From a45774ee31d9f35d4eff46d54d7deab719afb092 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 27 Sep 2011 09:15:20 +0100 Subject: [PATCH] apply version 2.7 copyright --- RELEASE | 4 +-- THIRDPARTYLIBS | 5 +++ build.xml | 4 +-- doc/AddingGroovySupport.html | 4 +-- doc/building.html | 4 +-- doc/developing.html | 4 +-- doc/index.html | 4 +-- doc/newdmobj.html | 4 +-- examples/javascript/deployJava.js | 5 ++- examples/javascript/jalview.js | 17 ++++++++++ help/helpTOC.xml | 4 +-- help/html/calculations/consensus.html | 4 +-- help/html/calculations/conservation.html | 4 +-- help/html/calculations/pairwise.html | 4 +-- help/html/calculations/pca.html | 4 +-- help/html/calculations/quality.html | 4 +-- help/html/calculations/recoverInputdata.html | 4 +-- help/html/calculations/redundancy.html | 4 +-- help/html/calculations/sorting.html | 4 +-- help/html/calculations/tree.html | 4 +-- help/html/calculations/treeviewer.html | 4 +-- help/html/colourSchemes/abovePID.html | 4 +-- 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+-- help/html/index.html | 4 +-- help/html/io/export.html | 4 +-- help/html/io/fileformats.html | 4 +-- help/html/io/index.html | 4 +-- help/html/io/modellerpir.html | 4 +-- help/html/jalviewjnlp.html | 4 +-- help/html/keys.html | 4 +-- help/html/memory.html | 4 +-- help/html/menus/alignmentMenu.html | 4 +-- help/html/menus/alwannotations.html | 4 +-- help/html/menus/alwcalculate.html | 4 +-- help/html/menus/alwcolour.html | 4 +-- help/html/menus/alwedit.html | 4 +-- help/html/menus/alwfile.html | 4 +-- help/html/menus/alwformat.html | 4 +-- help/html/menus/alwselect.html | 4 +-- help/html/menus/alwview.html | 4 +-- help/html/menus/desktopMenu.html | 4 +-- help/html/menus/index.html | 4 +-- help/html/menus/popupMenu.html | 4 +-- help/html/menus/wsmenu.html | 4 +-- help/html/misc/aaproperties.html | 4 +-- help/html/misc/aminoAcids.html | 4 +-- help/html/misc/geneticCode.html | 4 +-- help/html/privacy.html | 4 +-- help/html/releases.html | 4 +-- help/html/vamsas/index.html | 4 +-- help/html/webServices/JABAWS.html | 4 +-- help/html/webServices/dbreffetcher.html | 4 +-- help/html/webServices/index.html | 4 +-- help/html/webServices/jnet.html | 4 +-- help/html/webServices/msaclient.html | 4 +-- help/html/webServices/shmr.html | 4 +-- help/html/webServices/urllinks.html | 4 +-- help/html/webServices/webServicesParams.html | 4 +-- help/html/webServices/webServicesPrefs.html | 4 +-- help/html/whatsNew.html | 4 +-- jalview-jalopy.xml | 4 +-- nbbuild.xml | 19 ++++++++++- nbproject/genfiles.properties | 17 ++++++++++ nbproject/project.properties | 17 ++++++++++ nbproject/project.xml | 19 ++++++++++- resources/embl_mapping.xml | 4 +-- resources/uniprot_mapping.xml | 4 +-- schemas/JalviewUserColours.xsd | 4 +-- schemas/JalviewWsParamSet.xsd | 4 +-- schemas/castor-mapping.xsd | 4 +-- schemas/jalview.nodesc.properties | 17 ++++++++++ schemas/jalview.properties | 17 ++++++++++ schemas/jalview.xsd | 4 +-- schemas/jalviewJvV1.xsd | 4 +-- schemas/vamsas.xsd | 4 +-- 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++++++++++ .../schemabinding/version2/MapListFrom.java | 17 ++++++++++ src/jalview/schemabinding/version2/MapListTo.java | 17 ++++++++++ .../schemabinding/version2/MapListType.java | 17 ++++++++++ src/jalview/schemabinding/version2/Mapping.java | 17 ++++++++++ .../schemabinding/version2/MappingChoice.java | 17 ++++++++++ src/jalview/schemabinding/version2/OtherData.java | 17 ++++++++++ src/jalview/schemabinding/version2/Pdbentry.java | 17 ++++++++++ .../schemabinding/version2/PdbentryItem.java | 17 ++++++++++ src/jalview/schemabinding/version2/Pdbids.java | 17 ++++++++++ src/jalview/schemabinding/version2/Property.java | 17 ++++++++++ src/jalview/schemabinding/version2/Sequence.java | 17 ++++++++++ .../schemabinding/version2/SequenceSet.java | 17 ++++++++++ .../version2/SequenceSetProperties.java | 17 ++++++++++ .../schemabinding/version2/SequenceType.java | 17 ++++++++++ src/jalview/schemabinding/version2/Setting.java | 17 ++++++++++ .../schemabinding/version2/StructureState.java | 17 ++++++++++ .../schemabinding/version2/ThresholdLine.java | 17 ++++++++++ src/jalview/schemabinding/version2/Tree.java | 17 ++++++++++ .../schemabinding/version2/UserColourScheme.java | 17 ++++++++++ .../schemabinding/version2/UserColours.java | 17 ++++++++++ src/jalview/schemabinding/version2/VAMSAS.java | 17 ++++++++++ .../schemabinding/version2/VamsasModel.java | 17 ++++++++++ src/jalview/schemabinding/version2/Viewport.java | 17 ++++++++++ .../version2/WebServiceParameterSet.java | 17 ++++++++++ .../version2/descriptors/AlcodMapDescriptor.java | 17 ++++++++++ .../version2/descriptors/AlcodonDescriptor.java | 17 ++++++++++ .../descriptors/AlcodonFrameDescriptor.java | 17 ++++++++++ .../descriptors/AnnotationColoursDescriptor.java | 17 ++++++++++ .../version2/descriptors/AnnotationDescriptor.java | 17 ++++++++++ .../descriptors/AnnotationElementDescriptor.java | 17 ++++++++++ .../version2/descriptors/ColourDescriptor.java | 17 ++++++++++ .../version2/descriptors/DBRefDescriptor.java | 17 ++++++++++ .../version2/descriptors/FeatureDescriptor.java | 17 ++++++++++ .../descriptors/FeatureSettingsDescriptor.java | 17 ++++++++++ .../version2/descriptors/FeaturesDescriptor.java | 17 ++++++++++ .../version2/descriptors/GroupDescriptor.java | 17 ++++++++++ .../descriptors/HiddenColumnsDescriptor.java | 17 ++++++++++ .../version2/descriptors/JGroupDescriptor.java | 17 ++++++++++ .../version2/descriptors/JSeqDescriptor.java | 17 ++++++++++ .../descriptors/JalviewModelDescriptor.java | 17 ++++++++++ .../JalviewModelSequenceDescriptor.java | 17 ++++++++++ .../descriptors/JalviewUserColoursDescriptor.java | 17 ++++++++++ .../descriptors/MapListFromDescriptor.java | 17 ++++++++++ .../version2/descriptors/MapListToDescriptor.java | 17 ++++++++++ .../descriptors/MapListTypeDescriptor.java | 17 ++++++++++ .../descriptors/MappingChoiceDescriptor.java | 17 ++++++++++ .../version2/descriptors/MappingDescriptor.java | 17 ++++++++++ .../version2/descriptors/OtherDataDescriptor.java | 17 ++++++++++ .../version2/descriptors/PdbentryDescriptor.java | 17 ++++++++++ .../descriptors/PdbentryItemDescriptor.java | 17 ++++++++++ .../version2/descriptors/PdbidsDescriptor.java | 17 ++++++++++ .../version2/descriptors/PropertyDescriptor.java | 17 ++++++++++ .../version2/descriptors/SequenceDescriptor.java | 17 ++++++++++ .../descriptors/SequenceSetDescriptor.java | 17 ++++++++++ .../SequenceSetPropertiesDescriptor.java | 17 ++++++++++ .../descriptors/SequenceTypeDescriptor.java | 17 ++++++++++ .../version2/descriptors/SettingDescriptor.java | 17 ++++++++++ .../descriptors/StructureStateDescriptor.java | 17 ++++++++++ .../descriptors/ThresholdLineDescriptor.java | 17 ++++++++++ .../version2/descriptors/TreeDescriptor.java | 17 ++++++++++ .../descriptors/UserColourSchemeDescriptor.java | 17 ++++++++++ .../descriptors/UserColoursDescriptor.java | 17 ++++++++++ .../version2/descriptors/VAMSASDescriptor.java | 17 ++++++++++ .../descriptors/VamsasModelDescriptor.java | 17 ++++++++++ .../version2/descriptors/ViewportDescriptor.java | 17 ++++++++++ .../WebServiceParameterSetDescriptor.java | 17 ++++++++++ src/jalview/schemes/AnnotationColourGradient.java | 4 +-- src/jalview/schemes/Blosum62ColourScheme.java | 4 +-- src/jalview/schemes/BuriedColourScheme.java | 4 +-- src/jalview/schemes/ClustalxColourScheme.java | 4 +-- src/jalview/schemes/ColourSchemeI.java | 4 +-- src/jalview/schemes/ColourSchemeProperty.java | 4 +-- src/jalview/schemes/Consensus.java | 4 +-- src/jalview/schemes/GraduatedColor.java | 4 +-- src/jalview/schemes/HelixColourScheme.java | 4 +-- src/jalview/schemes/HydrophobicColourScheme.java | 4 +-- src/jalview/schemes/NucleotideColourScheme.java | 4 +-- src/jalview/schemes/PIDColourScheme.java | 4 +-- src/jalview/schemes/ResidueColourScheme.java | 4 +-- src/jalview/schemes/ResidueProperties.java | 4 +-- src/jalview/schemes/ScoreColourScheme.java | 4 +-- src/jalview/schemes/ScoreMatrix.java | 4 +-- src/jalview/schemes/StrandColourScheme.java | 4 +-- src/jalview/schemes/TaylorColourScheme.java | 4 +-- src/jalview/schemes/TurnColourScheme.java | 4 +-- src/jalview/schemes/UserColourScheme.java | 4 +-- src/jalview/schemes/ZappoColourScheme.java | 4 +-- .../structure/AlignmentViewPanelListener.java | 17 ++++++++++ src/jalview/structure/SelectionListener.java | 4 +-- src/jalview/structure/SelectionSource.java | 4 +-- src/jalview/structure/SequenceListener.java | 4 +-- src/jalview/structure/StructureListener.java | 4 +-- src/jalview/structure/StructureMapping.java | 4 +-- .../structure/StructureMappingcommandSet.java | 17 ++++++++++ .../structure/StructureSelectionManager.java | 4 +-- src/jalview/structure/VamsasListener.java | 4 +-- src/jalview/structure/VamsasSource.java | 17 ++++++++++ src/jalview/util/AWTConsole.java | 4 +-- src/jalview/util/BrowserLauncher.java | 4 +-- src/jalview/util/Comparison.java | 4 +-- src/jalview/util/DBRefUtils.java | 4 +-- src/jalview/util/Format.java | 4 +-- src/jalview/util/GroupUrlLink.java | 4 +-- src/jalview/util/ImageMaker.java | 4 +-- src/jalview/util/MapList.java | 4 +-- src/jalview/util/ParseHtmlBodyAndLinks.java | 17 ++++++++++ src/jalview/util/Platform.java | 4 +-- src/jalview/util/QuickSort.java | 4 +-- src/jalview/util/ShiftList.java | 4 +-- src/jalview/util/TableSorter.java | 4 +-- src/jalview/util/UrlLink.java | 4 +-- src/jalview/util/jarInputStreamProvider.java | 4 +-- src/jalview/ws/AWSThread.java | 4 +-- src/jalview/ws/AWsJob.java | 4 +-- src/jalview/ws/DBRefFetcher.java | 4 +-- src/jalview/ws/DasSequenceFeatureFetcher.java | 4 +-- src/jalview/ws/EnfinEnvision2OneWay.java | 4 +-- src/jalview/ws/JobStateSummary.java | 4 +-- src/jalview/ws/SequenceFetcher.java | 4 +-- src/jalview/ws/WSClient.java | 4 +-- src/jalview/ws/WSClientI.java | 4 +-- src/jalview/ws/WSMenuEntryProviderI.java | 4 +-- src/jalview/ws/dbsources/DasSequenceSource.java | 4 +-- .../ws/dbsources/EbiFileRetrievedProxy.java | 4 +-- src/jalview/ws/dbsources/EmblCdsSouce.java | 4 +-- src/jalview/ws/dbsources/EmblSource.java | 4 +-- src/jalview/ws/dbsources/EmblXmlSource.java | 4 +-- src/jalview/ws/dbsources/GeneDbSource.java | 4 +-- src/jalview/ws/dbsources/Pdb.java | 4 +-- src/jalview/ws/dbsources/Pfam.java | 4 +-- src/jalview/ws/dbsources/PfamFull.java | 4 +-- src/jalview/ws/dbsources/PfamSeed.java | 4 +-- src/jalview/ws/dbsources/Uniprot.java | 4 +-- src/jalview/ws/dbsources/UnprotName.java | 4 +-- .../dbsources/das/DasSequenceSourceListener.java | 4 +-- src/jalview/ws/ebi/EBIFetchClient.java | 4 +-- src/jalview/ws/io/mime/HttpContentHandler.java | 17 ++++++++++ .../ws/io/mime/JalviewMimeContentHandler.java | 17 ++++++++++ src/jalview/ws/io/mime/MimeTypes.java | 17 ++++++++++ src/jalview/ws/jws1/Discoverer.java | 25 ++------------ src/jalview/ws/jws1/JPredClient.java | 4 +-- src/jalview/ws/jws1/JPredThread.java | 4 +-- src/jalview/ws/jws1/JWS1Thread.java | 4 +-- src/jalview/ws/jws1/MsaWSClient.java | 4 +-- src/jalview/ws/jws1/MsaWSThread.java | 24 ++------------ src/jalview/ws/jws1/SeqSearchWSClient.java | 4 +-- src/jalview/ws/jws1/SeqSearchWSThread.java | 24 ++------------ src/jalview/ws/jws1/WS1Client.java | 4 +-- src/jalview/ws/jws1/WSJob.java | 4 +-- src/jalview/ws/jws2/AWS2Thread.java | 4 +-- src/jalview/ws/jws2/JWs2Job.java | 4 +-- src/jalview/ws/jws2/JabaParamStore.java | 4 +-- src/jalview/ws/jws2/JabaPreset.java | 4 +-- src/jalview/ws/jws2/JabaWsServerQuery.java | 17 ++++++++++ src/jalview/ws/jws2/Jws2Client.java | 4 +-- src/jalview/ws/jws2/Jws2Discoverer.java | 4 +-- src/jalview/ws/jws2/MsaWSClient.java | 4 +-- src/jalview/ws/jws2/MsaWSThread.java | 24 ++------------ src/jalview/ws/jws2/ParameterUtils.java | 4 +-- src/jalview/ws/jws2/dm/JabaOption.java | 4 +-- src/jalview/ws/jws2/dm/JabaParameter.java | 4 +-- src/jalview/ws/jws2/dm/JabaValueConstrain.java | 4 +-- src/jalview/ws/jws2/dm/JabaWsParamSet.java | 4 +-- src/jalview/ws/params/ArgumentI.java | 4 +-- .../ws/params/InvalidArgumentException.java | 17 ++++++++++ src/jalview/ws/params/OptionI.java | 4 +-- src/jalview/ws/params/ParamDatastoreI.java | 4 +-- src/jalview/ws/params/ParamManager.java | 4 +-- src/jalview/ws/params/ParameterI.java | 4 +-- src/jalview/ws/params/ValueConstrainI.java | 4 +-- src/jalview/ws/params/WsParamSetI.java | 4 +-- src/jalview/ws/params/simple/BooleanOption.java | 17 ++++++++++ src/jalview/ws/params/simple/IntegerParameter.java | 17 ++++++++++ src/jalview/ws/params/simple/Option.java | 17 ++++++++++ src/jalview/ws/params/simple/Parameter.java | 17 ++++++++++ .../ws/params/simple/StringChoiceParameter.java | 17 ++++++++++ src/jalview/ws/rest/AlignmentProcessor.java | 17 ++++++++++ src/jalview/ws/rest/HttpResultSet.java | 17 ++++++++++ src/jalview/ws/rest/InputType.java | 17 ++++++++++ src/jalview/ws/rest/NoValidInputDataException.java | 17 ++++++++++ src/jalview/ws/rest/RestClient.java | 17 ++++++++++ src/jalview/ws/rest/RestJob.java | 17 ++++++++++ src/jalview/ws/rest/RestJobThread.java | 17 ++++++++++ src/jalview/ws/rest/RestServiceDescription.java | 4 +-- src/jalview/ws/rest/params/Alignment.java | 17 ++++++++++ src/jalview/ws/rest/params/AnnotationFile.java | 17 ++++++++++ src/jalview/ws/rest/params/JobConstant.java | 17 ++++++++++ .../ws/rest/params/SeqGroupIndexVector.java | 17 ++++++++++ src/jalview/ws/rest/params/SeqIdVector.java | 17 ++++++++++ src/jalview/ws/rest/params/SeqVector.java | 17 ++++++++++ src/jalview/ws/rest/params/Tree.java | 17 ++++++++++ src/jalview/ws/seqfetcher/ASequenceFetcher.java | 4 +-- src/jalview/ws/seqfetcher/DbSourceProxy.java | 4 +-- src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 4 +-- src/uk/ac/ebi/picr/model/CrossReference.java | 4 +-- .../ac/ebi/picr/model/CrossReference_Helper.java | 4 +-- src/uk/ac/ebi/picr/model/UPEntry.java | 4 +-- src/uk/ac/ebi/picr/model/UPEntry_Helper.java | 4 +-- src/uk/ac/ebi/www/Data.java | 4 +-- src/uk/ac/ebi/www/InputParams.java | 4 +-- src/uk/ac/ebi/www/WSFile.java | 4 +-- src/uk/ac/ebi/www/WSWUBlast.java | 4 +-- src/uk/ac/ebi/www/WSWUBlastService.java | 4 +-- src/uk/ac/ebi/www/WSWUBlastServiceLocator.java | 4 +-- src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java | 4 +-- .../AccessionMapperBindingStub.java | 4 +-- .../AccessionMapperInterface.java | 4 +-- .../AccessionMapperService.java | 4 +-- .../AccessionMapperServiceLocator.java | 4 +-- src/vamsas/IMsaWS.java | 4 +-- src/vamsas/objects/simple/Alignment.java | 4 +-- src/vamsas/objects/simple/Alignment_Helper.java | 4 +-- src/vamsas/objects/simple/JpredResult.java | 4 +-- src/vamsas/objects/simple/JpredResult_Helper.java | 4 +-- src/vamsas/objects/simple/MsaResult.java | 4 +-- src/vamsas/objects/simple/MsaResult_Helper.java | 4 +-- src/vamsas/objects/simple/Msfalignment.java | 4 +-- src/vamsas/objects/simple/Msfalignment_Helper.java | 4 +-- src/vamsas/objects/simple/Object.java | 4 +-- src/vamsas/objects/simple/Object_Helper.java | 4 +-- src/vamsas/objects/simple/Result.java | 4 +-- src/vamsas/objects/simple/Result_Helper.java | 4 +-- src/vamsas/objects/simple/Secstructpred.java | 4 +-- .../objects/simple/Secstructpred_Helper.java | 4 +-- src/vamsas/objects/simple/SeqSearchResult.java | 4 +-- .../objects/simple/SeqSearchResult_Helper.java | 4 +-- src/vamsas/objects/simple/Sequence.java | 4 +-- src/vamsas/objects/simple/SequenceSet.java | 4 +-- src/vamsas/objects/simple/SequenceSet_Helper.java | 4 +-- src/vamsas/objects/simple/Sequence_Helper.java | 4 +-- src/vamsas/objects/simple/WsJobId.java | 4 +-- src/vamsas/objects/simple/WsJobId_Helper.java | 4 +-- utils/InstallAnywhere/jalview_buildinstaller.xml | 4 +-- utils/eclipse/JalviewCodeStyle.xml | 4 +-- utils/getJavaVersion.java | 4 +-- utils/gff2annot.pl | 33 +++++++++++++++++++ utils/help2Website.java | 4 +-- utils/jalopy/docs/acknowledge.html | 2 +- utils/jalopy/docs/bi01.html | 2 +- utils/jalopy/docs/build.html | 2 +- utils/jalopy/docs/comments.html | 2 +- utils/jalopy/docs/contact.html | 2 +- utils/jalopy/docs/contributors.html | 2 +- utils/jalopy/docs/dedication.html | 2 +- utils/jalopy/docs/dependencies.html | 2 +- utils/jalopy/docs/docs.html | 2 +- utils/jalopy/docs/download.html | 2 +- utils/jalopy/docs/environment.html | 2 +- utils/jalopy/docs/faq.html | 2 +- utils/jalopy/docs/features.html | 2 +- utils/jalopy/docs/footer.html | 2 +- utils/jalopy/docs/header.html | 2 +- utils/jalopy/docs/history.html | 2 +- utils/jalopy/docs/imports.html | 2 +- utils/jalopy/docs/indentation.html | 2 +- utils/jalopy/docs/index.html | 2 +- utils/jalopy/docs/inspector-naming.html | 2 +- utils/jalopy/docs/inspector.html | 2 +- utils/jalopy/docs/installation.html | 2 +- utils/jalopy/docs/introduction.html | 2 +- utils/jalopy/docs/ix01.html | 2 +- utils/jalopy/docs/javadoc.html | 2 +- utils/jalopy/docs/license-antlr.html | 2 +- utils/jalopy/docs/license-apache.html | 2 +- utils/jalopy/docs/license-common-public.html | 2 +- utils/jalopy/docs/license-gnu-doc.html | 2 +- utils/jalopy/docs/license-gnu.html | 2 +- utils/jalopy/docs/license-sun-public.html | 2 +- utils/jalopy/docs/links.html | 2 +- utils/jalopy/docs/manual.html | 2 +- utils/jalopy/docs/messages.html | 2 +- utils/jalopy/docs/misc.html | 2 +- utils/jalopy/docs/part-core.html | 2 +- utils/jalopy/docs/part-plugins.html | 2 +- utils/jalopy/docs/plugin-ant-config.html | 2 +- utils/jalopy/docs/plugin-ant-license.html | 2 +- utils/jalopy/docs/plugin-ant-usage.html | 2 +- utils/jalopy/docs/plugin-ant.html | 2 +- utils/jalopy/docs/plugin-console-license.html | 2 +- utils/jalopy/docs/plugin-console-usage.html | 2 +- utils/jalopy/docs/plugin-console.html | 2 +- utils/jalopy/docs/plugin-eclipse-integration.html | 2 +- utils/jalopy/docs/plugin-eclipse-license.html | 2 +- utils/jalopy/docs/plugin-eclipse.html | 2 +- utils/jalopy/docs/plugin-jbuilder-integration.html | 2 +- utils/jalopy/docs/plugin-jbuilder-license.html | 2 +- utils/jalopy/docs/plugin-jbuilder.html | 2 +- utils/jalopy/docs/plugin-jdev-integration.html | 2 +- utils/jalopy/docs/plugin-jdev-license.html | 2 +- utils/jalopy/docs/plugin-jdev.html | 2 +- utils/jalopy/docs/plugin-jedit-integration.html | 2 +- utils/jalopy/docs/plugin-jedit-license.html | 2 +- utils/jalopy/docs/plugin-jedit.html | 2 +- utils/jalopy/docs/plugin-netbeans-integration.html | 2 +- utils/jalopy/docs/plugin-netbeans-license.html | 2 +- utils/jalopy/docs/plugin-netbeans.html | 2 +- utils/jalopy/docs/plugins.html | 2 +- utils/jalopy/docs/printer.html | 2 +- utils/jalopy/docs/project.html | 2 +- utils/jalopy/docs/separation.html | 2 +- utils/jalopy/docs/settings.html | 2 +- utils/jalopy/docs/sorting.html | 2 +- utils/jalopy/docs/usage.html | 2 +- utils/jalopy/docs/whitespace.html | 2 +- utils/jalopy/docs/wrapping.html | 2 +- utils/jalopy/readme.html | 2 +- utils/jarunsigner.pl | 34 ++++++++++++++++++++ utils/patchGt.pl | 17 ++++++++++ utils/splitstockholm.pl | 17 ++++++++++ 756 files changed, 4109 insertions(+), 1330 deletions(-) diff --git a/RELEASE b/RELEASE index 8bd893d..a0d1141 100644 --- a/RELEASE +++ b/RELEASE @@ -1,3 +1,3 @@ -jalview.release=-r Release_2_6_Branch -jalview.version=2.6.1 +jalview.release=-b Release_2_7_Branch +jalview.version=2.7 diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index 5918fc2..e777ead 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -31,3 +31,8 @@ wsdl4j.jar xercesImpl.jar xml-apis.jar +Additional dependencies + +examples/javascript/deployJava.js : http://java.com/js/deployJava.js +examples/javascript/jquery*.js : BSD license +examples/javascript/jshashtable-2.1.js : Apache License diff --git a/build.xml b/build.xml index 7d63c56..e9528fc 100755 --- a/build.xml +++ b/build.xml @@ -1,7 +1,7 @@ + diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties index b52f0c2..3298729 100644 --- a/nbproject/genfiles.properties +++ b/nbproject/genfiles.properties @@ -1,3 +1,20 @@ +############################################################################### +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) +# Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle +# +# This file is part of Jalview. +# +# Jalview is free software: you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. +# +# Jalview is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty +# of MERCHANTABILITY or FITNESS FOR A PARTICULAR +# PURPOSE. See the GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along with Jalview. If not, see . +############################################################################### nbbuild.xml.data.CRC32=f5d3c6c2 nbbuild.xml.script.CRC32=307ee084 nbbuild.xml.stylesheet.CRC32=28e38971@1.43.1.45 diff --git a/nbproject/project.properties b/nbproject/project.properties index 87df84d..69d1428 100644 --- a/nbproject/project.properties +++ b/nbproject/project.properties @@ -1,3 +1,20 @@ +############################################################################### +# Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) +# Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle +# +# This file is part of Jalview. +# +# Jalview is free software: you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. +# +# Jalview is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty +# of MERCHANTABILITY or FITNESS FOR A PARTICULAR +# PURPOSE. See the GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along with Jalview. If not, see . +############################################################################### annotation.processing.enabled=true annotation.processing.enabled.in.editor=false annotation.processing.run.all.processors=true diff --git a/nbproject/project.xml b/nbproject/project.xml index 73b5c3a..f3db653 100644 --- a/nbproject/project.xml +++ b/nbproject/project.xml @@ -1,4 +1,21 @@ - + + org.netbeans.modules.java.j2seproject diff --git a/resources/embl_mapping.xml b/resources/embl_mapping.xml index c7b2538..d3af6c7 100644 --- a/resources/embl_mapping.xml +++ b/resources/embl_mapping.xml @@ -1,7 +1,7 @@