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Searched refs:entryGroup (Results 1 – 19 of 19) sorted by relevance

/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/uk/ac/sanger/artemis/components/variant/
H A DWriteVariantSitesTest.java40 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()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/uk/ac/sanger/artemis/components/
H A DTransferAnnotationToolTest.java65 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
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/digest/
H A DCircularGenomeController.java113 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()
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H A DUtils.java90 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()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/
H A DIOUtils.java185 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()
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H A DVCFview.java148 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()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/
H A DWizard.java263 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()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/
H A DMappedReads.java390 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()
H A DBamView.java3540 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()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/
H A DBasePlot.java137 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()
H A DTransferAnnotationTool.java128 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()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/
H A DIndexedGFFDocumentEntry.java69 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()
H A DDatabaseInferredFeature.java459 public static void addListenersToEntryGroup(EntryGroup entryGroup) in addListenersToEntryGroup() argument
461 FeatureVector features = entryGroup.getAllFeatures(); in addListenersToEntryGroup()
/dports/www/aria2/aria2-1.36.0/src/
H A DMetalink2RequestGroup.cc204 for (auto& entryGroup : entryGroups) { in createRequestGroup() local
205 auto& metaurl = entryGroup.first; in createRequestGroup()
206 auto& mes = entryGroup.second; in createRequestGroup()
/dports/security/openvpn-admin/openvpn-admin-1.9.4/src/
H A DDetailForm.cs62 [Widget] Gtk.Entry entryGroup; field in OpenVPN.Admin.DetailForm
236 entryGroup.Text = config["group"]; in RefreshEntries()
341 config["group"] = entryGroup.Text; in SaveEntries()
/dports/misc/tellico/tellico-3.4.2/src/
H A Dmainwindow.cpp1009 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()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/chado/
H A DChadoTransactionManager.java141 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()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/
H A DGeneUtils.java902 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()
/dports/lang/gnustep-base/libs-base-base-1_27_0/Source/
H A DGSAvahiNetService.m69 - (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