--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
- <classpathentry kind="src" path="src"/>
- <classpathentry kind="src" path="src2"/>
- <classpathentry kind="src" path="test"/>
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- <classpathentry kind="lib" path="lib/intervalstore-v1.0.jar"/>
- <classpathentry kind="output" path="classes"/>
++ <classpathentry kind="src" output="bin/main" path="src">
++ <attributes>
++ <attribute name="gradle_scope" value="main"/>
++ <attribute name="gradle_used_by_scope" value=""/>
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++ </classpathentry>
++ <classpathentry kind="src" output="bin/test" path="test">
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++ <classpathentry kind="lib" path="j11lib/groovy-macro-2.5.7.jar"/>
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++ <classpathentry kind="lib" path="j11lib/groovy-testng-2.5.7.jar"/>
++ <classpathentry kind="lib" path="j11lib/groovy-xml-2.5.7.jar"/>
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++ <attributes>
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++ <attributes>
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++ <classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
++ <attributes>
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++ <classpathentry kind="lib" path="utils/roxes-ant-tasks-1.2-2004-01-30.jar">
++ <attributes>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/bsh-2.0b4.jar">
++ <attributes>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
++ <attributes>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/testng.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/wsdl4j.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="output" path="bin/main"/>
+</classpath>
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
- <name>Jalview Release 2.7-old</name>
++ <name>Jalview with gradle build</name>
+ <comment></comment>
- <projects>
- </projects>
++ <projects/>
++ <natures>
++ <nature>org.eclipse.jdt.core.javanature</nature>
++ <nature>org.eclipse.jdt.groovy.core.groovyNature</nature>
++ <nature>org.eclipse.buildship.core.gradleprojectnature</nature>
++ </natures>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
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- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
- <arguments>
- </arguments>
++ <arguments/>
+ </buildCommand>
+ <buildCommand>
- <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
- <triggers>full,incremental,</triggers>
- <arguments>
- <dictionary>
- <key>LaunchConfigHandle</key>
- <value><project>/.externalToolBuilders/Jalview Release indices [Builder].launch</value>
- </dictionary>
- </arguments>
++ <name>org.eclipse.buildship.core.gradleprojectbuilder</name>
++ <arguments/>
+ </buildCommand>
+ </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.groovy.core.groovyNature</nature>
- <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
- <nature>de.tud.st.ispace.builder.ISpaceNature</nature>
- <nature>org.eclipse.jem.beaninfo.BeanInfoNature</nature>
- </natures>
++ <linkedResources/>
++ <filteredResources/>
+</projectDescription>
--- /dev/null
- eclipse.preferences.version=1
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- 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
destroyMenus();
embeddedPopup = null;
embeddedMenu = null;
- super.finalize();
- // no close for Frame
- // super.finalize();
}
}
@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);
}
// 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;
} 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));
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
--
-- class VersionChecker extends Thread
++ new Thread()
{
@Override
public void run()
setProperty("LATEST_VERSION", remoteVersion);
}
-- }
--
-- VersionChecker vc = new VersionChecker();
-- vc.start();
++ }.start();
}
else
{
}
}
- 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");
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
{
{
// 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;
// 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(
// 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;
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;
{
}
- /**
- *
- * @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);
// 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);
}
-
-
}
_isNa = Comparison.isNucleotide(this);
}
return !_isNa;
-- };
++ }
/*
* (non-Javadoc)
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<Object>) obj.get("alleles"));
String clinSig = JSONUtils
- .arrayToList(
- (JSONArray) obj.get("clinical_significance"));
+ .arrayToStringList(
+ (List<Object>) obj.get("clinical_significance"));
/*
* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GeneLociI;
+ import jalview.datamodel.GeneLocus;
+ import jalview.datamodel.Mapping;
import jalview.util.MapList;
-import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
- import jalview.util.JSONUtils;
+ import jalview.datamodel.GeneLocus;
+ import jalview.datamodel.Mapping;
import jalview.util.MapList;
--import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+ /**
+ * A client for the Ensembl REST service /map endpoint, to convert from
+ * coordinates of one genome assembly to another.
+ * <p>
+ * Note that species and assembly identifiers passed to this class must be valid
+ * in Ensembl. They are not case sensitive.
+ *
+ * @author gmcarstairs
+ * @see https://rest.ensembl.org/documentation/info/assembly_map
+ * @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
+ * @see https://rest.ensembl.org/info/species?content-type=text/xml
+ */
public class EnsemblMap extends EnsemblRestClient
{
private static final String MAPPED = "mapped";
try
{
- JSONObject parsed = (JSONObject) jp.parse(br);
- JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
-
- Iterator rvals = mappings.iterator();
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+ if (rvals == null)
- return null;
++ {
++ return null;
++ }
while (rvals.hasNext())
{
// todo check for "mapped"
try
{
- JSONObject parsed = (JSONObject) jp.parse(br);
- JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
-
- Iterator rvals = mappings.iterator();
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+ if (rvals == null)
- return null;
++ {
++ return null;
++ }
String assembly = null;
String chromosome = null;
int fromEnd = 0;
public static Iterator<Reader> processJsonResponseFor(Reader respons)
throws Exception
{
- org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
+ // BH 2019 never called?
try
{
- final JSONArray responses = (JSONArray) jp.parse(respons);
- final RvalsIterator rvals = new RvalsIterator(responses);
- return rvals;
+ @SuppressWarnings("unchecked")
+ final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
- return new Iterator<Reader>()
++ return new Iterator<>()
+ {
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public Reader next()
+ {
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
+
+ Object sval = null;
+ try
+ {
+ sval = val.get("2D");
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
- ;
+ if (sval == null)
+ {
+ System.err.println(
+ "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+ + val.toString());
+
+ sval = "";
+ }
+ return new StringReader(sval.toString());
+
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new Error(
+ MessageManager.getString("error.not_implemented_remove"));
+
+ }
+
+ @Override
+ protected Object clone() throws CloneNotSupportedException
+ {
+ throw new CloneNotSupportedException(
+ MessageManager.getString("error.not_implemented_clone"));
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+
+ @Override
+ protected void finalize() throws Throwable
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ super.finalize();
+ }
+ };
} catch (Exception foo)
{
throw new Exception(MessageManager.getString(
"exception.couldnt_parse_responde_from_annotated3d_server"),
foo);
}
--
}
public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
.queryParam("start", String.valueOf(offSet))
.queryParam("q", query).queryParam("sort", sortParam);
}
+
+ URI uri = webResource.getURI();
+
+ System.out.println(uri);
+
// Execute the REST request
ClientResponse clientResponse = webResource
- .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
+ .accept(MediaType.APPLICATION_JSON).get(clientResponseClass );
+
- int status = clientResponse.getStatus();
-
+ // Get the JSON string from the response object or directly from the
+ // client (JavaScript)
- Map<String, Object> jsonObj = (Platform.isJS() && status == 200
- ? clientResponse.getEntity(Map.class)
- : null);
- String responseString = (jsonObj == null
- ? clientResponse.getEntity(String.class)
- : null);
++ Map<String, Object> jsonObj = null;
++ String responseString = null;
// System.out.println("query >>>>>>> " + pdbRestRequest.toString());
// Check the response status and report exception if one occurs
- switch (status)
+ int responseStatus = clientResponse.getStatus();
- if (responseStatus != 200)
++ switch (responseStatus)
{
- String errorMessage = "";
- if (responseStatus == 400)
+ case 200:
++ if (Platform.isJS())
+ {
- errorMessage = parseJsonExceptionString(responseString);
- throw new Exception(errorMessage);
++ jsonObj = clientResponse.getEntity(Map.class);
+ }
+ else
+ {
- errorMessage = getMessageByHTTPStatusCode(
- responseStatus, "PDB");
- throw new Exception(errorMessage);
++ responseString = clientResponse.getEntity(String.class);
+ }
+ break;
+ case 400:
+ throw new Exception(parseJsonExceptionString(responseString));
+ default:
- throw new Exception(getMessageByHTTPStatusCode(status, "PDB"));
++ throw new Exception(
++ getMessageByHTTPStatusCode(responseStatus, "PDB"));
}
-- // Make redundant objects eligible for garbage collection to conserve
-- // memory
-- clientResponse = null;
-- client = null;
--
// Process the response and return the result to the caller.
- return parsePDBJsonResponse(responseString, pdbRestRequest);
+ return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest);
} catch (Exception e)
{
String exceptionMsg = e.getMessage();
--- /dev/null
+ package jalview.gui;
+
+ import jalview.util.MessageManager;
+ import jalview.util.Platform;
+
+ import java.awt.Desktop;
+ import java.awt.desktop.AboutEvent;
+ import java.awt.desktop.AboutHandler;
+ import java.awt.desktop.PreferencesEvent;
+ import java.awt.desktop.PreferencesHandler;
+ import java.awt.desktop.QuitEvent;
+ import java.awt.desktop.QuitHandler;
+ import java.awt.desktop.QuitResponse;
+ import java.awt.desktop.QuitStrategy;
+
+ import javax.swing.JOptionPane;
+
+ public class APQHandlers
+ {
+ private static boolean setAPQHandlers = false;
+
+ public APQHandlers() {
+ }
+
+ protected static boolean setAPQHandlers(jalview.gui.Desktop jalviewDesktop)
+ {
+ // flagging this test to avoid unnecessary reflection
+ if (!setAPQHandlers)
+ {
+ // see if the Quit, About and Preferences handlers are available
+ Class desktopClass = Desktop.class;
+ Desktop hdesktop = Desktop.getDesktop();
+
+ try
+ {
+ Float specversion = Float.parseFloat(
+ System.getProperty("java.specification.version"));
+
+ if (specversion >= 9)
+ {
- if (Platform.isAMac())
++ if (Platform.isAMacAndNotJS())
+ {
+ if (desktopClass.getDeclaredMethod("setAboutHandler",
+ new Class[]
+ { AboutHandler.class }) != null)
+ {
+
+ hdesktop.setAboutHandler(new AboutHandler()
+ {
+ @Override
+ public void handleAbout(AboutEvent e)
+ {
+ jalviewDesktop.aboutMenuItem_actionPerformed(null);
+ }
+ });
+
+ }
+
+ if (desktopClass.getDeclaredMethod("setPreferencesHandler",
+ new Class[]
+ { PreferencesHandler.class }) != null)
+ {
+
+ hdesktop.setPreferencesHandler(
+ new PreferencesHandler()
+ {
+ @Override
+ public void handlePreferences(
+ PreferencesEvent e)
+ {
+ jalviewDesktop.preferences_actionPerformed(null);
+ }
+ });
+
+ }
+
+ if (desktopClass.getDeclaredMethod("setQuitHandler",
+ new Class[]
+ { QuitHandler.class }) != null)
+ {
+
+ hdesktop.setQuitHandler(new QuitHandler()
+ {
+ @Override
+ public void handleQuitRequestWith(
+ QuitEvent e, QuitResponse r)
+ {
+ boolean confirmQuit = jalview.bin.Cache
+ .getDefault(
+ jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT,
+ true);
+ int n;
+ if (confirmQuit)
+ {
+ n = JOptionPane.showConfirmDialog(null,
+ MessageManager.getString("label.quit_jalview"),
+ MessageManager.getString("action.quit"),
+ JOptionPane.OK_CANCEL_OPTION,
+ JOptionPane.PLAIN_MESSAGE, null);
+ }
+ else
+ {
+ n = JOptionPane.OK_OPTION;
+ }
+ if (n == JOptionPane.OK_OPTION)
+ {
+ System.out.println("Shortcut Quit confirmed by user");
+ jalviewDesktop.quit();
+ r.performQuit(); // probably won't reach this line, but just
+ // in
+ // case
+ }
+ else
+ {
+ r.cancelQuit();
+ System.out.println("Shortcut Quit cancelled by user");
+ }
+ }
+ });
+ hdesktop.setQuitStrategy(
+ QuitStrategy.CLOSE_ALL_WINDOWS);
+
+ }
+ }
+ setAPQHandlers = true;
+ }
+ else
+ {
+ System.out.println(
+ "Not going to try setting APQ Handlers as java.spec.version is "
+ + specversion);
+ }
+
+ } catch (Exception e)
+ {
+ System.out.println(
+ "Exception when looking for About, Preferences, Quit Handlers");
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println(
+ "Throwable when looking for About, Preferences, Quit Handlers");
+ // t.printStackTrace();
+ }
+
+ }
+
+ return setAPQHandlers;
+ }
+
+ }
import jalview.project.Jalview2XML;
import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
-import jalview.util.ImageMaker;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
++import jalview.util.ShortcutKeyMaskExWrapper;
import jalview.util.UrlConstants;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.ParamManager;
* constructor.
*/
instance = this;
- if (!Platform.isJS())
+
+ doConfigureStructurePrefs();
- setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
++ setTitle("Jalview " + Cache.getProperty("VERSION"));
+ /*
+ if (!Platform.isAMac())
{
- doVamsasClientCheck();
+ // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
}
+ else
+ {
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ }
+ */
- doConfigureStructurePrefs();
- setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+ try
+ {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Exception e)
+ {
+ System.out.println("Cannot set APQHandlers");
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println("Cannot set APQHandlers");
+ // t.printStackTrace();
+ }
+
+
+ addWindowListener(new WindowAdapter()
+ {
+
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
+
- boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
++ boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
false);
- boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
+
- boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
++ boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE",
false);
desktop = new MyDesktopPane(selmemusage);
+
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
+
getContentPane().setLayout(new BorderLayout());
// alternate config - have scrollbars - see notes in JAL-153
// JScrollPane sp = new JScrollPane();
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
- 900, 650);
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
}
- jconsole = new Console(this, showjconsole);
- // add essential build information
- jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
- showConsole(showjconsole);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+
+ jconsole = new Console(this, showjconsole);
+ // add essential build information
+ jconsole.setHeader("Jalview Version: "
- + jalview.bin.Cache.getProperty("VERSION") + "\n"
++ + Cache.getProperty("VERSION") + "\n"
+ + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
++ + Cache.getDefault("INSTALLATION", "unknown")
+ + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
++ + Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ + "Java version: " + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
- showNews.setVisible(false);
+ showConsole(showjconsole);
- experimentalFeatures.setSelected(showExperimental());
+ showNews.setVisible(false);
- getIdentifiersOrgData();
+ experimentalFeatures.setSelected(showExperimental());
- checkURLLinks();
+ getIdentifiersOrgData();
+
+ checkURLLinks();
+
+ // Spawn a thread that shows the splashscreen
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen();
+ }
+ });
+
+ // Thread off a new instance of the file chooser - this reduces the time
+ // it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
-
+ });
-
+ }
+
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
this.addWindowListener(new WindowAdapter()
{
// configure services
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(this);
-- if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
++ if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
-- ssm.setAddTempFacAnnot(jalview.bin.Cache
++ ssm.setAddTempFacAnnot(Cache
.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
-- ssm.setProcessSecondaryStructure(jalview.bin.Cache
++ ssm.setProcessSecondaryStructure(Cache
.getDefault(Preferences.STRUCT_FROM_PDB, true));
ssm.setSecStructServices(
-- jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
++ Cache.getDefault(Preferences.USE_RNAVIEW, true));
}
else
{
public void run()
{
Cache.log.debug("Downloading data from identifiers.org");
-- UrlDownloadClient client = new UrlDownloadClient();
try
{
-- client.download(IdOrgSettings.getUrl(),
++ UrlDownloadClient.download(IdOrgSettings.getUrl(),
IdOrgSettings.getDownloadLocation());
} catch (IOException e)
{
}
}
}).start();
-- ;
++
}
@Override
{
// TODO: lock aspect ratio for scaling desktop Bug #0058199
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-- String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
-- String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
-- String width = jalview.bin.Cache
++ String x = Cache.getProperty(windowName + "SCREEN_X");
++ String y = Cache.getProperty(windowName + "SCREEN_Y");
++ String width = Cache
.getProperty(windowName + "SCREEN_WIDTH");
-- String height = jalview.bin.Cache
++ String height = Cache
.getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
iw = Integer.parseInt(width), ih = Integer.parseInt(height);
-- if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
++ if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
{
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
-- jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
++ Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
-- jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
++ Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
-- jalview.bin.Cache.log.debug(
++ Cache.log.debug(
"Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
-- jalview.bin.Cache.log.debug(
++ Cache.log.debug(
"Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
-- jalview.bin.Cache.log.debug(
++ Cache.log.debug(
"Got last known dimensions for " + windowName + ": x:" + ix
+ " y:" + iy + " width:" + iw + " height:" + ih);
}
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
-- };
++ }
});
menuItem.addActionListener(new ActionListener()
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
InputEvent.CTRL_DOWN_MASK);
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
++ ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
-- jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
++ Cache.setProperty("SCREENGEOMETRY_WIDTH",
screen.width + "");
-- jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
++ Cache.setProperty("SCREENGEOMETRY_HEIGHT",
screen.height + "");
storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
getWidth(), getHeight()));
private void storeLastKnownDimensions(String string, Rectangle jc)
{
-- jalview.bin.Cache.log.debug("Storing last known dimensions for "
++ Cache.log.debug("Storing last known dimensions for "
+ string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ " height:" + jc.height);
-- jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
-- jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
-- jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
-- jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
++ Cache.setProperty(string + "SCREEN_X", jc.x + "");
++ Cache.setProperty(string + "SCREEN_Y", jc.y + "");
++ Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
++ Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
}
/**
if (shortv)
{
message.append("<h1><strong>Version: "
-- + jalview.bin.Cache.getProperty("VERSION")
++ + Cache.getProperty("VERSION")
+ "</strong></h1>");
- message.append("<strong>Last Updated: <em>"
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em></strong>");
+ message.append("<strong>Built: <em>"
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
++ + Cache.getDefault("BUILD_DATE", "unknown") + "</em> from "
++ + Cache.getBuildDetailsForSplash()
+ + "</strong>");
}
else
{
message.append("<strong>Version "
-- + jalview.bin.Cache.getProperty("VERSION")
++ + Cache.getProperty("VERSION")
+ "; last updated: "
-- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
++ + Cache.getDefault("BUILD_DATE", "unknown"));
}
-- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
++ if (Cache.getDefault("LATEST_VERSION", "Checking")
.equals("Checking"))
{
- message.append("<br>...Checking latest version...</br>");
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("<br>...Checking latest version...</br>");
}
-- else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
-- .equals(jalview.bin.Cache.getProperty("VERSION")))
++ else if (!Cache.getDefault("LATEST_VERSION", "Checking")
++ .equals(Cache.getProperty("VERSION")))
{
boolean red = false;
-- if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
++ if (Cache.getProperty("VERSION").toLowerCase()
.indexOf("automated build") == -1)
{
red = true;
}
message.append("<br>!! Version "
-- + jalview.bin.Cache.getDefault("LATEST_VERSION",
++ + Cache.getDefault("LATEST_VERSION",
"..Checking..")
+ " is available for download from "
-- + jalview.bin.Cache.getDefault("www.jalview.org",
++ + Cache.getDefault("www.jalview.org",
"http://www.jalview.org")
+ " !!");
if (red)
message.append("</div>");
}
}
-- message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
++ message.append("<br>Authors: " + Cache.getDefault(
"AUTHORFNAMES",
"The Jalview Authors (See AUTHORS file for current list)")
+ "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
-- jalview.bin.Cache.log.debug("Collecting garbage...");
++ Cache.log.debug("Collecting garbage...");
System.gc();
-- jalview.bin.Cache.log.debug("Finished garbage collection.");
++ Cache.log.debug("Finished garbage collection.");
}
/*
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
{ chosenFile.getName() }), chosenFile.hashCode());
-- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
++ Cache.setProperty("LAST_DIRECTORY",
chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
}
}
}
--
- }
-
- jalview.gui.VamsasApplication v_client = null;
-
- @Override
- public void vamsasImport_actionPerformed(ActionEvent e)
- {
- // TODO: JAL-3048 not needed for Jalview-JS
-
- if (v_client == null)
- {
- // Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager.getString(
- "label.select_vamsas_session_opened_as_new_vamsas_session"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String fle = chooser.getSelectedFile().toString();
- if (!vamsasImport(chooser.getSelectedFile()))
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[]
- { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- else
- {
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- }
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(URL url)
- {
- // TODO: create progress bar
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- try
- {
- // copy the URL content to a temporary local file
- // TODO: be a bit cleverer here with nio (?!)
- File file = File.createTempFile("vdocfromurl", ".vdj");
- FileOutputStream fos = new FileOutputStream(file);
- BufferedInputStream bis = new BufferedInputStream(url.openStream());
- byte[] buffer = new byte[2048];
- int ln;
- while ((ln = bis.read(buffer)) > -1)
- {
- fos.write(buffer, 0, ln);
- }
- bis.close();
- fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file,
- url.toExternalForm());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "
- + url,
- ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- return v_client.inSession();
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(File file)
- {
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, file, null);
- } catch (Exception ex)
- {
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:", ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- return v_client.inSession();
- }
-
- public boolean joinVamsasSession(String mysesid)
- {
- if (v_client != null)
- {
- throw new Error(MessageManager
- .getString("error.try_join_vamsas_session_another"));
- }
- if (mysesid == null)
- {
- throw new Error(
- MessageManager.getString("error.invalid_vamsas_session_id"));
- }
- v_client = new VamsasApplication(this, mysesid);
- setupVamsasConnectedGui();
- v_client.initial_update();
- return (v_client.inSession());
- }
-
- @Override
- public void vamsasStart_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Start a session.
- // we just start a default session for moment.
- /*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView());
- * chooser.setDialogTitle("Load Vamsas file");
- * chooser.setToolTipText("Import");
- *
- * int value = chooser.showOpenDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
- * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- */
- v_client = new VamsasApplication(this);
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- }
- else
- {
- // store current data in session.
- v_client.push_update(); // TODO: thread
- }
- }
-
- protected void setupVamsasConnectedGui()
- {
- vamsasStart.setText(MessageManager.getString("label.session_update"));
- vamsasSave.setVisible(true);
- vamsasStop.setVisible(true);
- vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
- }
-
- protected void setupVamsasDisconnectedGui()
- {
- vamsasSave.setVisible(false);
- vamsasStop.setVisible(false);
- vamsasImport.setVisible(true);
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- }
-
- @Override
- public void vamsasStop_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- v_client.end_session();
- v_client = null;
- setupVamsasDisconnectedGui();
- }
- }
-
- protected void buildVamsasStMenu()
- {
- if (v_client == null)
- {
- String[] sess = null;
- try
- {
- sess = VamsasApplication.getSessionList();
- } catch (Exception e)
- {
- jalview.bin.Cache.log.warn("Problem getting current sessions list.",
- e);
- sess = null;
- }
- if (sess != null)
- {
- jalview.bin.Cache.log.debug(
- "Got current sessions list: " + sess.length + " entries.");
- VamsasStMenu.removeAll();
- for (int i = 0; i < sess.length; i++)
- {
- JMenuItem sessit = new JMenuItem();
- sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager
- .formatMessage("label.connect_to_session", new Object[]
- { sess[i] }));
- final Desktop dsktp = this;
- final String mysesid = sess[i];
- sessit.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (dsktp.v_client == null)
- {
- Thread rthr = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- });
- rthr.start();
- }
- };
- });
- VamsasStMenu.add(sessit);
- }
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
- }
- else
- {
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
- }
- }
- else
- {
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
- }
- }
-
- @Override
- public void vamsasSave_actionPerformed(ActionEvent e)
- {
- // TODO: JAL-3048 not needed for Jalview-JS
-
- if (v_client != null)
- {
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_vamsas_document_archive"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager
- .formatMessage("label.saving_vamsas_doc", new Object[]
- { choice.getName() }));
- Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String warnmsg = null;
- String warnttl = null;
- try
- {
- v_client.vclient.storeDocument(choice);
- } catch (Error ex)
- {
- warnttl = "Serious Problem saving Vamsas Document";
- warnmsg = ex.toString();
- jalview.bin.Cache.log
- .error("Error Whilst saving document to " + choice, ex);
-
- } catch (Exception ex)
- {
- warnttl = "Problem saving Vamsas Document.";
- warnmsg = ex.toString();
- jalview.bin.Cache.log.warn(
- "Exception Whilst saving document to " + choice, ex);
-
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- }
-
- JPanel vamUpdate = null;
-
- /**
- * hide vamsas user gui bits when a vamsas document event is being handled.
- *
- * @param b
- * true to hide gui, false to reveal gui
- */
- public void setVamsasUpdate(boolean b)
- {
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
-
- if (vamUpdate != null)
- {
- this.removeProgressPanel(vamUpdate);
- }
- if (b)
- {
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
- }
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
}
public JInternalFrame[] getAllFrames()
openGroovyConsole();
} catch (Exception ex)
{
-- jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
++ Cache.log.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
} catch (InterruptedException x)
{
}
-- ;
}
if (instance == null)
{
System.err.println(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
-- ;
}
} catch (Throwable ex)
{
*/
package jalview.gui;
- import java.awt.Color;
-
-import jalview.api.FeatureColourI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.FeaturesFile;
-import jalview.schemes.FeatureColour;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.swing.JColorChooser;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JSpinner;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-import javax.swing.SwingConstants;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-
/**
-- * DOCUMENT ME!
-- *
-- * @author $author$
-- * @version $Revision$
++ * A class that manages drawing of sequence features for the Swing gui
*/
public class FeatureRenderer
extends jalview.renderer.seqfeatures.FeatureRenderer
{
- Color resBoxColour;
-
- /*
- * defaults for creating a new feature are the last created
- * feature type and group
- */
- static String lastFeatureAdded = "feature_1";
-
- static String lastFeatureGroupAdded = "Jalview";
-
- Color resBoxColour;
-
AlignmentPanel ap;
/**
JPanel singleColour = new JPanel();
- private JPanel minColour = new JPanel();
+ JPanel minColour = new JPanel();
- private JPanel maxColour = new JPanel();
+ JPanel maxColour = new JPanel();
- private JComboBox<String> threshold = new JComboBox<>();
+ private JComboBox<Object> threshold = new JComboBox<>();
- private JSlider slider = new JSlider();
+ JSlider slider = new JSlider();
- private JTextField thresholdValue = new JTextField(20);
+ JTextField thresholdValue = new JTextField(20);
private JCheckBox thresholdIsMin = new JCheckBox();
if (!patternField.isEnabled()
|| (pattern != null && pattern.trim().length() > 0))
{
-- JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
++ JButton removeCondition = new JButton("\u2717");
++ // Dingbats cursive x
+ removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
+ removeCondition.setBackground(Color.WHITE);
+ removeCondition.setPreferredSize(new Dimension(23, 17));
- removeCondition
- .setToolTipText(MessageManager.getString("label.delete_row"));
+ removeCondition.setToolTipText(
+ MessageManager.getString("label.delete_condition"));
- removeCondition.setBorder(new EmptyBorder(0, 0, 0, 0));
removeCondition.addActionListener(new ActionListener()
{
@Override
import javax.swing.JTextArea;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkListener;
++import javax.swing.event.InternalFrameAdapter;
++import javax.swing.event.InternalFrameEvent;
import javax.swing.text.html.HTMLEditorKit;
import javax.swing.text.html.StyleSheet;
{
super.setVisible(aFlag);
frame.setVisible(aFlag);
-- };
++ }
JTabbedPane subjobs = null;
thread.start();
final WebserviceInfo thisinfo = this;
frame.addInternalFrameListener(
-- new javax.swing.event.InternalFrameAdapter()
++ new InternalFrameAdapter()
{
@Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
++ public void internalFrameClosed(InternalFrameEvent evt)
{
// System.out.println("Shutting down webservice client");
WSClientI service = thisinfo.getthisService();
{
service.cancelJob();
}
-- };
++ }
});
frame.validate();
public static void classInit()
{
- setEnabled(Cache.getDefault(ENABLED, true));
+ setEnabled(Cache.getDefault(ENABLED, !Platform.isJS()));
- setConfirmDelete(Cache.getDefault(CONFIRM_DELETE_OLD, true));
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ setConfirmDelete(bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
*/
protected AlignFrame _LoadFileWaitTillLoaded()
{
- Thread loader = new Thread(this);
- loader.start();
-
- while (loader.isAlive())
- {
- try
- {
- Thread.sleep(500);
- } catch (Exception ex)
- {
- System.out.println(
- "Exception caught while waiting for FileLoader thread");
- ex.printStackTrace();
- }
- }
+ this.run();
+
return alignFrame;
}
e.printStackTrace();
}
- if (!Platform.isAMac())
+ if (Platform.allowMnemonics())
{
+ //BH was !Platform.isAMacAndNotJS()) i.e. "JS or not Mac"
+ // but here we want just not a Mac, period, right?
FileMenu.setMnemonic('F');
inputLocalFileMenuItem.setMnemonic('L');
- VamsasMenu.setMnemonic('V');
inputURLMenuItem.setMnemonic('U');
inputTextboxMenuItem.setMnemonic('C');
quit.setMnemonic('Q');
*/
private void jbInit() throws Exception
{
-
+ setName("jalview-desktop");
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
- VamsasMenu.setText("Vamsas");
- VamsasMenu.setToolTipText(MessageManager
- .getString("label.share_data_vamsas_applications"));
- VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
- VamsasStMenu.setToolTipText(
- MessageManager.getString("label.join_existing_vamsas_session"));
inputLocalFileMenuItem
.setText(MessageManager.getString("label.load_tree_from_file"));
inputLocalFileMenuItem.setAccelerator(
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
HelpMenu.add(documentationMenuItem);
- VamsasMenu.add(VamsasStMenu);
- VamsasStMenu.setVisible(false);
- VamsasMenu.add(vamsasStart);
- VamsasMenu.add(vamsasImport);
- VamsasMenu.add(vamsasSave);
- VamsasMenu.add(vamsasStop);
- toolsMenu.add(preferences);
- if (!Platform.isJS())
- if (!Platform.isAMac() || specversion < 11)
++ if (!Platform.isAMacAndNotJS() || specversion < 11)
{
- toolsMenu.add(showMemusage);
- toolsMenu.add(showConsole);
+ toolsMenu.add(preferences);
}
- toolsMenu.add(showMemusage);
- toolsMenu.add(showConsole);
- toolsMenu.add(showNews);
- toolsMenu.add(garbageCollect);
- toolsMenu.add(groovyShell);
+ if (!Platform.isJS())
+ {
++ toolsMenu.add(showMemusage);
++ toolsMenu.add(showConsole);
+ toolsMenu.add(showNews);
+ toolsMenu.add(garbageCollect);
+ toolsMenu.add(groovyShell);
+ }
toolsMenu.add(experimentalFeatures);
// toolsMenu.add(snapShotWindow);
inputMenu.add(inputLocalFileMenuItem);
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.BackupFilenameParts;
import jalview.io.BackupFiles;
+ import jalview.io.BackupFilesPresetEntry;
+ import jalview.io.IntKeyStringValueEntry;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
protected void loadLastSavedBackupsOptions()
{
+ BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+ .getSavedBackupEntry();
enableBackupFiles
- .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+ .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+
+ BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
+ .createBackupFilesPresetEntry(Cache
+ .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
+ if (backupfilesCustomEntry == null)
+ {
+ backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
+ }
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
+ backupfilesCustomEntry);
+
setComboIntStringKey(backupfilesPresetsCombo,
- Cache.getDefault(BackupFiles.NS + "_PRESET", 1));
- suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
- ".bak" + BackupFiles.NUM_PLACEHOLDER));
- suffixDigitsSpinner
- .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
- suffixReverse.setSelected(
- Cache.getDefault(BackupFiles.REVERSE_ORDER, false));
- backupfilesKeepAll
- .setSelected(Cache.getDefault(BackupFiles.NO_MAX, false));
- backupfilesRollMaxSpinner
- .setValue(Cache.getDefault(BackupFiles.ROLL_MAX, 3));
- backupfilesConfirmDelete.setSelected(
- Cache.getDefault(BackupFiles.CONFIRM_DELETE_OLD, true));
+ Cache.getDefault(BackupFiles.NS + "_PRESET",
+ BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
+
+ backupsSetOptions(savedPreset);
backupsOptionsSetEnabled();
updateBackupFilesExampleLabel();
parentseq = jds;
}
}
+
+ /*
+ * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+ */
if (dbrefs != null)
{
- for (int d = 0; d < dbrefs.length; d++)
+ for (int d = 0, nd = dbrefs.size(); d < nd; d++)
{
DBRef dbref = new DBRef();
- DBRefEntry dbRefEntry = dbrefs[d];
- dbref.setSource(dbRefEntry.getSource());
- dbref.setVersion(dbRefEntry.getVersion());
- dbref.setAccessionId(dbRefEntry.getAccessionId());
- if (dbRefEntry instanceof GeneLocus)
+ DBRefEntry ref = dbrefs.get(d);
+ dbref.setSource(ref.getSource());
+ dbref.setVersion(ref.getVersion());
+ dbref.setAccessionId(ref.getAccessionId());
++ if (ref instanceof GeneLocus)
+ {
+ dbref.setLocus(true);
+ }
- if (dbRefEntry.hasMap())
+ if (ref.hasMap())
{
- Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq,
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
jds, recurse);
dbref.setMapping(mp);
}
}
- public ImageMaker(Component parent, TYPE type, String title, int width,
- int height, File file, String fileTitle,
- IProgressIndicator pIndicator, long pSessionId, boolean headless)
+ /**
+ * Constructor configures the graphics context ready for writing to
+ *
+ * @param imageType
+ * @param width
+ * @param height
+ * @param file
+ * @param fileTitle
+ * @param useLineart
+ * @throws IOException
+ */
+ public ImageMaker(TYPE imageType, int width, int height,
+ File file, String fileTitle, boolean useLineart)
+ throws IOException
{
- this.pIndicator = pIndicator;
- this.type = type;
- this.pSessionId = pSessionId;
- this.headless = headless;
- if (file == null)
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.waiting_for_user_to_select_output_file", type.name));
- JalviewFileChooser chooser;
- chooser = type.getFileChooser();
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(title);
- chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(parent);
-
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
- file = chooser.getSelectedFile();
- }
- else
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", type.name));
- }
- }
-
- if (file != null)
- {
- try
- {
- out = new FileOutputStream(file);
- setProgressMessage(null);
- setProgressMessage(MessageManager.formatMessage(
- "status.exporting_alignment_as_x_file", type.getName()));
- if (type == TYPE.SVG)
- {
- setupSVG(width, height, fileTitle);
- }
- else if (type == TYPE.EPS)
- {
- setupEPS(width, height, fileTitle);
- }
- else if (type == TYPE.PNG)
- {
- setupPNG(width, height);
- }
-
- } catch (Exception ex)
- {
- System.out.println("Error creating " + type.getName() + " file.");
-
- setProgressMessage(MessageManager
- .formatMessage("info.error_creating_file", type.getName()));
- }
+ this.type = imageType;
+
+ out = new FileOutputStream(file);
- if (imageType == TYPE.SVG)
++ switch (imageType)
+ {
++ case SVG:
+ setupSVG(width, height, useLineart);
- }
- else if (imageType == TYPE.EPS)
- {
++ break;
++ case EPS:
+ setupEPS(width, height, fileTitle, useLineart);
- }
- else if (imageType == TYPE.PNG)
- {
++ break;
++ case PNG:
+ setupPNG(width, height);
++ break;
++ default:
}
}
*/
protected static boolean isControlDown(MouseEvent e, boolean aMac)
{
- if (aMac)
+ if (!aMac)
{
- /*
- * answer false for right mouse button
- */
- if (e.isPopupTrigger())
+ return e.isControlDown();
++
++ // Jalview 2.11 code below: above is as amended for JalviewJS
++ // /*
++ // * answer false for right mouse button
++ // */
++ // if (e.isPopupTrigger())
++ // {
++ // return false;
++ // }
++ // return
++ // (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() //
++ // .getMenuShortcutKeyMaskEx()
++ // & jalview.util.ShortcutKeyMaskExWrapper
++ // .getModifiersEx(e)) != 0; // getModifiers()) != 0;
+ }
+ // answer false for right mouse button
+ // shortcut key will be META for a Mac
+ return !e.isPopupTrigger()
+ && (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ & e.getModifiers()) != 0;
+ // could we use e.isMetaDown() here?
+ }
+
+ // BH: I don't know about that previous method. Here is what SwingJS uses.
+ // Notice the distinction in mouse events. (BUTTON3_MASK == META)
+ //
+ // private static boolean isPopupTrigger(int id, int mods, boolean isWin) {
+ // boolean rt = ((mods & InputEvent.BUTTON3_MASK) != 0);
+ // if (isWin) {
+ // if (id != MouseEvent.MOUSE_RELEASED)
+ // return false;
+ ////
+ //// // Oddly, Windows returns InputEvent.META_DOWN_MASK on release, though
+ //// // BUTTON3_DOWN_MASK for pressed. So here we just accept both.
+ ////
+ //// actually, we can use XXX_MASK, not XXX_DOWN_MASK and avoid this issue,
+ // because
+ //// J2S adds the appropriate extended (0x3FC0) and simple (0x3F) modifiers.
+ ////
+ // return rt;
+ // } else {
+ // // mac, linux, unix
+ // if (id != MouseEvent.MOUSE_PRESSED)
+ // return false;
+ // boolean lt = ((mods & InputEvent.BUTTON1_MASK) != 0);
+ // boolean ctrl = ((mods & InputEvent.CTRL_MASK) != 0);
+ // return rt || (ctrl && lt);
+ // }
+ // }
+ //
+
+ /**
+ * Windows (not Mac, Linux, or Unix) and right button to test for the
+ * right-mouse pressed event in Windows that would have opened a menu or a
+ * Mac.
+ *
+ * @param e
+ * @return
+ */
+ public static boolean isWinRightButton(MouseEvent e)
+ {
+ // was !isAMac(), but that is true also for Linux and Unix and JS,
+
+ return isWin() && SwingUtilities.isRightMouseButton(e);
+ }
+
+ /**
+ * Windows (not Mac, Linux, or Unix) and middle button -- for mouse wheeling
+ * without pressing the button.
+ *
+ * @param e
+ * @return
+ */
+ public static boolean isWinMiddleButton(MouseEvent e)
+ {
+ // was !isAMac(), but that is true also for Linux and Unix and JS
+ return isWin() && SwingUtilities.isMiddleMouseButton(e);
+ }
+
+ public static boolean allowMnemonics()
+ {
+ return !isMac();
+ }
+
+ public final static int TIME_RESET = 0;
+
+ public final static int TIME_MARK = 1;
+
+ public static final int TIME_SET = 2;
+
+ public static final int TIME_GET = 3;
+
+ public static long time, mark, set, duration;
+
+ public static void timeCheck(String msg, int mode)
+ {
+ long t = System.currentTimeMillis();
+ switch (mode)
+ {
+ case TIME_RESET:
+ time = mark = t;
+ if (msg != null)
+ {
+ System.err.println("Platform: timer reset\t\t\t" + msg);
+ }
+ break;
+ case TIME_MARK:
+ if (set > 0)
+ {
+ duration += (t - set);
+ }
+ else
{
- return false;
+ if (time == 0)
+ {
+ time = mark = t;
+ }
+ if (msg != null)
+ {
+ System.err.println("Platform: timer mark\t" + ((t - time) / 1000f)
+ + "\t" + ((t - mark) / 1000f) + "\t" + msg);
+ }
+ mark = t;
}
- return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
- & jalview.util.ShortcutKeyMaskExWrapper
- .getModifiersEx(e)) != 0; // getModifiers()) != 0;
+ break;
+ case TIME_SET:
+ set = t;
+ break;
+ case TIME_GET:
+ if (msg != null)
+ {
+ System.err.println("Platform: timer dur\t" + ((t - time) / 1000f)
+ + "\t" + ((duration) / 1000f) + "\t" + msg);
+ }
+ set = 0;
+ break;
+ }
+ }
+
+ public static void cacheFileData(String path, Object data)
+ {
+ if (!isJS() || data == null)
+ {
+ return;
+ }
+ /**
+ * @j2sNative
+ *
+ * swingjs.JSUtil.cacheFileData$S$O(path, data);
+ *
+ */
+ }
+
+ public static void cacheFileData(File file)
+ {
+ byte[] data;
+ if (!isJS() || (data = Platform.getFileBytes(file)) == null)
+ {
+ return;
+ }
+ cacheFileData(file.toString(), data);
+ }
+
+ public static byte[] getFileBytes(File f)
+ {
+ return /** @j2sNative f && f._bytes || */
+ null;
+ }
+
+ public static byte[] getFileAsBytes(String fileStr)
+ {
+ byte[] bytes = null;
+ // BH 2018 hack for no support for access-origin
+ /**
+ * @j2sNative bytes = swingjs.JSUtil.getFileAsBytes$O(fileStr)
+ */
+ cacheFileData(fileStr, bytes);
+ return bytes;
+ }
+
+ @SuppressWarnings("unused")
+ public static String getFileAsString(String url)
+ {
+ String ret = null;
+ /**
+ * @j2sNative
+ *
+ * ret = swingjs.JSUtil.getFileAsString$S(url);
+ *
+ *
+ */
+ cacheFileData(url, ret);
+ return ret;
+ }
+
+ public static boolean setFileBytes(File f, String urlstring)
+ {
+ if (!isJS())
+ {
+ return false;
}
- return e.isControlDown();
+ @SuppressWarnings("unused")
+ byte[] bytes = getFileAsBytes(urlstring);
+ /**
+ * @j2sNative f._bytes = bytes;
+ */
+ return true;
+ }
+
+ public static void addJ2SBinaryType(String ext)
+ {
+ /**
+ * @j2sNative
+ *
+ * J2S._binaryTypes.push("." + ext + "?");
+ *
+ */
+ }
+
+ /**
+ * Encode the URI using JavaScript encodeURIComponent
+ *
+ * @param value
+ * @return encoded value
+ */
+ public static String encodeURI(String value)
+ {
+ /**
+ * @j2sNative value = encodeURIComponent(value);
+ */
+ return value;
+ }
+
+ /**
+ * Open the URL using a simple window call if this is JavaScript
+ *
+ * @param url
+ * @return true if window has been opened
+ */
+ public static boolean openURL(String url)
+ {
+ if (!isJS())
+ {
+ return false;
+ }
+ /**
+ * @j2sNative
+ *
+ *
+ * window.open(url);
+ */
+ return true;
+ }
+
+ public static String getUniqueAppletID()
+ {
+ @SuppressWarnings("unused")
+ ThreadGroup g = Thread.currentThread().getThreadGroup();
+ /**
+ * @j2sNative return g.html5Applet._uniqueId;
+ *
+ */
+ return null;
+
+ }
+
+ /**
+ * Read the Info block for this applet.
+ *
+ * @param prefix
+ * "jalview_"
+ * @param p
+ * @return unique id for this applet
+ */
+ public static void readInfoProperties(String prefix, Properties p)
+ {
+ if (!isJS())
+ {
+ return;
+ }
+ @SuppressWarnings("unused")
+ ThreadGroup g = Thread.currentThread().getThreadGroup();
+ String id = getUniqueAppletID();
+ String key = "", value = "";
+ /**
+ * @j2sNative var info = g.html5Applet.__Info || {}; for (var key in info) {
+ * if (key.indexOf(prefix) == 0) { value = "" + info[key];
+ */
+
+ System.out.println(
+ "Platform id=" + id + " reading Info." + key + " = " + value);
+ p.put(id + "_" + key, value);
+
+ /**
+ * @j2sNative
+ *
+ *
+ * } }
+ */
+ }
+
+ public static void setAjaxJSON(URL url)
+ {
+ if (isJS())
+ {
+ JSON.setAjax(url);
+ }
+ }
+
+ public static Object parseJSON(InputStream response)
+ throws IOException, ParseException
+ {
+ if (isJS())
+ {
+ return JSON.parse(response);
+ }
+
+ BufferedReader br = null;
+ try
+ {
+ br = new BufferedReader(new InputStreamReader(response, "UTF-8"));
+ return new JSONParser().parse(br);
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ public static Object parseJSON(String json) throws ParseException
+ {
+ return (isJS() ? JSON.parse(json)
+ : new JSONParser().parse(json));
+ }
+
+ public static Object parseJSON(Reader r)
+ throws IOException, ParseException
+ {
+ if (r == null)
+ {
+ return null;
+ }
+
+ if (!isJS())
+ {
+ return new JSONParser().parse(r);
+ }
+ // Using a file reader is not currently supported in SwingJS JavaScript
+
+ if (r instanceof FileReader)
+ {
+ throw new IOException(
+ "StringJS does not support FileReader parsing for JSON -- but it could...");
+ }
+ return JSON.parse(r);
+
+ }
+
+ /**
+ * Dump the input stream to an output file.
+ *
+ * @param is
+ * @param outFile
+ * @throws IOException
+ * if the file cannot be created or there is a problem reading the
+ * input stream.
+ */
+ public static void streamToFile(InputStream is, File outFile)
+ throws IOException
+ {
+ FileOutputStream fio = new FileOutputStream(outFile);
+ try
+ {
+ if (isJS()
+ && /**
+ * @j2sNative outFile.setBytes$O && outFile.setBytes$O(is) &&
+ */
+ true)
+ {
+ return;
+ }
+ byte[] bb = new byte[32 * 1024];
+ int l;
+ while ((l = is.read(bb)) > 0)
+ {
+ fio.write(bb, 0, l);
+ }
+ } finally
+ {
+ fio.close();
+ }
+ }
+
+ /**
+ * Add a known domain that implements access-control-allow-origin:*
+ *
+ * These should be reviewed periodically.
+ *
+ * @param domain
+ * for a service that is not allowing ajax
+ *
+ * @author hansonr@stolaf.edu
+ *
+ */
+ public static void addJ2SDirectDatabaseCall(String domain)
+ {
+
+ if (isJS())
+ {
+ System.out.println(
+ "Platform adding known access-control-allow-origin * for domain "
+ + domain);
+ /**
+ * @j2sNative
+ *
+ * J2S.addDirectDatabaseCall(domain);
+ */
+ }
+
+ }
+
+ public static void getURLCommandArguments()
+ {
+
+ /**
+ * Retrieve the first query field as command arguments to Jalview. Include
+ * only if prior to "?j2s" or "&j2s" or "#". Assign the applet's __Info.args
+ * element to this value.
+ *
+ * @j2sNative var a =
+ * decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
+ * + "?").split("?")[1].split("#")[0]); a &&
+ * (J2S.thisApplet.__Info.args = a.split(" "));
+ */
+
}
+ /**
+ * A (case sensitive) file path comparator that ignores the difference between /
+ * and \
+ *
+ * @param path1
+ * @param path2
+ * @return
+ */
+ public static boolean pathEquals(String path1, String path2)
+ {
+ if (path1 == null)
+ {
+ return path2 == null;
+ }
+ if (path2 == null)
+ {
+ return false;
+ }
+ String p1 = path1.replace('\\', '/');
+ String p2 = path2.replace('\\', '/');
+ return p1.equals(p2);
+ }
}
src.add(srcs[i]);
}
}
- String[] tosort = src.toArray(new String[0]),
- sorted = src.toArray(new String[0]);
- for (int j = 0, jSize = sorted.length; j < jSize; j++)
- {
- tosort[j] = tosort[j].toLowerCase();
- }
- jalview.util.QuickSort.sort(tosort, sorted);
- // construct array with all sources listed
- int i = 0;
- for (int j = sorted.length - 1; j >= 0; j--, i++)
- {
- tosort[i] = sorted[j];
- }
- return tosort;
++
+ Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+ return src.toArray(new String[src.size()]);
}
}
git://source.jalview.org / jalview.git / commitdiff