Merge branch 'j2s/develop-toc' into j2s/develop
[jalview.git] / .j2s
1 #Java2Script Configuration
2 #Mon Jul 20 15:52:45 BST 2015
3 j2s.resources.list=../../eclipseJ2ee/eclipse/plugins/net.sf.j2s.lib_2.0.0/j2slib/java.runtime.j2x,classes/vamsas/objects/simple/WsJobId_Helper.js,classes/vamsas/objects/simple/WsJobId.js,classes/vamsas/objects/simple/Sequence_Helper.js,classes/vamsas/objects/simple/SequenceSet_Helper.js,classes/vamsas/objects/simple/SequenceSet.js,classes/vamsas/objects/simple/Sequence.js,classes/vamsas/objects/simple/SeqSearchResult_Helper.js,classes/vamsas/objects/simple/SeqSearchResult.js,classes/vamsas/objects/simple/Secstructpred_Helper.js,classes/vamsas/objects/simple/Secstructpred.js,classes/vamsas/objects/simple/Result_Helper.js,classes/vamsas/objects/simple/Result.js,classes/vamsas/objects/simple/Object_Helper.js,classes/vamsas/objects/simple/Object.js,classes/vamsas/objects/simple/Msfalignment_Helper.js,classes/vamsas/objects/simple/Msfalignment.js,classes/vamsas/objects/simple/MsaResult_Helper.js,classes/vamsas/objects/simple/MsaResult.js,classes/vamsas/objects/simple/JpredResult_Helper.js,classes/vamsas/objects/simple/JpredResult.js,classes/vamsas/objects/simple/Alignment_Helper.js,classes/vamsas/objects/simple/Alignment.js,classes/vamsas/IMsaWS.js,classes/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.js,classes/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.js,classes/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.js,classes/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.js,classes/uk/ac/ebi/www/WSWUBlastSoapBindingStub.js,classes/uk/ac/ebi/www/WSWUBlastServiceLocator.js,classes/uk/ac/ebi/www/WSWUBlastService.js,classes/uk/ac/ebi/www/WSWUBlast.js,classes/uk/ac/ebi/www/WSFile.js,classes/uk/ac/ebi/www/InputParams.js,classes/uk/ac/ebi/www/Data.js,classes/uk/ac/ebi/picr/model/UPEntry_Helper.js,classes/uk/ac/ebi/picr/model/UPEntry.js,classes/uk/ac/ebi/picr/model/CrossReference_Helper.js,classes/uk/ac/ebi/picr/model/CrossReference.js,classes/org/jibble/epsgraphics/EpsGraphics2D.js,classes/org/jibble/epsgraphics/EpsException.js,classes/org/jibble/epsgraphics/EpsDocument.js,classes/jalview/ws/uimodel/PDBRestResponse.js,classes/jalview/ws/uimodel/PDBRestRequest.js,classes/jalview/ws/uimodel/AlignAnalysisUIText.js,classes/jalview/ws/seqfetcher/DbSourceProxyImpl.js,classes/jalview/ws/seqfetcher/DbSourceProxy.js,classes/jalview/ws/seqfetcher/ASequenceFetcher.js,classes/jalview/ws/rest/params/Tree.js,classes/jalview/ws/rest/params/SeqVector.js,classes/jalview/ws/rest/params/SeqIdVector.js,classes/jalview/ws/rest/params/SeqGroupIndexVector.js,classes/jalview/ws/rest/params/JobConstant.js,classes/jalview/ws/rest/params/AnnotationFile.js,classes/jalview/ws/rest/params/Alignment.js,classes/jalview/ws/rest/RestServiceDescription.js,classes/jalview/ws/rest/RestJobThread.js,classes/jalview/ws/rest/RestJob.js,classes/jalview/ws/rest/RestClient.js,classes/jalview/ws/rest/NoValidInputDataException.js,classes/jalview/ws/rest/InputType.js,classes/jalview/ws/rest/HttpResultSet.js,classes/jalview/ws/rest/AlignmentProcessor.js,classes/jalview/ws/params/simple/StringChoiceParameter.js,classes/jalview/ws/params/simple/Parameter.js,classes/jalview/ws/params/simple/Option.js,classes/jalview/ws/params/simple/IntegerParameter.js,classes/jalview/ws/params/simple/BooleanOption.js,classes/jalview/ws/params/WsParamSetI.js,classes/jalview/ws/params/ValueConstrainI.js,classes/jalview/ws/params/ParameterI.js,classes/jalview/ws/params/ParamManager.js,classes/jalview/ws/params/ParamDatastoreI.js,classes/jalview/ws/params/OptionI.js,classes/jalview/ws/params/InvalidArgumentException.js,classes/jalview/ws/params/AutoCalcSetting.js,classes/jalview/ws/params/ArgumentI.js,classes/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.js,classes/jalview/ws/jws2/jabaws2/Jws2Instance.js,classes/jalview/ws/jws2/dm/JabaWsParamSet.js,classes/jalview/ws/jws2/dm/JabaValueConstrain.js,classes/jalview/ws/jws2/dm/JabaParameter.js,classes/jalview/ws/jws2/dm/JabaOption.js,classes/jalview/ws/jws2/dm/AAConSettings.js,classes/jalview/ws/jws2/SequenceAnnotationWSClient.js,classes/jalview/ws/jws2/RNAalifoldClient.js,classes/jalview/ws/jws2/ParameterUtils.js,classes/jalview/ws/jws2/MsaWSThread.js,classes/jalview/ws/jws2/MsaWSClient.js,classes/jalview/ws/jws2/Jws2Discoverer.js,classes/jalview/ws/jws2/Jws2Client.js,classes/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.js,classes/jalview/ws/jws2/JabawsCalcWorker.js,classes/jalview/ws/jws2/JabaWsServerQuery.js,classes/jalview/ws/jws2/JabaPreset.js,classes/jalview/ws/jws2/JabaParamStore.js,classes/jalview/ws/jws2/JWs2Job.js,classes/jalview/ws/jws2/JPred301Client.js,classes/jalview/ws/jws2/AbstractJabaCalcWorker.js,classes/jalview/ws/jws2/AWS2Thread.js,classes/jalview/ws/jws2/AADisorderClient.js,classes/jalview/ws/jws2/AAConClient.js,classes/jalview/ws/jws1/WSJob.js,classes/jalview/ws/jws1/WS1Client.js,classes/jalview/ws/jws1/SeqSearchWSThread.js,classes/jalview/ws/jws1/SeqSearchWSClient.js,classes/jalview/ws/jws1/MsaWSThread.js,classes/jalview/ws/jws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