[med-svn] [apollo] 06/08: Merge tag 'upstream/2.0.8'
Andreas Tille
tille at debian.org
Fri Dec 1 15:43:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository apollo.
commit ebed210211af57ab5cfe1517e0b0c38cd52f8bbb
Merge: d9458fe 2c78426
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 1 16:37:20 2017 +0100
Merge tag 'upstream/2.0.8'
Upstream version 2.0.8
.coveralls.yml | 2 +
.github/CONTRIBUTING.md | 309 +
.github/ISSUE_TEMPLATE.md | 8 +
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ChangeLog.md | 648 +
LICENSE.md | 13 +
README.md | 74 +
apollo | 244 +
application.properties | 6 +
build.gradle | 440 +
build.xml | 256 +
client/apollo/css/add_sequence_alteration.css | 34 +
client/apollo/css/annotation_info_editor.css | 145 +
client/apollo/css/confirm_dialog.css | 19 +
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client/apollo/css/flat.css | 29 +
client/apollo/css/genome.css | 67 +
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client/apollo/css/get_sequence.css | 35 +
client/apollo/css/information_editor_panel.css | 57 +
client/apollo/css/main.css | 20 +
client/apollo/css/maker.css | 292 +
client/apollo/css/maker_darkbackground.css | 357 +
client/apollo/css/maker_styles.css | 448 +
client/apollo/css/search_sequence.css | 76 +
client/apollo/css/webapollo_track_styles.css | 882 +
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client/apollo/js/FeatureSelectionManager.js | 184 +
client/apollo/js/FormatUtils.js | 25 +
client/apollo/js/InformationEditor.js | 72 +
client/apollo/js/JSONUtils.js | 422 +
client/apollo/js/Permission.js | 11 +
client/apollo/js/SequenceFeatureDialog.js | 170 +
client/apollo/js/SequenceOntologyUtils.js | 415 +
client/apollo/js/SequenceSearch.js | 243 +
client/apollo/js/Store/SeqFeature/ApolloGFF3.js | 132 +
client/apollo/js/Store/SeqFeature/PseudoNCList.js | 22 +
client/apollo/js/Store/SeqFeature/ScratchPad.js | 75 +
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client/apollo/js/View/Dialog/Help.js | 60 +
client/apollo/js/View/Track/AnnotSequenceTrack.js | 18 +
client/apollo/js/View/Track/AnnotTrack.js | 5934 +++++++
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client/apollo/jslib/bbop/search_box.js | 178 +
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client/apollo/jslib/jqueryui/datepicker-pl.js | 26 +
client/apollo/jslib/jqueryui/datepicker-pt-BR.js | 25 +
client/apollo/jslib/jqueryui/datepicker-pt.js | 24 +
client/apollo/jslib/jqueryui/datepicker-rm.js | 24 +
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client/apollo/jslib/jqueryui/datepicker-sk.js | 26 +
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client/apollo/jslib/jqueryui/datepicker-sv.js | 26 +
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client/apollo/jslib/jqueryui/datepicker-zh-TW.js | 26 +
client/apollo/jslib/jqueryui/datepicker.js | 1829 ++
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client/apollo/jslib/jqueryui/draggable.js | 828 +
client/apollo/jslib/jqueryui/droppable.js | 299 +
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client/apollo/jslib/jqueryui/effects/pulsate.js | 54 +
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client/apollo/jslib/jqueryui/effects/shake.js | 60 +
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client/apollo/jslib/jqueryui/selectable.js | 270 +
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client/apollo/jslib/jqueryui/sortable.js | 1084 ++
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.../vendor/jquery-ui-menubar/jquery-1.8.2.js | 9440 +++++++++++
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.../vendor/jquery-ui-menubar/jquery.ui.all.css | 12 +
.../jquery-ui-menubar/jquery.ui.autocomplete.css | 18 +
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.../jquery-ui-menubar/jquery.ui.datepicker.css | 67 +
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.../vendor/jquery-ui-menubar/jquery.ui.menubar.js | 327 +
.../vendor/jquery-ui-menubar/jquery.ui.position.js | 517 +
.../jquery-ui-menubar/jquery.ui.progressbar.css | 12 +
.../jquery-ui-menubar/jquery.ui.resizable.css | 21 +
.../jquery-ui-menubar/jquery.ui.selectable.css | 11 +
.../vendor/jquery-ui-menubar/jquery.ui.slider.css | 25 +
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.../vendor/jquery-ui-menubar/jquery.ui.tooltip.css | 22 +
.../vendor/jquery-ui-menubar/jquery.ui.widget.js | 502 +
grails-app/assets/javascripts/vendor/raf/index.js | 31 +
.../javascripts/vendor/ui-bootstrap-0.11.0.min.js | 9 +
.../vendor/ui-bootstrap-custom-0.13.4-csp.css | 6 +
.../vendor/ui-bootstrap-custom-0.13.4.js | 5450 ++++++
.../vendor/ui-bootstrap-custom-0.13.4.min.js | 10 +
.../vendor/ui-bootstrap-custom-tpls-0.13.4.js | 5836 +++++++
.../vendor/ui-bootstrap-custom-tpls-0.13.4.min.js | 10 +
grails-app/assets/javascripts/vendor/ui-layout.js | 123 +
.../assets/javascripts/vendor/ui-layout.min.js | 7 +
grails-app/assets/stylesheets/annotator.css | 126 +
grails-app/assets/stylesheets/application.css | 55 +
grails-app/assets/stylesheets/errors.css | 109 +
grails-app/assets/stylesheets/login.css | 22 +
grails-app/assets/stylesheets/main.css | 649 +
grails-app/assets/stylesheets/mobile.css | 82 +
grails-app/assets/stylesheets/oldlook.css | 171 +
grails-app/assets/stylesheets/search_sequence.css | 78 +
.../stylesheets/ui-bootstrap-custom-0.13.4-csp.css | 6 +
grails-app/assets/stylesheets/ui-layout.css | 49 +
.../assets/stylesheets/web_api_stylesheet.css | 39 +
grails-app/conf/AppNavigation.groovy | 26 +
grails-app/conf/BootStrap.groovy | 60 +
grails-app/conf/BuildConfig.groovy | 191 +
grails-app/conf/Config.groovy | 435 +
grails-app/conf/DataSource.groovy | 107 +
grails-app/conf/UrlMappings.groovy | 132 +
.../conf/org/bbop/apollo/SecurityFilters.groovy | 100 +
grails-app/conf/spring/resources.groovy | 3 +
.../bbop/apollo/AbstractApolloController.groovy | 48 +
.../bbop/apollo/AnnotationEditorController.groovy | 1291 ++
.../org/bbop/apollo/AnnotatorController.groovy | 507 +
.../org/bbop/apollo/AuthController.groovy | 97 +
.../bbop/apollo/AvailableStatusController.groovy | 329 +
.../org/bbop/apollo/CannedCommentController.groovy | 335 +
.../org/bbop/apollo/CannedKeyController.groovy | 337 +
.../org/bbop/apollo/CannedValueController.groovy | 334 +
.../org/bbop/apollo/FeatureEventController.groovy | 301 +
.../org/bbop/apollo/FeatureTypeController.groovy | 113 +
.../org/bbop/apollo/GroupController.groovy | 377 +
.../org/bbop/apollo/HomeController.groovy | 127 +
.../org/bbop/apollo/IOServiceController.groovy | 251 +
.../org/bbop/apollo/JbrowseController.groovy | 575 +
.../org/bbop/apollo/LoginController.groovy | 239 +
.../bbop/apollo/NcbiProxyServiceController.groovy | 46 +
.../org/bbop/apollo/OrganismController.groovy | 1087 ++
.../org/bbop/apollo/ProxyController.groovy | 152 +
.../org/bbop/apollo/SequenceController.groovy | 380 +
.../org/bbop/apollo/TrackController.groovy | 309 +
.../org/bbop/apollo/UserController.groovy | 578 +
.../org/bbop/apollo/WebServicesController.groovy | 15 +
grails-app/domain/org/bbop/apollo/Analysis.groovy | 65 +
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.../domain/org/bbop/apollo/AnalysisProperty.groovy | 38 +
.../domain/org/bbop/apollo/AvailableStatus.groovy | 17 +
.../apollo/AvailableStatusOrganismFilter.groovy | 10 +
.../domain/org/bbop/apollo/BiologicalRegion.groovy | 17 +
grails-app/domain/org/bbop/apollo/CDS.groovy | 15 +
grails-app/domain/org/bbop/apollo/CV.groovy | 13 +
grails-app/domain/org/bbop/apollo/CVTerm.groovy | 68 +
.../domain/org/bbop/apollo/CVTermPath.groovy | 45 +
.../org/bbop/apollo/CVTermRelationship.groovy | 39 +
.../domain/org/bbop/apollo/CannedComment.groovy | 16 +
.../bbop/apollo/CannedCommentOrganismFilter.groovy | 10 +
grails-app/domain/org/bbop/apollo/CannedKey.groovy | 16 +
.../org/bbop/apollo/CannedKeyOrganismFilter.groovy | 10 +
.../domain/org/bbop/apollo/CannedValue.groovy | 16 +
.../bbop/apollo/CannedValueOrganismFilter.groovy | 10 +
.../domain/org/bbop/apollo/Chromosome.groovy | 14 +
grails-app/domain/org/bbop/apollo/Comment.groovy | 10 +
grails-app/domain/org/bbop/apollo/Contig.groovy | 15 +
.../org/bbop/apollo/CustomDomainMapping.groovy | 15 +
.../domain/org/bbop/apollo/CustomFeature.groovy | 66 +
.../domain/org/bbop/apollo/CustomTranscript.groovy | 67 +
grails-app/domain/org/bbop/apollo/DB.groovy | 44 +
grails-app/domain/org/bbop/apollo/DBXref.groovy | 66 +
.../domain/org/bbop/apollo/DBXrefProperty.groovy | 40 +
.../domain/org/bbop/apollo/DataAdapter.groovy | 40 +
grails-app/domain/org/bbop/apollo/Deletion.groovy | 19 +
.../domain/org/bbop/apollo/Environment.groovy | 42 +
.../org/bbop/apollo/EnvironmentCVTerm.groovy | 35 +
grails-app/domain/org/bbop/apollo/Exon.groovy | 16 +
grails-app/domain/org/bbop/apollo/Feature.groovy | 167 +
.../domain/org/bbop/apollo/FeatureAttribute.groovy | 14 +
.../domain/org/bbop/apollo/FeatureCVTerm.groovy | 50 +
.../domain/org/bbop/apollo/FeatureEvent.groovy | 63 +
.../domain/org/bbop/apollo/FeatureGenotype.groovy | 49 +
.../org/bbop/apollo/FeatureLazyResidues.groovy | 16 +
.../domain/org/bbop/apollo/FeatureLocation.groovy | 86 +
.../domain/org/bbop/apollo/FeatureProperty.groovy | 59 +
.../org/bbop/apollo/FeatureRelationship.groovy | 52 +
.../domain/org/bbop/apollo/FeatureSynonym.groovy | 45 +
.../domain/org/bbop/apollo/FeatureType.groovy | 12 +
.../domain/org/bbop/apollo/Frameshift.groovy | 33 +
grails-app/domain/org/bbop/apollo/Gene.groovy | 19 +
.../domain/org/bbop/apollo/GeneMemberRegion.groovy | 14 +
grails-app/domain/org/bbop/apollo/Genotype.groovy | 51 +
.../org/bbop/apollo/GroupOrganismPermission.groovy | 31 +
.../domain/org/bbop/apollo/GroupPermission.groovy | 13 +
.../org/bbop/apollo/GroupTrackPermission.groovy | 13 +
grails-app/domain/org/bbop/apollo/Insertion.groovy | 17 +
grails-app/domain/org/bbop/apollo/Intron.groovy | 15 +
grails-app/domain/org/bbop/apollo/MRNA.groovy | 11 +
grails-app/domain/org/bbop/apollo/Match.groovy | 76 +
grails-app/domain/org/bbop/apollo/MiRNA.groovy | 11 +
.../domain/org/bbop/apollo/Minus1Frameshift.groovy | 24 +
.../domain/org/bbop/apollo/Minus2Frameshift.groovy | 24 +
grails-app/domain/org/bbop/apollo/NcRNA.groovy | 11 +
.../apollo/NonCanonicalFivePrimeSpliceSite.groovy | 15 +
.../apollo/NonCanonicalThreePrimeSpliceSite.groovy | 14 +
grails-app/domain/org/bbop/apollo/Operation.groovy | 36 +
grails-app/domain/org/bbop/apollo/Organism.groovy | 76 +
.../domain/org/bbop/apollo/OrganismDBXref.groovy | 35 +
.../domain/org/bbop/apollo/OrganismFilter.groovy | 10 +
.../domain/org/bbop/apollo/OrganismProperty.groovy | 54 +
grails-app/domain/org/bbop/apollo/PartOf.groovy | 10 +
.../domain/org/bbop/apollo/Permission.groovy | 16 +
grails-app/domain/org/bbop/apollo/Phenotype.groovy | 56 +
.../org/bbop/apollo/PhenotypeDescription.groovy | 44 +
.../org/bbop/apollo/PhenotypeStatement.groovy | 46 +
.../domain/org/bbop/apollo/Plus1Frameshift.groovy | 24 +
.../domain/org/bbop/apollo/Plus2Frameshift.groovy | 24 +
.../domain/org/bbop/apollo/Preference.groovy | 18 +
grails-app/domain/org/bbop/apollo/Proxy.groovy | 24 +
.../domain/org/bbop/apollo/Pseudogene.groovy | 16 +
.../domain/org/bbop/apollo/Publication.groovy | 90 +
.../org/bbop/apollo/PublicationAuthor.groovy | 47 +
.../org/bbop/apollo/PublicationDBXref.groovy | 40 +
.../org/bbop/apollo/PublicationRelationship.groovy | 37 +
grails-app/domain/org/bbop/apollo/RRNA.groovy | 11 +
grails-app/domain/org/bbop/apollo/Region.groovy | 16 +
.../domain/org/bbop/apollo/RepeatRegion.groovy | 14 +
grails-app/domain/org/bbop/apollo/Role.groovy | 15 +
.../domain/org/bbop/apollo/SearchTool.groovy | 19 +
grails-app/domain/org/bbop/apollo/Sequence.groovy | 39 +
.../org/bbop/apollo/SequenceAlteration.groovy | 24 +
.../org/bbop/apollo/SequenceAttribute.groovy | 14 +
.../domain/org/bbop/apollo/SequenceCache.groovy | 32 +
.../domain/org/bbop/apollo/SequenceChunk.groovy | 16 +
.../domain/org/bbop/apollo/SequenceFeature.groovy | 14 +
.../domain/org/bbop/apollo/ServerData.groovy | 21 +
grails-app/domain/org/bbop/apollo/SnRNA.groovy | 12 +
grails-app/domain/org/bbop/apollo/SnoRNA.groovy | 11 +
.../domain/org/bbop/apollo/SpliceSite.groovy | 13 +
grails-app/domain/org/bbop/apollo/Status.groovy | 11 +
.../org/bbop/apollo/StopCodonReadThrough.groovy | 19 +
.../domain/org/bbop/apollo/Substitution.groovy | 14 +
.../domain/org/bbop/apollo/SuperContig.groovy | 13 +
grails-app/domain/org/bbop/apollo/Synonym.groovy | 39 +
grails-app/domain/org/bbop/apollo/TRNA.groovy | 12 +
.../domain/org/bbop/apollo/TrackCache.groovy | 36 +
.../domain/org/bbop/apollo/Transcript.groovy | 16 +
.../org/bbop/apollo/TranscriptAttribute.groovy | 14 +
.../domain/org/bbop/apollo/TranscriptRegion.groovy | 13 +
.../org/bbop/apollo/TransposableElement.groovy | 14 +
grails-app/domain/org/bbop/apollo/User.groovy | 75 +
grails-app/domain/org/bbop/apollo/UserGroup.groovy | 14 +
.../org/bbop/apollo/UserOrganismPermission.groovy | 32 +
.../org/bbop/apollo/UserOrganismPreference.groovy | 41 +
.../domain/org/bbop/apollo/UserPermission.groovy | 15 +
.../domain/org/bbop/apollo/UserPreference.groovy | 10 +
.../org/bbop/apollo/UserTrackPermission.groovy | 13 +
grails-app/domain/org/gmod/chado/Chadoprop.groovy | 24 +
grails-app/domain/org/gmod/chado/Cv.groovy | 22 +
grails-app/domain/org/gmod/chado/Cvprop.groovy | 25 +
grails-app/domain/org/gmod/chado/Cvterm.groovy | 157 +
.../domain/org/gmod/chado/CvtermDbxref.groovy | 16 +
.../org/gmod/chado/CvtermRelationship.groovy | 16 +
grails-app/domain/org/gmod/chado/Cvtermpath.groovy | 23 +
grails-app/domain/org/gmod/chado/Cvtermprop.groovy | 22 +
.../domain/org/gmod/chado/Cvtermsynonym.groovy | 21 +
grails-app/domain/org/gmod/chado/Db.groovy | 24 +
grails-app/domain/org/gmod/chado/Dbxref.groovy | 48 +
grails-app/domain/org/gmod/chado/Dbxrefprop.groovy | 22 +
grails-app/domain/org/gmod/chado/Eimage.groovy | 21 +
.../domain/org/gmod/chado/Environment.groovy | 30 +
.../domain/org/gmod/chado/EnvironmentCvterm.groovy | 15 +
grails-app/domain/org/gmod/chado/Expression.groovy | 26 +
.../domain/org/gmod/chado/ExpressionCvterm.groovy | 18 +
.../org/gmod/chado/ExpressionCvtermprop.groovy | 23 +
.../domain/org/gmod/chado/ExpressionImage.groovy | 15 +
.../domain/org/gmod/chado/ExpressionPub.groovy | 15 +
.../domain/org/gmod/chado/Expressionprop.groovy | 23 +
grails-app/domain/org/gmod/chado/Feature.groovy | 81 +
.../domain/org/gmod/chado/FeatureContains.groovy | 38 +
.../domain/org/gmod/chado/FeatureCvterm.groovy | 26 +
.../org/gmod/chado/FeatureCvtermDbxref.groovy | 15 +
.../domain/org/gmod/chado/FeatureCvtermPub.groovy | 15 +
.../domain/org/gmod/chado/FeatureCvtermprop.groovy | 23 +
.../domain/org/gmod/chado/FeatureDbxref.groovy | 16 +
.../domain/org/gmod/chado/FeatureExpression.groovy | 17 +
.../org/gmod/chado/FeatureExpressionprop.groovy | 23 +
.../domain/org/gmod/chado/FeatureGenotype.groovy | 24 +
.../org/gmod/chado/FeatureIntersection.groovy | 58 +
.../domain/org/gmod/chado/FeaturePhenotype.groovy | 15 +
grails-app/domain/org/gmod/chado/FeaturePub.groovy | 16 +
.../domain/org/gmod/chado/FeaturePubprop.groovy | 23 +
.../org/gmod/chado/FeatureRelationship.groovy | 26 +
.../org/gmod/chado/FeatureRelationshipPub.groovy | 15 +
.../org/gmod/chado/FeatureRelationshipprop.groovy | 24 +
.../gmod/chado/FeatureRelationshippropPub.groovy | 15 +
.../domain/org/gmod/chado/FeatureSynonym.groovy | 18 +
grails-app/domain/org/gmod/chado/Featureloc.groovy | 35 +
.../domain/org/gmod/chado/FeaturelocPub.groovy | 15 +
grails-app/domain/org/gmod/chado/Featuremap.groovy | 24 +
.../domain/org/gmod/chado/FeaturemapPub.groovy | 15 +
grails-app/domain/org/gmod/chado/Featurepos.groovy | 21 +
.../domain/org/gmod/chado/Featureprop.groovy | 24 +
.../domain/org/gmod/chado/FeaturepropPub.groovy | 15 +
.../domain/org/gmod/chado/Featurerange.groovy | 26 +
.../domain/org/gmod/chado/FeaturesetMeets.groovy | 38 +
grails-app/domain/org/gmod/chado/Genotype.groovy | 35 +
.../domain/org/gmod/chado/Genotypeprop.groovy | 24 +
grails-app/domain/org/gmod/chado/Organism.groovy | 36 +
.../domain/org/gmod/chado/OrganismDbxref.groovy | 15 +
.../org/gmod/chado/OrganismFeatureCount.groovy | 58 +
.../domain/org/gmod/chado/Organismprop.groovy | 23 +
grails-app/domain/org/gmod/chado/Phendesc.groovy | 18 +
grails-app/domain/org/gmod/chado/Phenotype.groovy | 41 +
.../org/gmod/chado/PhenotypeComparison.groovy | 22 +
.../gmod/chado/PhenotypeComparisonCvterm.groovy | 17 +
.../domain/org/gmod/chado/PhenotypeCvterm.groovy | 21 +
.../domain/org/gmod/chado/Phenstatement.groovy | 18 +
grails-app/domain/org/gmod/chado/Phylonode.groovy | 42 +
.../domain/org/gmod/chado/PhylonodeDbxref.groovy | 15 +
.../domain/org/gmod/chado/PhylonodeOrganism.groovy | 15 +
.../domain/org/gmod/chado/PhylonodePub.groovy | 15 +
.../org/gmod/chado/PhylonodeRelationship.groovy | 22 +
.../domain/org/gmod/chado/Phylonodeprop.groovy | 22 +
grails-app/domain/org/gmod/chado/Phylotree.groovy | 27 +
.../domain/org/gmod/chado/PhylotreePub.groovy | 15 +
grails-app/domain/org/gmod/chado/Pub.groovy | 89 +
grails-app/domain/org/gmod/chado/PubDbxref.groovy | 16 +
.../domain/org/gmod/chado/PubRelationship.groovy | 16 +
grails-app/domain/org/gmod/chado/Pubauthor.groovy | 28 +
grails-app/domain/org/gmod/chado/Pubprop.groovy | 22 +
grails-app/domain/org/gmod/chado/Synonym.groovy | 26 +
grails-app/i18n/messages.properties | 55 +
grails-app/i18n/messages_cs_CZ.properties | 55 +
grails-app/i18n/messages_da.properties | 56 +
grails-app/i18n/messages_de.properties | 55 +
grails-app/i18n/messages_es.properties | 55 +
grails-app/i18n/messages_fr.properties | 19 +
grails-app/i18n/messages_it.properties | 55 +
grails-app/i18n/messages_ja.properties | 55 +
grails-app/i18n/messages_nb.properties | 56 +
grails-app/i18n/messages_nl.properties | 55 +
grails-app/i18n/messages_pl.properties | 59 +
grails-app/i18n/messages_pt_BR.properties | 59 +
grails-app/i18n/messages_pt_PT.properties | 34 +
grails-app/i18n/messages_ru.properties | 31 +
grails-app/i18n/messages_sv.properties | 55 +
grails-app/i18n/messages_th.properties | 55 +
grails-app/i18n/messages_zh_CN.properties | 18 +
grails-app/i18n/shiro.properties | 1 +
.../org/bbop/apollo/CleanupPreferencesJob.groovy | 18 +
.../jobs/org/bbop/apollo/PhoneHomeJob.groovy | 20 +
grails-app/migrations/changelog-2_0_0.groovy | 2192 +++
grails-app/migrations/changelog-2_0_1.groovy | 117 +
grails-app/migrations/changelog-2_0_2.groovy | 12 +
grails-app/migrations/changelog-2_0_3.groovy | 24 +
grails-app/migrations/changelog-2_0_7.groovy | 7 +
grails-app/migrations/changelog-2_0_8.groovy | 7 +
grails-app/migrations/changelog.groovy | 7 +
grails-app/realms/org/bbop/apollo/DbRealm.groovy | 132 +
.../org/bbop/apollo/AnnotationEditorService.groovy | 20 +
.../org/bbop/apollo/AnnotatorService.groovy | 92 +
.../services/org/bbop/apollo/CdsService.groovy | 169 +
.../org/bbop/apollo/ChadoHandlerService.groovy | 1459 ++
.../org/bbop/apollo/ConfigWrapperService.groovy | 129 +
.../bbop/apollo/ConfigurableFeatureService.groovy | 61 +
.../services/org/bbop/apollo/CvTermService.groovy | 54 +
.../org/bbop/apollo/DomainMarshallerService.groovy | 88 +
.../services/org/bbop/apollo/ExonService.groovy | 481 +
.../org/bbop/apollo/FastaHandlerService.groovy | 264 +
.../org/bbop/apollo/FeatureEventService.groovy | 910 +
.../org/bbop/apollo/FeaturePropertyService.groovy | 114 +
.../bbop/apollo/FeatureRelationshipService.groovy | 226 +
.../services/org/bbop/apollo/FeatureService.groovy | 2977 ++++
.../org/bbop/apollo/FeatureTypeService.groovy | 34 +
.../services/org/bbop/apollo/FileService.groovy | 210 +
.../org/bbop/apollo/Gff3HandlerService.groovy | 439 +
.../services/org/bbop/apollo/JbrowseService.groovy | 41 +
.../services/org/bbop/apollo/NameService.groovy | 156 +
.../apollo/NonCanonicalSplitSiteService.groovy | 281 +
.../org/bbop/apollo/OrganismService.groovy | 86 +
.../org/bbop/apollo/OverlapperService.groovy | 186 +
.../org/bbop/apollo/PermissionService.groovy | 669 +
.../org/bbop/apollo/PhoneHomeService.groovy | 71 +
.../org/bbop/apollo/PreferenceService.groovy | 756 +
.../org/bbop/apollo/ProjectionService.groovy | 35 +
.../services/org/bbop/apollo/ProxyService.groovy | 68 +
.../services/org/bbop/apollo/ReportService.groovy | 222 +
.../org/bbop/apollo/RequestHandlingService.groovy | 2360 +++
.../org/bbop/apollo/SequenceSearchService.groovy | 81 +
.../org/bbop/apollo/SequenceService.groovy | 595 +
.../services/org/bbop/apollo/SvgService.groovy | 177 +
.../org/bbop/apollo/TrackMapperService.groovy | 69 +
.../services/org/bbop/apollo/TrackService.groovy | 558 +
.../org/bbop/apollo/TranscriptService.groovy | 508 +
.../services/org/bbop/apollo/UserService.groovy | 115 +
.../authenticator/AuthenticatorService.groovy | 16 +
.../RemoteUserAuthenticatorService.groovy | 125 +
.../UsernamePasswordAuthenticatorService.groovy | 41 +
.../taglib/org/bbop/apollo/PermissionTagLib.groovy | 29 +
grails-app/views/annotator/adminPanel.gsp | 18 +
grails-app/views/annotator/componentDiv.gsp | 53 +
grails-app/views/annotator/demo.gsp | 40 +
grails-app/views/annotator/detail.gsp | 156 +
grails-app/views/annotator/index.gsp | 54 +
grails-app/views/annotator/notAuthorized.gsp | 17 +
grails-app/views/annotator/report.gsp | 117 +
grails-app/views/annotator/splitter.gsp | 52 +
grails-app/views/annotator/version.gsp | 49 +
grails-app/views/annotator/workingDiv.gsp | 53 +
grails-app/views/auth/login.gsp | 68 +
grails-app/views/auth/unauthorized.gsp | 24 +
grails-app/views/availableStatus/_form.gsp | 38 +
grails-app/views/availableStatus/create.gsp | 38 +
grails-app/views/availableStatus/edit.gsp | 41 +
grails-app/views/availableStatus/index.gsp | 58 +
grails-app/views/availableStatus/show.gsp | 79 +
grails-app/views/cannedComment/_form.gsp | 47 +
grails-app/views/cannedComment/create.gsp | 38 +
grails-app/views/cannedComment/edit.gsp | 41 +
grails-app/views/cannedComment/index.gsp | 64 +
grails-app/views/cannedComment/show.gsp | 91 +
grails-app/views/cannedKey/_form.gsp | 45 +
grails-app/views/cannedKey/create.gsp | 38 +
grails-app/views/cannedKey/edit.gsp | 41 +
grails-app/views/cannedKey/index.gsp | 63 +
grails-app/views/cannedKey/show.gsp | 102 +
grails-app/views/cannedValue/_form.gsp | 43 +
grails-app/views/cannedValue/create.gsp | 38 +
grails-app/views/cannedValue/edit.gsp | 41 +
grails-app/views/cannedValue/index.gsp | 70 +
grails-app/views/cannedValue/show.gsp | 88 +
grails-app/views/error.gsp | 18 +
grails-app/views/featureEvent/_form.gsp | 112 +
grails-app/views/featureEvent/create.gsp | 38 +
grails-app/views/featureEvent/edit.gsp | 41 +
grails-app/views/featureEvent/index.gsp | 66 +
grails-app/views/featureEvent/report.gsp | 166 +
grails-app/views/featureEvent/show.gsp | 161 +
grails-app/views/featureType/_form.gsp | 40 +
grails-app/views/featureType/create.gsp | 38 +
grails-app/views/featureType/edit.gsp | 41 +
grails-app/views/featureType/index.gsp | 59 +
grails-app/views/featureType/show.gsp | 72 +
grails-app/views/google_analytics.gsp | 26 +
grails-app/views/home/metrics.gsp | 66 +
grails-app/views/home/systemInfo.gsp | 90 +
grails-app/views/index.gsp | 122 +
.../views/jbrowse/chooseOrganismForJbrowse.gsp | 46 +
grails-app/views/layouts/_reportHeader.gsp | 47 +
grails-app/views/layouts/annotator.gsp | 63 +
grails-app/views/layouts/annotator2.gsp | 67 +
grails-app/views/layouts/embedded.gsp | 71 +
grails-app/views/layouts/login.gsp | 89 +
grails-app/views/layouts/main.gsp | 71 +
grails-app/views/layouts/oldlook.gsp | 64 +
grails-app/views/layouts/report.gsp | 67 +
grails-app/views/login/doLogin.gsp | 109 +
grails-app/views/menu.gsp | 43 +
grails-app/views/organism/_summaryEntry.gsp | 49 +
grails-app/views/organism/report.gsp | 38 +
grails-app/views/proxy/_form.gsp | 41 +
grails-app/views/proxy/create.gsp | 38 +
grails-app/views/proxy/edit.gsp | 41 +
grails-app/views/proxy/index.gsp | 73 +
grails-app/views/proxy/show.gsp | 82 +
grails-app/views/sequence/index.gsp | 194 +
grails-app/views/sequence/permissions.gsp | 50 +
grails-app/views/sequence/report.gsp | 109 +
grails-app/views/sequence/singleUser.gsp | 69 +
grails-app/views/sequence/websocketTest.gsp | 91 +
grails-app/views/webServices/index.gsp | 171 +
grails-app/views/web_services.gsp | 2176 +++
grailsw | 363 +
grailsw.bat | 186 +
gwt-sdk/gwt-dev.jar | Bin 0 -> 38520843 bytes
gwt-sdk/gwt-user.jar | Bin 0 -> 32026261 bytes
gwt-sdk/validation-api-1.0.0.GA-sources.jar | Bin 0 -> 65220 bytes
gwt-sdk/validation-api-1.0.0.GA.jar | Bin 0 -> 47433 bytes
index.html | 10 +
install_jbrowse.sh | 36 +
lib/gbol/resources/1.0/resources-1.0.jar | Bin 0 -> 900 bytes
lib/gwt/gwt-servlet-deps.jar | Bin 0 -> 276574 bytes
lib/gwt/gwt-servlet.jar | Bin 0 -> 9426252 bytes
lib/gwt/gwtbootstrap3-0.9.4.jar | Bin 0 -> 1635022 bytes
lib/gwt/gwtbootstrap3-extras-0.9.4.jar | Bin 0 -> 1218547 bytes
package.json | 33 +
sample-docker-apollo-config.groovy | 3 +
sample-h2-apollo-config.groovy | 111 +
sample-mysql-apollo-config.groovy | 110 +
sample-postgres-apollo-config.groovy | 158 +
scripts/_Events.groovy | 202 +
scripts/chado-schema-with-ontologies.sql.gz | Bin 0 -> 5358015 bytes
scripts/clean_organism.sh | 24 +
scripts/copy_client.sh | 10 +
scripts/delete_all_features.sh | 20 +
scripts/delete_only_features.sh | 19 +
scripts/load_chado_schema.sh | 147 +
scripts/print_all_features.sh | 34 +
scripts/version-template.jsp | 1 +
settings.gradle | 19 +
setup.py | 0
.../org/bbop/apollo/ConfigurableFeature.groovy | 20 +
src/groovy/org/bbop/apollo/CvTermStringEnum.groovy | 17 +
.../org/bbop/apollo/DefaultPaddingStrategy.groovy | 10 +
.../bbop/apollo/FeaturePositionComparator.groovy | 51 +
src/groovy/org/bbop/apollo/FlankingRegion.groovy | 17 +
src/groovy/org/bbop/apollo/FormatUtil.groovy | 78 +
src/groovy/org/bbop/apollo/GFF3Entry.groovy | 124 +
.../org/bbop/apollo/LeftPaddingStrategy.groovy | 15 +
.../org/bbop/apollo/LetterPaddingStrategy.groovy | 18 +
src/groovy/org/bbop/apollo/Ontological.groovy | 11 +
src/groovy/org/bbop/apollo/PaddingStrategy.groovy | 9 +
src/groovy/org/bbop/apollo/PhoneHomeEnum.groovy | 31 +
src/groovy/org/bbop/apollo/TermTypeEnum.groovy | 12 +
.../alteration/SequenceAlterationInContext.groovy | 16 +
.../org/bbop/apollo/event/AnnotationEvent.groovy | 33 +
.../apollo/event/AnnotationEventListener.groovy | 9 +
.../bbop/apollo/event/AnnotationListener.groovy | 9 +
.../org/bbop/apollo/filter/Cds3Filter.groovy | 28 +
.../org/bbop/apollo/filter/FeatureFilter.groovy | 13 +
.../org/bbop/apollo/filter/StopCodonFilter.groovy | 27 +
.../bbop/apollo/history/FeatureEventView.groovy | 16 +
.../bbop/apollo/history/FeatureOperation.groovy | 34 +
.../org/bbop/apollo/operation/OperationEnum.groovy | 43 +
.../org/bbop/apollo/preference/OrganismDTO.groovy | 8 +
.../org/bbop/apollo/preference/SequenceDTO.groovy | 12 +
.../org/bbop/apollo/preference/UserDTO.groovy | 7 +
.../preference/UserOrganismPreferenceDTO.groovy | 43 +
.../apollo/projection/AbstractProjection.groovy | 21 +
.../org/bbop/apollo/projection/Coordinate.groovy | 35 +
.../projection/DiscontinuousProjection.groovy | 121 +
.../DiscontinuousProjectionFactory.groovy | 36 +
.../projection/DuplicateTrackProjection.groovy | 17 +
.../org/bbop/apollo/projection/Projection.groovy | 27 +
.../bbop/apollo/projection/RefSeqProjector.groovy | 15 +
.../bbop/apollo/projection/ReferenceTrack.groovy | 11 +
.../apollo/projection/ReverseProjection.groovy | 29 +
src/groovy/org/bbop/apollo/projection/Track.groovy | 44 +
.../bbop/apollo/projection/TrackProjector.groovy | 9 +
.../org/bbop/apollo/report/AnnotatorSummary.groovy | 15 +
.../apollo/report/OrganismPermissionSummary.groovy | 12 +
.../org/bbop/apollo/report/OrganismSummary.groovy | 36 +
.../bbop/apollo/report/PerformanceMetric.groovy | 13 +
.../org/bbop/apollo/report/SequenceSummary.groovy | 15 +
.../org/bbop/apollo/sequence/DownloadFile.groovy | 10 +
.../org/bbop/apollo/sequence/Overlapper.groovy | 13 +
src/groovy/org/bbop/apollo/sequence/Range.groovy | 25 +
.../org/bbop/apollo/sequence/SequenceDTO.groovy | 11 +
.../apollo/sequence/SequenceLocationDTO.groovy | 27 +
.../sequence/SequenceTranslationHandler.groovy | 230 +
.../sequence/StandardTranslationTable.groovy | 86 +
src/groovy/org/bbop/apollo/sequence/Strand.groovy | 36 +
.../bbop/apollo/sequence/TranslationTable.groovy | 93 +
.../org/bbop/apollo/sequence/search/Alignment.java | 9 +
.../sequence/search/AlignmentParsingException.java | 11 +
.../apollo/sequence/search/SequenceSearchTool.java | 22 +
.../search/SequenceSearchToolException.java | 15 +
.../sequence/search/blast/BlastAlignment.java | 135 +
.../sequence/search/blast/BlastCommandLine.java | 156 +
.../search/blast/TabDelimittedAlignment.java | 43 +
.../sequence/search/blat/BlatCommandLine.java | 153 +
.../BlatCommandLineNucleotideToNucleotide.java | 5 +
.../blat/BlatCommandLineProteinToNucleotide.java | 9 +
.../org/bbop/apollo/track/RenderObject.groovy | 15 +
src/gwt/org/bbop/apollo/gwt/Annotator.gwt.xml | 43 +
.../gwt/client/AnnotationContainerWidget.java | 43 +
src/gwt/org/bbop/apollo/gwt/client/Annotator.java | 170 +
.../org/bbop/apollo/gwt/client/AnnotatorPanel.java | 836 +
.../bbop/apollo/gwt/client/AnnotatorPanel.ui.xml | 175 +
.../org/bbop/apollo/gwt/client/ErrorDialog.java | 57 +
.../bbop/apollo/gwt/client/ExonDetailPanel.java | 411 +
.../bbop/apollo/gwt/client/ExonDetailPanel.ui.xml | 89 +
.../org/bbop/apollo/gwt/client/ExportPanel.java | 298 +
.../bbop/apollo/gwt/client/GeneDetailPanel.java | 135 +
.../bbop/apollo/gwt/client/GeneDetailPanel.ui.xml | 72 +
src/gwt/org/bbop/apollo/gwt/client/GroupPanel.java | 522 +
.../org/bbop/apollo/gwt/client/GroupPanel.ui.xml | 144 +
src/gwt/org/bbop/apollo/gwt/client/LinkDialog.java | 31 +
.../org/bbop/apollo/gwt/client/LoadingDialog.java | 44 +
.../org/bbop/apollo/gwt/client/LoginDialog.java | 101 +
.../org/bbop/apollo/gwt/client/LoginDialog.ui.xml | 49 +
src/gwt/org/bbop/apollo/gwt/client/MainPanel.java | 1138 ++
.../org/bbop/apollo/gwt/client/MainPanel.ui.xml | 191 +
.../org/bbop/apollo/gwt/client/MutableBoolean.java | 21 +
.../org/bbop/apollo/gwt/client/OrganismPanel.java | 486 +
.../bbop/apollo/gwt/client/OrganismPanel.ui.xml | 116 +
.../bbop/apollo/gwt/client/PreferencePanel.java | 103 +
.../bbop/apollo/gwt/client/PreferencePanel.ui.xml | 66 +
.../apollo/gwt/client/ReferenceSequenceOracle.java | 74 +
.../org/bbop/apollo/gwt/client/RegisterDialog.java | 144 +
.../apollo/gwt/client/RepeatRegionDetailPanel.java | 117 +
.../gwt/client/RepeatRegionDetailPanel.ui.xml | 64 +
.../org/bbop/apollo/gwt/client/SequencePanel.java | 453 +
.../bbop/apollo/gwt/client/SequencePanel.ui.xml | 218 +
src/gwt/org/bbop/apollo/gwt/client/TrackPanel.java | 501 +
.../org/bbop/apollo/gwt/client/TrackPanel.ui.xml | 120 +
.../apollo/gwt/client/TranscriptDetailPanel.java | 124 +
.../apollo/gwt/client/TranscriptDetailPanel.ui.xml | 74 +
.../org/bbop/apollo/gwt/client/UrlDialogBox.java | 41 +
src/gwt/org/bbop/apollo/gwt/client/UserPanel.java | 718 +
.../org/bbop/apollo/gwt/client/UserPanel.ui.xml | 181 +
.../apollo/gwt/client/WebApolloSimplePager.java | 37 +
.../gwt/client/comparators/AlphanumericSorter.java | 96 +
.../bbop/apollo/gwt/client/dto/AnnotationInfo.java | 149 +
.../gwt/client/dto/AnnotationInfoConverter.java | 72 +
.../apollo/gwt/client/dto/AppInfoConverter.java | 33 +
.../bbop/apollo/gwt/client/dto/AppStateInfo.java | 95 +
.../org/bbop/apollo/gwt/client/dto/ExportInfo.java | 37 +
.../org/bbop/apollo/gwt/client/dto/GroupInfo.java | 118 +
.../client/dto/GroupOrganismPermissionInfo.java | 39 +
.../org/bbop/apollo/gwt/client/dto/HasJSON.java | 13 +
.../bbop/apollo/gwt/client/dto/OrganismInfo.java | 184 +
.../gwt/client/dto/OrganismInfoConverter.java | 113 +
.../gwt/client/dto/OrganismPermissionInfo.java | 76 +
.../bbop/apollo/gwt/client/dto/SequenceInfo.java | 140 +
.../gwt/client/dto/SequenceInfoConverter.java | 46 +
.../org/bbop/apollo/gwt/client/dto/TrackInfo.java | 122 +
.../org/bbop/apollo/gwt/client/dto/UserInfo.java | 198 +
.../apollo/gwt/client/dto/UserInfoConverter.java | 112 +
.../gwt/client/dto/UserOrganismPermissionInfo.java | 38 +
.../client/event/AnnotationInfoChangeEvent.java | 53 +
.../event/AnnotationInfoChangeEventHandler.java | 13 +
.../bbop/apollo/gwt/client/event/ExportEvent.java | 49 +
.../gwt/client/event/ExportEventHandler.java | 13 +
.../apollo/gwt/client/event/GroupChangeEvent.java | 69 +
.../gwt/client/event/GroupChangeEventHandler.java | 12 +
.../gwt/client/event/OrganismChangeEvent.java | 74 +
.../client/event/OrganismChangeEventHandler.java | 13 +
.../apollo/gwt/client/event/UserChangeEvent.java | 89 +
.../gwt/client/event/UserChangeEventHandler.java | 12 +
.../org/bbop/apollo/gwt/client/resources/Table.css | 141 +
.../gwt/client/resources/TableResources.java | 18 +
.../org/bbop/apollo/gwt/client/resources/Tree.css | 83 +
.../apollo/gwt/client/resources/TreeResources.java | 9 +
.../gwt/client/rest/AnnotationRestService.java | 30 +
.../apollo/gwt/client/rest/GroupRestService.java | 193 +
.../gwt/client/rest/OrganismRestService.java | 129 +
.../bbop/apollo/gwt/client/rest/RestService.java | 61 +
.../gwt/client/rest/SequenceRestService.java | 146 +
.../apollo/gwt/client/rest/UserRestService.java | 252 +
src/gwt/org/bbop/apollo/gwt/public/theme.css | 66 +
.../apollo/gwt/shared/ClientTokenGenerator.java | 30 +
.../bbop/apollo/gwt/shared/FeatureStringEnum.java | 166 +
.../org/bbop/apollo/gwt/shared/PermissionEnum.java | 72 +
.../apollo/gwt/shared/track/NclistColumnEnum.java | 37 +
.../bbop/apollo/gwt/shared/track/TrackIndex.java | 194 +
.../org/bbop/apollo/AnnotationException.groovy | 10 +
src/java/org/bbop/apollo/ImprovedH2Dialect.java | 19 +
.../org/bbop/apollo/ImprovedPostgresDialect.java | 19 +
src/java/org/bbop/apollo/Pair.java | 29 +
.../org/bbop/apollo/PermissionException.groovy | 10 +
src/templates/war/web.xml | 92 +
.../client/data/MAKER/Group1.33_Amel_4.5.maker.gff | 12 +
.../Group1.33_Amel_4.5.maker.jbrowse.expected.json | 44 +
...Amel_4.5.maker.jbrowse.expected_PRETTIFIED.json | 43 +
...roup1.33_Amel_4.5.maker.webapollo.expected.json | 45 +
test/client/data/heterozygous_snv.vcf | 9 +
test/client/js_tests/index.html | 55 +
test/client/js_tests/lib/jasmine-1.2.0/MIT.LICENSE | 20 +
.../js_tests/lib/jasmine-1.2.0/jasmine-html.js | 616 +
test/client/js_tests/lib/jasmine-1.2.0/jasmine.css | 81 +
test/client/js_tests/lib/jasmine-1.2.0/jasmine.js | 2529 +++
test/client/js_tests/spec/GFF3toJbrowseJsonSpec.js | 135 +
test/client/js_tests/spec/JSONUtilsSpec.js | 130 +
test/client/selenium_tests/lib/WebApolloTest.py | 35 +
test/client/selenium_tests/lib/__init__.py | 2 +
test/client/selenium_tests/pythium_test.py | 29 +
test/config/mysql.travis | 21 +
test/config/postgres.travis | 18 +
.../org/bbop/apollo/AbstractIntegrationSpec.groovy | 78 +
.../bbop/apollo/CdsServiceIntegrationSpec.groovy | 68 +
.../ChadoHandlerServiceIntegrationSpec.groovy | 358 +
.../bbop/apollo/ExonServiceIntegrationSpec.groovy | 97 +
.../FastaHandlerServiceIntegrationSpec.groovy | 48 +
.../FeatureEventServiceIntegrationSpec.groovy | 1454 ++
...eatureRelationshipServiceIntegrationSpec.groovy | 83 +
.../apollo/FeatureServiceIntegrationSpec.groovy | 318 +
.../Gff3HandlerServiceIntegrationSpec.groovy | 61 +
.../apollo/OrganismServiceIntegrationSpec.groovy | 55 +
.../apollo/OverlapperServiceIntegrationSpec.groovy | 247 +
.../apollo/PhoneHomeServiceIntegrationSpec.groovy | 15 +
.../apollo/PreferenceServiceIntegrationSpec.groovy | 1020 ++
.../RequestHandlingServiceIntegrationSpec.groovy | 3899 +++++
.../apollo/SequenceServiceIntegrationSpec.groovy | 352 +
.../seq/f78/c6f/0c/Group1.10-0.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-1.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-10.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-11.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-12.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-13.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-14.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-15.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-16.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-17.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-18.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-19.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-2.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-20.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-21.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-22.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-23.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-24.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-25.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-26.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-27.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-28.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-29.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-3.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-30.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-31.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-32.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-33.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-34.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-35.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-36.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-37.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-38.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-39.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-4.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-40.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-41.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-42.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-43.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-44.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-45.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-46.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-47.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-48.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-49.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-5.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-50.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-51.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-52.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-53.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-54.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-55.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-56.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-57.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-58.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-59.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-6.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-60.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-61.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-62.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-63.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-64.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-65.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-66.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-67.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-68.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-69.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-7.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-70.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-8.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-9.txt | 1 +
.../sequences/honeybee-Group1.10/seq/refSeqs.json | 1 +
.../sequences/honeybee-Group1.10/trackList.json | 1 +
.../sequences/honeybee-Group1.10/tracks.conf | 0
.../honeybee-tracks/seq/2ac/141/c6/Group11.4-0.txt | 1 +
.../honeybee-tracks/seq/2ac/141/c6/Group11.4-1.txt | 1 +
.../honeybee-tracks/seq/2ac/141/c6/Group11.4-2.txt | 1 +
.../honeybee-tracks/seq/2ac/141/c6/Group11.4-3.txt | 1 +
.../honeybee-tracks/seq/7cf/4ac/72/GroupUn87-0.txt | 1 +
.../honeybee-tracks/seq/7cf/4ac/72/GroupUn87-1.txt | 1 +
.../honeybee-tracks/seq/7cf/4ac/72/GroupUn87-2.txt | 1 +
.../honeybee-tracks/seq/7cf/4ac/72/GroupUn87-3.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-0.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-1.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-10.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-11.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-12.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-13.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-14.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-15.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-16.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-17.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-18.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-19.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-2.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-20.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-21.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-22.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-23.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-24.txt | 1 +
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.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-4.txt | 1 +
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.../seq/f78/c6f/0c/Group1.10-48.txt | 1 +
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.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-5.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-50.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-51.txt | 1 +
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.../seq/f78/c6f/0c/Group1.10-59.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-6.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-60.txt | 1 +
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.../seq/f78/c6f/0c/Group1.10-66.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-67.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-68.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-69.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-7.txt | 1 +
.../seq/f78/c6f/0c/Group1.10-70.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-8.txt | 1 +
.../honeybee-tracks/seq/f78/c6f/0c/Group1.10-9.txt | 1 +
.../sequences/honeybee-tracks/trackList.json | 1 +
.../Group1.1/hist-100000-0.json | 1 +
.../Official Gene Set v3.2/Group1.1/names.txt | 56 +
.../Official Gene Set v3.2/Group1.1/trackData.json | 1 +
.../Group1.10/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/Group1.10/lf-1.json | 1 +
.../Official Gene Set v3.2/Group1.10/lf-2.json | 1 +
.../Official Gene Set v3.2/Group1.10/lf-3.json | 1 +
.../Official Gene Set v3.2/Group1.10/names.txt | 143 +
.../Group1.10/trackData.json | 1 +
.../Group11.4/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/Group11.4/names.txt | 6 +
.../Group11.4/trackData.json | 1 +
.../Group11.6/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/Group11.6/lf-1.json | 1 +
.../Official Gene Set v3.2/Group11.6/lf-2.json | 1 +
.../Official Gene Set v3.2/Group11.6/names.txt | 109 +
.../Group11.6/trackData.json | 1 +
.../Group2.19/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-1.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-2.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-3.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-4.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-5.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-6.json | 1 +
.../Official Gene Set v3.2/Group2.19/lf-7.json | 1 +
.../Official Gene Set v3.2/Group2.19/names.txt | 313 +
.../Group2.19/trackData.json | 1 +
.../Group4.1/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/Group4.1/names.txt | 29 +
.../Official Gene Set v3.2/Group4.1/trackData.json | 1 +
.../Group6.10/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/Group6.10/names.txt | 35 +
.../Group6.10/trackData.json | 1 +
.../GroupUn87/hist-50000-0.json | 1 +
.../Official Gene Set v3.2/GroupUn87/names.txt | 4 +
.../GroupUn87/trackData.json | 1 +
.../resources/sequences/yeast/.htaccess | 10 +
.../resources/sequences/yeast/names/0.json | 1 +
.../resources/sequences/yeast/names/1.json | 1 +
.../resources/sequences/yeast/names/2.json | 1 +
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.../resources/sequences/yeast/names/9.json | 1 +
.../resources/sequences/yeast/names/a.json | 1 +
.../resources/sequences/yeast/names/b.json | 1 +
.../resources/sequences/yeast/names/c.json | 1 +
.../resources/sequences/yeast/names/d.json | 1 +
.../resources/sequences/yeast/names/e.json | 1 +
.../resources/sequences/yeast/names/f.json | 1 +
.../resources/sequences/yeast/names/meta.json | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-0.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-1.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-10.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-11.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-2.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-3.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-4.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-5.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-6.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-7.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-8.txt | 1 +
.../sequences/yeast/seq/5c1/aff/29/chrI-9.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-0.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-1.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-10.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-11.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-12.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-13.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-14.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-15.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-16.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-17.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-18.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-19.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-2.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-20.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-21.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-22.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-23.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-24.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-25.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-26.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-27.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-28.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-29.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-3.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-30.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-31.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-32.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-33.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-34.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-35.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-36.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-37.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-38.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-39.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-4.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-40.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-5.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-6.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-7.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-8.txt | 1 +
.../sequences/yeast/seq/9fe/c94/2a/chrII-9.txt | 1 +
.../resources/sequences/yeast/seq/refSeqs.json | 1 +
.../resources/sequences/yeast/trackList.json | 71 +
.../resources/sequences/yeast/tracks.conf | 0
.../yeast/tracks/Genes/chrI/hist-5000-0.json | 1 +
.../sequences/yeast/tracks/Genes/chrI/names.txt | 117 +
.../yeast/tracks/Genes/chrI/trackData.json | 1 +
.../yeast/tracks/Genes/chrII/hist-10000-0.json | 1 +
.../yeast/tracks/Genes/chrII/hist-5000-0.json | 1 +
.../sequences/yeast/tracks/Genes/chrII/lf-1.json | 1 +
.../sequences/yeast/tracks/Genes/chrII/lf-2.json | 1 +
.../sequences/yeast/tracks/Genes/chrII/lf-3.json | 1 +
.../sequences/yeast/tracks/Genes/chrII/lf-4.json | 1 +
.../sequences/yeast/tracks/Genes/chrII/names.txt | 456 +
.../yeast/tracks/Genes/chrII/trackData.json | 1 +
.../resources/track-data/inputNcList.json | 357 +
.../resources/track-data/mouseMsx2.json | 156 +
.../resources/track-data/trackClasses.json | 1 +
.../resources/track-data/wormGeneflp-1.json | 1258 ++
.../apollo/AbstractApolloControllerSpec.groovy | 20 +
.../bbop/apollo/AnnotationEditorServiceSpec.groovy | 30 +
.../apollo/AvailableStatusControllerSpec.groovy | 151 +
.../bbop/apollo/CannedCommentControllerSpec.groovy | 151 +
.../org/bbop/apollo/CannedKeyControllerSpec.groovy | 152 +
.../bbop/apollo/CannedValueControllerSpec.groovy | 152 +
.../org/bbop/apollo/ChadoHandlerServiceSpec.groovy | 20 +
.../bbop/apollo/FeatureEventControllerSpec.groovy | 156 +
.../org/bbop/apollo/FeatureEventServiceSpec.groovy | 1201 ++
.../apollo/FeatureRelationshipServiceSpec.groovy | 71 +
.../unit/org/bbop/apollo/FeatureServiceSpec.groovy | 64 +
test/unit/org/bbop/apollo/FeatureSpec.groovy | 130 +
.../bbop/apollo/FeatureTypeControllerSpec.groovy | 155 +
.../org/bbop/apollo/FeatureTypeServiceSpec.groovy | 36 +
.../org/bbop/apollo/Gff3HandlerServiceSpec.groovy | 48 +
.../unit/org/bbop/apollo/JbrowseServiceSpec.groovy | 44 +
test/unit/org/bbop/apollo/NameServiceSpec.groovy | 29 +
.../org/bbop/apollo/PermissionServiceSpec.groovy | 139 +
test/unit/org/bbop/apollo/ProjectionSpec.groovy | 187 +
.../org/bbop/apollo/ProxyControllerSpec.groovy | 154 +
.../bbop/apollo/RequestHandlingServiceSpec.groovy | 30 +
test/unit/org/bbop/apollo/SvgServiceSpec.groovy | 20 +
test/unit/org/bbop/apollo/TrackServiceSpec.groovy | 129 +
.../org/bbop/apollo/TranslationTableSpec.groovy | 73 +
test/unit/org/bbop/apollo/UserSpec.groovy | 63 +
tools/cleanup/remove_temporary_files.sh | 30 +
.../data/add_features_from_gff3_to_annotations.pl | 920 +
.../add_transcripts_from_gff3_to_annotations.pl | 749 +
web-app/WEB-INF/applicationContext.xml | 31 +
web-app/WEB-INF/sitemesh.xml | 14 +
web-app/WEB-INF/tld/c.tld | 572 +
web-app/WEB-INF/tld/fmt.tld | 671 +
web-app/WEB-INF/tld/grails.tld | 550 +
web-app/WEB-INF/tld/spring-form.tld | 2411 +++
web-app/WEB-INF/tld/spring.tld | 457 +
web-app/css/Annotator.css | 42 +
web-app/css/chado.css | 20 +
web-app/css/login.css | 22 +
web-app/css/search_sequence.css | 78 +
web-app/css/ui-layout.css | 49 +
web-app/css/web_api_stylesheet.css | 31 +
web-app/images/ApolloLogo_100x36.png | Bin 0 -> 3071 bytes
web-app/images/loading.gif | Bin 0 -> 673 bytes
web-app/images/qrcode.26636394.png | Bin 0 -> 377 bytes
web-app/images/sign_in_green.png | Bin 0 -> 1803 bytes
web-app/images/user_icon_16px.png | Bin 0 -> 470 bytes
web-app/images/webapollo_favicon.ico | Bin 0 -> 1150 bytes
web-app/js/DataTables-plugins/dataTablesPlugins.js | 36 +
web-app/js/DataTables/css/demo_table.css | 577 +
web-app/js/DataTables/images/Sorting icons.psd | Bin 0 -> 27490 bytes
web-app/js/DataTables/images/back_disabled.png | Bin 0 -> 1361 bytes
web-app/js/DataTables/images/back_enabled.png | Bin 0 -> 1379 bytes
.../js/DataTables/images/back_enabled_hover.png | Bin 0 -> 1375 bytes
web-app/js/DataTables/images/favicon.ico | Bin 0 -> 894 bytes
web-app/js/DataTables/images/forward_disabled.png | Bin 0 -> 1363 bytes
web-app/js/DataTables/images/forward_enabled.png | Bin 0 -> 1380 bytes
.../js/DataTables/images/forward_enabled_hover.png | Bin 0 -> 1379 bytes
web-app/js/DataTables/images/sort_asc.png | Bin 0 -> 1118 bytes
web-app/js/DataTables/images/sort_asc_disabled.png | Bin 0 -> 1050 bytes
web-app/js/DataTables/images/sort_both.png | Bin 0 -> 1136 bytes
web-app/js/DataTables/images/sort_desc.png | Bin 0 -> 1127 bytes
.../js/DataTables/images/sort_desc_disabled.png | Bin 0 -> 1045 bytes
web-app/js/DataTables/js/jquery.dataTables.js | 12099 ++++++++++++++
web-app/js/DataTables/js/jquery.dataTables.min.js | 155 +
web-app/js/DataTables/js/jquery.js | 2 +
web-app/js/jQueryUtils.js | 11 +
.../images/ui-bg_flat_0_aaaaaa_40x100.png | Bin 0 -> 180 bytes
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.../images/ui-bg_glass_55_fbf9ee_1x400.png | Bin 0 -> 120 bytes
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.../ui-bg_highlight-soft_75_cccccc_1x100.png | Bin 0 -> 101 bytes
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.../images/ui-icons_888888_256x240.png | Bin 0 -> 4369 bytes
.../images/ui-icons_cd0a0a_256x240.png | Bin 0 -> 4369 bytes
web-app/js/jquery-ui-menubar/jquery-1.8.2.js | 9440 +++++++++++
.../js/jquery-ui-menubar/jquery.ui.accordion.css | 16 +
web-app/js/jquery-ui-menubar/jquery.ui.all.css | 12 +
.../jquery-ui-menubar/jquery.ui.autocomplete.css | 18 +
web-app/js/jquery-ui-menubar/jquery.ui.base.css | 26 +
web-app/js/jquery-ui-menubar/jquery.ui.button.css | 40 +
web-app/js/jquery-ui-menubar/jquery.ui.button.js | 415 +
web-app/js/jquery-ui-menubar/jquery.ui.core.css | 39 +
web-app/js/jquery-ui-menubar/jquery.ui.core.js | 343 +
.../js/jquery-ui-menubar/jquery.ui.datepicker.css | 67 +
web-app/js/jquery-ui-menubar/jquery.ui.dialog.css | 22 +
web-app/js/jquery-ui-menubar/jquery.ui.dialog.js | 847 +
web-app/js/jquery-ui-menubar/jquery.ui.menu.css | 30 +
web-app/js/jquery-ui-menubar/jquery.ui.menu.js | 628 +
web-app/js/jquery-ui-menubar/jquery.ui.menubar.css | 15 +
web-app/js/jquery-ui-menubar/jquery.ui.menubar.js | 327 +
web-app/js/jquery-ui-menubar/jquery.ui.position.js | 517 +
.../js/jquery-ui-menubar/jquery.ui.progressbar.css | 12 +
.../js/jquery-ui-menubar/jquery.ui.resizable.css | 21 +
.../js/jquery-ui-menubar/jquery.ui.selectable.css | 11 +
web-app/js/jquery-ui-menubar/jquery.ui.slider.css | 25 +
web-app/js/jquery-ui-menubar/jquery.ui.spinner.css | 24 +
web-app/js/jquery-ui-menubar/jquery.ui.tabs.css | 18 +
web-app/js/jquery-ui-menubar/jquery.ui.theme.css | 247 +
web-app/js/jquery-ui-menubar/jquery.ui.tooltip.css | 22 +
web-app/js/jquery-ui-menubar/jquery.ui.widget.js | 502 +
web-app/js/restapidoc/restapidoc.json | 6886 ++++++++
.../ncbi_10_translation_table.txt | 1 +
.../ncbi_11_translation_table.txt | 6 +
.../ncbi_12_translation_table.txt | 1 +
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.../ncbi_14_translation_table.txt | 5 +
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.../ncbi_5_translation_table.txt | 5 +
.../ncbi_6_translation_table.txt | 2 +
.../ncbi_9_translation_table.txt | 5 +
wrapper/grails-wrapper-runtime-2.5.5.jar | Bin 0 -> 6110 bytes
wrapper/grails-wrapper.properties | 1 +
1410 files changed, 254513 insertions(+), 66 deletions(-)
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