); in initContig() 1197 if(entryGroup.getSequenceEntry().getFeatureCount() == sequenceNames.length) in checkOffset() 1200 uk.ac.sanger.artemis.FeatureVector features = entryGroup.getSequenceEntry().getAllFeatures(); in checkOffset() 1343 if(entryGroup == null) in hasMoreFeatures() 1351 new Range(1, entryGroup.getSequenceLength())); in hasMoreFeatures()
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H A D | DatabaseInferredFeature.java | 459 public static void addListenersToEntryGroup(EntryGroup entryGroup) in addListenersToEntryGroup() argument 461 FeatureVector features = entryGroup.getAllFeatures(); in addListenersToEntryGroup()
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/dports/www/aria2/aria2-1.36.0/src/ |
H A D | Metalink2RequestGroup.cc | 204 for (auto& entryGroup : entryGroups) { in createRequestGroup() local 205 auto& metaurl = entryGroup.first; in createRequestGroup() 206 auto& mes = entryGroup.second; in createRequestGroup()
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/dports/security/openvpn-admin/openvpn-admin-1.9.4/src/ |
H A D | DetailForm.cs | 62 [Widget] Gtk.Entry entryGroup; field in OpenVPN.Admin.DetailForm 236 entryGroup.Text = config["group"]; in RefreshEntries() 341 config["group"] = entryGroup.Text; in SaveEntries()
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/dports/misc/tellico/tellico-3.4.2/src/ |
H A D | mainwindow.cpp | 1009 QString entryGroup, groupSortField; in readCollectionOptions() local 1011 entryGroup = group.readEntry("Group By", defaultGroup); in readCollectionOptions() 1018 entryGroup = group.readEntry(QStringLiteral("Group By_%1").arg(i), defaultGroup); in readCollectionOptions() 1024 if(entryGroup.isEmpty()) { in readCollectionOptions() 1025 entryGroup = group.readEntry("Group By", defaultGroup); in readCollectionOptions() 1028 if(entryGroup.isEmpty() || in readCollectionOptions() 1029 …(!coll_->entryGroups().contains(entryGroup) && entryGroup != Data::Collection::s_peopleGroupName))… in readCollectionOptions() 1030 entryGroup = defaultGroup; in readCollectionOptions() 1032 m_groupView->setGroupField(entryGroup); in readCollectionOptions()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/chado/ |
H A D | ChadoTransactionManager.java | 141 private EntryGroup entryGroup; field in ChadoTransactionManager 195 public void setEntryGroup(final EntryGroup entryGroup) in setEntryGroup() argument 197 this.entryGroup = entryGroup; in setEntryGroup() 205 ((DocumentEntry)entryGroup.getSequenceEntry().getEMBLEntry()).getDocument()); in logMDC() 225 ((DocumentEntry)entryGroup.getSequenceEntry().getEMBLEntry()).getDocument(); in sequenceChanged() 226 int newSequenceLength = entryGroup.getSequenceEntry().getEMBLEntry().getSequence().length(); in sequenceChanged() 275 entryGroup.getSequenceEntry().getEMBLEntry().getSequence().length())); in sequenceChanged()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/ |
H A D | GeneUtils.java | 902 public static boolean isDatabaseEntry(final EntryGroup entryGroup) in isDatabaseEntry() argument 904 final EntryVector entries = entryGroup.getActiveEntries(); in isDatabaseEntry() 919 public static boolean isGFFEntry(final EntryGroup entryGroup) in isGFFEntry() argument 921 final EntryVector entries = entryGroup.getActiveEntries(); in isGFFEntry()
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/dports/lang/gnustep-base/libs-base-base-1_27_0/Source/ |
H A D | GSAvahiNetService.m | 69 - (void) entryGroup: (AvahiEntryGroup*)group 516 [(GSAvahiNetService*)userInfo entryGroup: group 934 // The entryGroup is active: 940 // The entryGroup is not properly set up for publication: 1948 - (void) entryGroup: (AvahiEntryGroup*)group
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