From: gmungoc Date: Tue, 16 Jul 2019 07:14:32 +0000 (+0100) Subject: JAL-3210 Merge branch 'develop' into trialMerge X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~127 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=17e4ea278bc9a5fb280db1252ce78b7a295215f5 JAL-3210 Merge branch 'develop' into trialMerge Conflicts: .classpath .project .settings/org.eclipse.jdt.core.prefs .settings/org.eclipse.jdt.ui.prefs build.xml resources/lang/Messages_es.properties src/MCview/AppletPDBCanvas.java src/MCview/Atom.java src/MCview/PDBCanvas.java src/jalview/analysis/AAFrequency.java src/jalview/appletgui/EmbmenuFrame.java src/jalview/appletgui/OverviewPanel.java src/jalview/appletgui/SeqPanel.java src/jalview/bin/Cache.java src/jalview/bin/Jalview.java src/jalview/datamodel/DBRefEntry.java src/jalview/datamodel/Sequence.java src/jalview/ext/ensembl/EnsemblMap.java src/jalview/ext/paradise/Annotate3D.java src/jalview/fts/service/pdb/PDBFTSRestClient.java src/jalview/gui/Desktop.java src/jalview/gui/FeatureRenderer.java src/jalview/gui/FeatureTypeSettings.java src/jalview/gui/WebserviceInfo.java src/jalview/io/BackupFiles.java src/jalview/io/FileLoader.java src/jalview/jbgui/GDesktop.java src/jalview/jbgui/GPreferences.java src/jalview/project/Jalview2XML.java src/jalview/util/ImageMaker.java src/jalview/util/Platform.java src/jalview/ws/SequenceFetcher.java --- 17e4ea278bc9a5fb280db1252ce78b7a295215f5 diff --cc .classpath index 004d432,0000000..0a7e4b3 mode 100644,000000..100644 --- a/.classpath +++ b/.classpath @@@ -1,74 -1,0 +1,206 @@@ + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ + diff --cc .project index 6c40472,0000000..d4d0c20 mode 100644,000000..100644 --- a/.project +++ b/.project @@@ -1,37 -1,0 +1,23 @@@ + + - Jalview Release 2.7-old ++ Jalview with gradle build + - - ++ ++ ++ org.eclipse.jdt.core.javanature ++ org.eclipse.jdt.groovy.core.groovyNature ++ org.eclipse.buildship.core.gradleprojectnature ++ + + + org.eclipse.jdt.core.javabuilder - - - - - org.eclipse.wst.common.project.facet.core.builder - - ++ + + - org.eclipse.ui.externaltools.ExternalToolBuilder - full,incremental, - - - LaunchConfigHandle - <project>/.externalToolBuilders/Jalview Release indices [Builder].launch - - ++ org.eclipse.buildship.core.gradleprojectbuilder ++ + + - - org.eclipse.jdt.groovy.core.groovyNature - org.eclipse.jem.workbench.JavaEMFNature - org.eclipse.jdt.core.javanature - org.eclipse.wst.common.project.facet.core.nature - de.tud.st.ispace.builder.ISpaceNature - org.eclipse.jem.beaninfo.BeanInfoNature - ++ ++ + diff --cc .settings/org.eclipse.jdt.core.prefs index 32ad05c,0000000..11ddce1 mode 100644,000000..100644 --- a/.settings/org.eclipse.jdt.core.prefs +++ b/.settings/org.eclipse.jdt.core.prefs @@@ -1,421 -1,0 +1,299 @@@ - eclipse.preferences.version=1 - org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled - org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore - org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull - org.eclipse.jdt.core.compiler.annotation.nonnull.secondary= - org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault - org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary= - org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable - org.eclipse.jdt.core.compiler.annotation.nullable.secondary= - org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled - org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled - org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate - org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8 - org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve - org.eclipse.jdt.core.compiler.compliance=1.8 - org.eclipse.jdt.core.compiler.debug.lineNumber=generate - org.eclipse.jdt.core.compiler.debug.localVariable=generate - org.eclipse.jdt.core.compiler.debug.sourceFile=generate - org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning - org.eclipse.jdt.core.compiler.problem.assertIdentifier=error - org.eclipse.jdt.core.compiler.problem.autoboxing=ignore - org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning - org.eclipse.jdt.core.compiler.problem.deadCode=warning - org.eclipse.jdt.core.compiler.problem.deprecation=warning - org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled - org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled - org.eclipse.jdt.core.compiler.problem.discouragedReference=warning - org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore - org.eclipse.jdt.core.compiler.problem.enumIdentifier=error - org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore - org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore - org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled - org.eclipse.jdt.core.compiler.problem.fieldHiding=ignore - org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning - org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning - org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning - org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning - org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled - org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning - org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning - org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore - org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore - org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning - org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore - org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore - org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled - org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=ignore - org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=ignore - org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled - org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning - org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore - org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning - org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning - org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore - org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning - org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning - org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error - org.eclipse.jdt.core.compiler.problem.nullReference=warning - org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error - org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning - org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning - org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore - org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning - org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore - org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore - org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore - org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning - org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning - org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore - org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore - org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore - org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore - org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore - org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled - org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning - org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled - org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled - org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled - org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=warning - org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning - org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled - org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning - org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning - org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore - org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning - org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore - org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore - org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore - org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore - org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled - org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled - org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled - org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore - org.eclipse.jdt.core.compiler.problem.unusedImport=warning - org.eclipse.jdt.core.compiler.problem.unusedLabel=warning - org.eclipse.jdt.core.compiler.problem.unusedLocal=warning - org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore - org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore - org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled - org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled - org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled - org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning - org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore - org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning - org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning - org.eclipse.jdt.core.compiler.release=disabled - org.eclipse.jdt.core.compiler.source=1.8 - org.eclipse.jdt.core.formatter.align_assignment_statements_on_columns=false - org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647 - org.eclipse.jdt.core.formatter.align_type_members_on_columns=false - org.eclipse.jdt.core.formatter.align_variable_declarations_on_columns=false - org.eclipse.jdt.core.formatter.align_with_spaces=false - org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16 - org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52 - org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16 - org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=16 - org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation=16 - org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16 - org.eclipse.jdt.core.formatter.alignment_for_assignment=0 - org.eclipse.jdt.core.formatter.alignment_for_binary_expression=16 - org.eclipse.jdt.core.formatter.alignment_for_compact_if=16 - org.eclipse.jdt.core.formatter.alignment_for_compact_loops=16 - org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80 - org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16 - org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16 - org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header=0 - org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0 - org.eclipse.jdt.core.formatter.alignment_for_module_statements=16 - org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16 - org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0 - org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80 - org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16 - org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16 - org.eclipse.jdt.core.formatter.alignment_for_type_arguments=0 - org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0 - org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16 ++# ++#Tue Jul 16 08:09:58 BST 2019 ++org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert ++org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters=insert ++org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert ++org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert ++org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert +org.eclipse.jdt.core.formatter.blank_lines_after_imports=1 - org.eclipse.jdt.core.formatter.blank_lines_after_package=1 - org.eclipse.jdt.core.formatter.blank_lines_before_field=1 - org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration=0 ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert ++org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert ++org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert ++org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true ++org.eclipse.jdt.core.formatter.indentation.size=8 ++org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert ++org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert ++org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off ++org.eclipse.jdt.core.formatter.continuation_indentation=4 +org.eclipse.jdt.core.formatter.blank_lines_before_imports=1 - org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1 - org.eclipse.jdt.core.formatter.blank_lines_before_method=1 - org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1 - org.eclipse.jdt.core.formatter.blank_lines_before_package=0 - org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1 ++org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16 ++org.eclipse.jdt.core.formatter.blank_lines_after_package=1 ++org.eclipse.jdt.core.formatter.insert_space_after_binary_operator=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert ++org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16 ++org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference=do not insert ++org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true ++org.eclipse.jdt.core.formatter.comment.indent_root_tags=true ++org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on ++org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block=insert ++org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert ++org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16 ++org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert ++org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false ++org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments=insert ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=insert ++org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer=insert +org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations=1 - org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=next_line ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments=do not insert ++org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression=do not insert ++org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false ++org.eclipse.jdt.core.compiler.problem.enumIdentifier=error ++org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits=insert ++org.eclipse.jdt.core.formatter.indent_statements_compare_to_block=true +org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration=next_line - org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=next_line_on_wrap ++org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert ++org.eclipse.jdt.core.formatter.comment.line_length=80 ++org.eclipse.jdt.core.formatter.use_on_off_tags=true ++org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert ++org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for=do not insert ++org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false ++org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert ++org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=next_line ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation=do not insert ++org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16 ++org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for=insert ++org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0 ++org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments=insert ++org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false ++org.eclipse.jdt.core.formatter.alignment_for_binary_expression=16 ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert ++org.eclipse.jdt.core.compiler.debug.localVariable=generate ++org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve ++org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=16 ++org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces=insert ++org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional=insert +org.eclipse.jdt.core.formatter.brace_position_for_block=next_line - org.eclipse.jdt.core.formatter.brace_position_for_block_in_case=next_line +org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration=next_line - org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=next_line - org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=next_line +org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line - org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=next_line - org.eclipse.jdt.core.formatter.brace_position_for_switch=next_line - org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line - org.eclipse.jdt.core.formatter.comment.align_tags_descriptions_grouped=false - org.eclipse.jdt.core.formatter.comment.align_tags_names_descriptions=false ++org.eclipse.jdt.core.formatter.compact_else_if=true ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert ++org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true ++org.eclipse.jdt.core.compiler.debug.lineNumber=generate ++org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16 ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments=insert ++org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation=16 ++org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16 ++org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false ++org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert ++org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing=do not insert +org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false - org.eclipse.jdt.core.formatter.comment.count_line_length_from_starting_position=false - org.eclipse.jdt.core.formatter.comment.format_block_comments=false - org.eclipse.jdt.core.formatter.comment.format_header=false - org.eclipse.jdt.core.formatter.comment.format_html=true - org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true - org.eclipse.jdt.core.formatter.comment.format_line_comments=true - org.eclipse.jdt.core.formatter.comment.format_source_code=true - org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true - org.eclipse.jdt.core.formatter.comment.indent_root_tags=true - org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert - org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert - org.eclipse.jdt.core.formatter.comment.line_length=80 - org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true - org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true - org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false - org.eclipse.jdt.core.formatter.compact_else_if=true - org.eclipse.jdt.core.formatter.continuation_indentation=4 - org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2 - org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off - org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on - org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line=false ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer=insert ++org.eclipse.jdt.core.formatter.insert_space_before_binary_operator=insert ++org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert ++org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16 +org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column=true - org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true - org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true - org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true - org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header=true - org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true - org.eclipse.jdt.core.formatter.indent_empty_lines=false - org.eclipse.jdt.core.formatter.indent_statements_compare_to_block=true - org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true - org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true - org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false - org.eclipse.jdt.core.formatter.indentation.size=2 - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_enum_constant=insert - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type=insert - org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_after_type_annotation=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=insert - org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement=do not insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=insert - org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter=insert - org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator=insert - org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_binary_operator=insert - org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments=insert - org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters=insert - org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block=insert - org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast=insert - org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert=insert ++org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1 +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_case=insert - org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional=insert - org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for=insert ++org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert=insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter=insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression=do not insert ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=insert ++org.eclipse.jdt.core.formatter.comment.format_line_comments=true +org.eclipse.jdt.core.formatter.insert_space_after_colon_in_labeled_statement=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert - org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert - org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert - org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer=insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration=do not insert ++org.eclipse.jdt.core.formatter.align_type_members_on_columns=false ++org.eclipse.jdt.core.formatter.alignment_for_assignment=0 ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=insert ++org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header=true ++org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_enum_constant=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration=do not insert ++org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16 ++org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration=0 ++org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80 ++org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line=false ++org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert ++org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block=insert ++org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration=next_line ++org.eclipse.jdt.core.formatter.brace_position_for_block_in_case=next_line ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration=do not insert ++org.eclipse.jdt.core.formatter.comment.format_header=false ++org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert ++org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=do not insert ++org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0 ++org.eclipse.jdt.core.formatter.join_wrapped_lines=true ++org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert ++org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true ++org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized=do not insert ++org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true ++org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=next_line ++org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert ++org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80 ++org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false ++org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16 ++org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false ++org.eclipse.jdt.core.compiler.source=11 +org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_try=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional=insert - org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard=do not insert - org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws=insert ++org.eclipse.jdt.core.formatter.tabulation.size=2 ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression=insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional=insert ++org.eclipse.jdt.core.formatter.comment.format_source_code=true ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_try=do not insert ++org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate +org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_try_resources=insert ++org.eclipse.jdt.core.formatter.blank_lines_before_field=1 ++org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation=do not insert ++org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2 ++org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard=do not insert ++org.eclipse.jdt.core.formatter.blank_lines_before_method=1 ++org.eclipse.jdt.core.compiler.debug.sourceFile=generate ++org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16 ++org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=16 ++org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert ++org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert ++org.eclipse.jdt.core.compiler.codegen.targetPlatform=11 ++org.eclipse.jdt.core.formatter.brace_position_for_switch=next_line ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters=insert ++org.eclipse.jdt.core.formatter.insert_new_line_after_type_annotation=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert ++org.eclipse.jdt.core.formatter.comment.format_html=true ++org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters=insert ++org.eclipse.jdt.core.formatter.alignment_for_compact_if=16 ++org.eclipse.jdt.core.formatter.indent_empty_lines=false ++eclipse.preferences.version=1 ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert +org.eclipse.jdt.core.formatter.insert_space_after_unary_operator=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert ++org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52 ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert ++org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=true ++org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false ++org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=insert +org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator=insert - org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_before_binary_operator=insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert ++org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1 ++org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert ++org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true ++org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer=insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_cast=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_try=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert=insert - org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert - org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert - org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_ellipsis=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement=do not insert ++org.eclipse.jdt.core.formatter.blank_lines_before_member_type=1 ++org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference=do not insert ++org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16 ++org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer=do not insert ++org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert ++org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_try=do not insert +org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast=do not insert ++org.eclipse.jdt.core.formatter.comment.format_block_comments=false ++org.eclipse.jdt.core.formatter.insert_space_before_lambda_arrow=insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration=do not insert ++org.eclipse.jdt.core.compiler.problem.discouragedReference=warning ++org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false +org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert ++org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16 ++org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws=insert +org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression=do not insert ++org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true ++org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16 ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments=insert ++org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert ++org.eclipse.jdt.core.formatter.brace_position_for_array_initializer=next_line_on_wrap ++org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert ++org.eclipse.jdt.core.compiler.compliance=11 ++org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert ++org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration=insert +org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if=insert +org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert ++org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true ++org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast=insert ++org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line ++org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=next_line ++org.eclipse.jdt.core.formatter.blank_lines_before_package=0 ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert +org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try=insert - org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while=insert - org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert - org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert - org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert - org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_semicolon=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources=do not insert - org.eclipse.jdt.core.formatter.insert_space_before_unary_operator=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration=do not insert - org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert ++org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters=do not insert ++org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true ++org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration=insert ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws=do not insert +org.eclipse.jdt.core.formatter.join_lines_in_comments=true - org.eclipse.jdt.core.formatter.join_wrapped_lines=true - org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false - org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=true - org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false - org.eclipse.jdt.core.formatter.keep_simple_do_while_body_on_same_line=false - org.eclipse.jdt.core.formatter.keep_simple_for_body_on_same_line=false - org.eclipse.jdt.core.formatter.keep_simple_while_body_on_same_line=false - org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false - org.eclipse.jdt.core.formatter.lineSplit=76 - org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false - org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false - org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0 - org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1 - org.eclipse.jdt.core.formatter.parentheses_positions_in_annotation=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_catch_clause=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines - org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines - org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true ++org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional=insert ++org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true ++org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert +org.eclipse.jdt.core.formatter.tabulation.char=space - org.eclipse.jdt.core.formatter.tabulation.size=2 - org.eclipse.jdt.core.formatter.use_on_off_tags=true - org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false - org.eclipse.jdt.core.formatter.wrap_before_assignment_operator=false - org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true - org.eclipse.jdt.core.formatter.wrap_before_conditional_operator=true - org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true - org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true - org.eclipse.jdt.core.javaFormatter=org.eclipse.jdt.core.defaultJavaFormatter ++org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert ++org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1 ++org.eclipse.jdt.core.formatter.lineSplit=76 ++org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation=do not insert ++org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch=insert diff --cc src/jalview/appletgui/EmbmenuFrame.java index b6b81fa,7b489ea..8b2b279 --- a/src/jalview/appletgui/EmbmenuFrame.java +++ b/src/jalview/appletgui/EmbmenuFrame.java @@@ -270,6 -274,7 +276,5 @@@ public class EmbmenuFrame extends Fram destroyMenus(); embeddedPopup = null; embeddedMenu = null; - super.finalize(); - // no close for Frame - // super.finalize(); } } diff --cc src/jalview/appletgui/OverviewPanel.java index 4e69399,8f72260..9cbdd36 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@@ -142,10 -140,10 +142,10 @@@ public class OverviewPanel extends Pane @Override public void mousePressed(MouseEvent evt) { - if ((evt.getModifiers() - & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) + if ((evt.getModifiersEx() + & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK) { - if (!Platform.isAMac()) + if (!Platform.isMac()) // BH was excluding JavaScript { showPopupMenu(evt); } diff --cc src/jalview/appletgui/SeqPanel.java index 32f0abb,fee68c8..5becbc1 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@@ -500,8 -499,9 +500,7 @@@ public class SeqPanel extends Panel imp // For now, ignore the mouseWheel font resizing on Macs // As the Button2_mask always seems to be true - - if ((evt.getModifiersEx() - & InputEvent.BUTTON2_DOWN_MASK) == InputEvent.BUTTON2_DOWN_MASK - && !av.MAC) + if (Platform.isWinMiddleButton(evt)) { mouseWheelPressed = true; return; diff --cc src/jalview/bin/Cache.java index 362fca8,8418d68..9e28f5d --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@@ -410,53 -400,12 +410,16 @@@ public class Cach } catch (Exception ex) { System.out.println("Error reading author details: " + ex); - applicationProperties.remove("AUTHORS"); - applicationProperties.remove("AUTHORFNAMES"); - applicationProperties.remove("YEAR"); + authorDetails = null; + } + if (authorDetails == null) + { + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + applicationProperties.remove("YEAR"); } - // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar - // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE - // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW - String buildDetails = resolveResourceURLFor("/.build_properties"); - - if (buildDetails != null) - { - try - { - java.net.URL localJarFileURL = new java.net.URL(buildDetails); - InputStream in = localJarFileURL.openStream(); - applicationProperties.load(in); - in.close(); - } catch (Exception ex) - { - System.out.println("Error reading build details: " + ex); - buildDetails = null; - } - } - if (buildDetails == null) - { - applicationProperties.remove("VERSION"); - } - String jnlpVersion = System.getProperty("jalview.version"); - String codeVersion = getProperty("VERSION"); - String codeInstallation = getProperty("INSTALLATION"); - if (codeVersion == null) - { - // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! - codeVersion = "Test"; - jnlpVersion = "Test"; - codeInstallation = ""; - } - else - { - codeInstallation = " (" + codeInstallation + ")"; - } - new BuildDetails(codeVersion, null, codeInstallation); + loadBuildProperties(false); SiftsSettings .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); @@@ -492,8 -443,8 +457,7 @@@ && (System.getProperty("java.awt.headless") == null || System .getProperty("java.awt.headless").equals("false"))) { -- -- class VersionChecker extends Thread ++ new Thread() { @Override public void run() @@@ -541,10 -492,10 +505,7 @@@ setProperty("LATEST_VERSION", remoteVersion); } -- } -- -- VersionChecker vc = new VersionChecker(); -- vc.start(); ++ }.start(); } else { @@@ -558,44 -509,57 +519,84 @@@ } } - setProperty("VERSION", codeVersion); - // LOAD USERDEFINED COLOURS -- jalview.bin.Cache -- .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); ++ Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false); } - + /** + * construct a resource URL for the given absolute resource pathname + * + * @param resourcePath + * @return + */ + private static String resolveResourceURLFor(String resourcePath) + { + String url = null; + if (Platform.isJS() || !Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString().endsWith(".jar")) + { + try + { + url = Cache.class.getResource(resourcePath).toString(); + } catch (Exception ex) + { + + } + } + else + { + url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource() + .getLocation().toString().concat("!" + resourcePath)); + } + return url; + } + + public static void loadBuildProperties(boolean reportVersion) + { + String codeInstallation = getProperty("INSTALLATION"); + boolean printV = codeInstallation == null; + + // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar + try + { + String buildDetails = "jar:".concat(Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString() + .concat("!/.build_properties")); + + java.net.URL localJarFileURL = new java.net.URL(buildDetails); + + InputStream in = localJarFileURL.openStream(); + applicationProperties.load(in); + in.close(); + } catch (Exception ex) + { + System.out.println("Error reading build details: " + ex); + applicationProperties.remove("VERSION"); + } + String codeVersion = getProperty("VERSION"); + codeInstallation = getProperty("INSTALLATION"); + + if (codeVersion == null) + { + // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! + codeVersion = "Test"; + codeInstallation = ""; + } + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + setProperty("VERSION", codeVersion); + new BuildDetails(codeVersion, null, codeInstallation); + if (printV && reportVersion) + { + System.out + .println("Jalview Version: " + codeVersion + codeInstallation); + } + } + private static void deleteBuildProperties() { applicationProperties.remove("LATEST_VERSION"); diff --cc src/jalview/bin/Jalview.java index 694fe00,ca2a584..521b674 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@@ -406,30 -338,44 +411,44 @@@ public class Jalvie if (!headless) { - desktop = new Desktop(); + desktop = new Desktop() +// { +// // BH testing +// @Override +// protected void processEvent(AWTEvent e) { +// System.out.println("Jalview.java " + e); +// super.processEvent(e); +// } +// } + ; desktop.setInBatchMode(true); // indicate we are starting up + + try + { + JalviewTaskbar.setTaskbar(this); + } catch (Exception e) + { + System.out.println("Cannot set Taskbar"); + // e.printStackTrace(); + } catch (Throwable t) + { + System.out.println("Cannot set Taskbar"); + // t.printStackTrace(); + } + desktop.setVisible(true); - desktop.startServiceDiscovery(); - if (!aparser.contains("nousagestats")) - { - startUsageStats(desktop); - } - else - { - System.err.println("CMD [-nousagestats] executed successfully!"); - } - if (!aparser.contains("noquestionnaire")) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - String url = aparser.getValue("questionnaire"); - if (url != null) + desktop.startServiceDiscovery(); + if (!aparser.contains("nousagestats")) { - // Start the desktop questionnaire prompter with the specified - // questionnaire - Cache.log.debug("Starting questionnaire url at " + url); - desktop.checkForQuestionnaire(url); - System.out.println( - "CMD questionnaire[-" + url + "] executed successfully!"); + startUsageStats(desktop); } else { @@@ -443,42 -383,48 +462,61 @@@ { // Start the desktop questionnaire prompter with the specified // questionnaire - // String defurl = - // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; - // // - String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; - Cache.log.debug( - "Starting questionnaire with default url: " + defurl); - desktop.checkForQuestionnaire(defurl); + Cache.log.debug("Starting questionnaire url at " + url); + desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); + } + else + { + if (Cache.getProperty("NOQUESTIONNAIRES") == null) + { + // Start the desktop questionnaire prompter with the specified + // questionnaire + // String defurl = + // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; + // // + String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; + Cache.log.debug( + "Starting questionnaire with default url: " + defurl); + desktop.checkForQuestionnaire(defurl); + } } } - } - else - { - System.err.println("CMD [-noquestionnaire] executed successfully!"); - } + else + { + System.err + .println("CMD [-noquestionnaire] executed successfully!"); + } - if (!aparser.contains("nonews")) - { - desktop.checkForNews(); - } + if (!aparser.contains("nonews")) + { + desktop.checkForNews(); + } - BioJsHTMLOutput.updateBioJS(); + BioJsHTMLOutput.updateBioJS(); + } } + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 0) + { + final File appdir = new File(appdirString); + new Thread() + { + @Override + public void run() + { + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); + } + String file = null, data = null; FileFormatI format = null; DataSourceType protocol = null; @@@ -826,17 -676,11 +778,16 @@@ // And the user // //////////////////// - if (!headless && file == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + if (!Platform.isJS() && !headless && file == null - && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) ++ && Cache.getDefault("SHOW_STARTUP_FILE", true)) + /** + * Java only + * + * @j2sIgnore + */ { -- file = jalview.bin.Cache.getDefault("STARTUP_FILE", -- jalview.bin.Cache.getDefault("www.jalview.org", ++ file = Cache.getDefault("STARTUP_FILE", ++ Cache.getDefault("www.jalview.org", "http://www.jalview.org") + "/examples/exampleFile_2_7.jar"); if (file.equals( @@@ -845,7 -689,7 +796,7 @@@ // hardwire upgrade of the startup file file.replace("_2_3.jar", "_2_7.jar"); // and remove the stale setting -- jalview.bin.Cache.removeProperty("STARTUP_FILE"); ++ Cache.removeProperty("STARTUP_FILE"); } protocol = DataSourceType.FILE; diff --cc src/jalview/datamodel/DBRefEntry.java index 54e8379,bc8d0cf..f557ff8 --- a/src/jalview/datamodel/DBRefEntry.java +++ b/src/jalview/datamodel/DBRefEntry.java @@@ -21,37 -21,19 +21,26 @@@ package jalview.datamodel; import jalview.api.DBRefEntryI; - import jalview.io.vamsas.Dbref; +import jalview.util.DBRefUtils; +import jalview.util.MapList; -import java.util.Arrays; import java.util.List; public class DBRefEntry implements DBRefEntryI { - /* - * the mapping to chromosome (genome) is held as an instance with - * source = speciesId - * version = assemblyId - * accessionId = "chromosome:" + chromosomeId - * map = mapping from sequence to reference assembly - */ - public static final String CHROMOSOME = "chromosome"; - - private String source = ""; + String source = ""; - String version = ""; + private String version = ""; + + private String ucversion; - String accessionId = ""; + private String accessionId = ""; + + int sourceKey = Integer.MIN_VALUE; - /** + String canonicalSourceName; + - - /** ++ /* * maps from associated sequence to the database sequence's coordinate system */ Mapping map = null; @@@ -60,12 -42,7 +49,16 @@@ { } - /** - * - * @param source may not be null - * @param version may be null - * @param accessionId may be null - */ + ++ /** ++ * ++ * @param source ++ * may not be null ++ * @param version ++ * may be null ++ * @param accessionId ++ * may be null ++ */ public DBRefEntry(String source, String version, String accessionId) { this(source, version, accessionId, null); @@@ -375,31 -319,20 +368,19 @@@ // no version string implies the reference has not been verified at all. return false; } - // tricky - this test really needs to search the sequence's set of dbrefs to - // see if there is a primary reference that derived this reference. - String ucv = version.toUpperCase(); - for (String primsrc : Arrays.asList(DBRefSource.allSources())) - { - if (ucv.startsWith(primsrc.toUpperCase())) - { - // by convention, many secondary references inherit the primary - // reference's - // source string as a prefix for any version information from the - // secondary reference. - return false; - } - } - return true; + + return DBRefSource.isPrimaryCandidate(ucversion); + } + + /** - * Mappings to chromosome are held with accessionId as "chromosome:id" - * - * @return - */ - public boolean isChromosome() - { - return accessionId != null && accessionId.startsWith(CHROMOSOME + ":"); - } - - /** + * stores the upper-case canonical name of the source for use in + * Sequence.getPrimaryDBRefs(). + * + * @author Bob Hanson + * + * @return + */ + public String getCanonicalSourceName() { + return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName); } - - } diff --cc src/jalview/datamodel/Sequence.java index ca2b6d4,6f5c18a..950ee05 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@@ -1612,7 -1553,7 +1580,7 @@@ public class Sequence extends ASequenc _isNa = Comparison.isNucleotide(this); } return !_isNa; -- }; ++ } /* * (non-Javadoc) diff --cc src/jalview/ext/ensembl/EnsemblFeatures.java index 2dd6ebb,99ebc69..e28cc7f --- a/src/jalview/ext/ensembl/EnsemblFeatures.java +++ b/src/jalview/ext/ensembl/EnsemblFeatures.java @@@ -129,11 -130,12 +129,12 @@@ class EnsemblFeatures extends EnsemblRe int end = Integer.parseInt(obj.get("end").toString()); String source = obj.get("source").toString(); String strand = obj.get("strand").toString(); + Object phase = obj.get("phase"); String alleles = JSONUtils - .arrayToList((JSONArray) obj.get("alleles")); + .arrayToStringList((List

Version: " -- + jalview.bin.Cache.getProperty("VERSION") ++ + Cache.getProperty("VERSION") + "