--- /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
eclipse.preferences.version=1
editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
formatter_profile=_Jalview
- formatter_settings_version=14
+ formatter_settings_version=16
org.eclipse.jdt.ui.ignorelowercasenames=true
org.eclipse.jdt.ui.importorder=jalview;java;javax;org;com;
org.eclipse.jdt.ui.ondemandthreshold=99
sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
sp_cleanup.remove_private_constructors=true
sp_cleanup.remove_redundant_modifiers=false
+sp_cleanup.remove_redundant_semicolons=true
sp_cleanup.remove_redundant_type_arguments=true
sp_cleanup.remove_trailing_whitespaces=false
sp_cleanup.remove_trailing_whitespaces_all=true
action.save_project = Save Project
action.save_project_as = Save Project as...
action.quit = Quit
+ label.quit_jalview = Quit Jalview?
action.expand_views = Expand Views
action.gather_views = Gather Views
action.page_setup = Page Setup...
label.groovy_console = Groovy Console...
label.lineart = Lineart
label.dont_ask_me_again = Don't ask me again
-label.select_eps_character_rendering_style = Select EPS character rendering style
+label.select_character_rendering_style = {0} character rendering style
+label.select_character_style_title = {0} Rendering options
label.invert_selection = Invert Selection
label.optimise_order = Optimise Order
label.seq_sort_by_score = Sequence sort by Score
label.input_alignment = Input Alignment
label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
label.vamsas_document_import_failed = Vamsas Document Import Failed
-label.couldnt_locate = Could not locate {0}
+label.couldnt_locate = Couldn''t locate {0}
label.url_not_found = URL not found
label.new_sequence_url_link = New sequence URL link
label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
label.check_for_latest_version = Check for latest version
label.url_linkfrom_sequence_id = URL link from Sequence ID
label.use_proxy_server = Use a proxy server
-label.eps_rendering_style = EPS rendering style
+label.rendering_style = {0} rendering style
label.append_start_end = Append /start-end (/15-380)
label.full_sequence_id = Full Sequence Id
label.smooth_font = Smooth Font
label.sequence_name = Sequence Name
label.sequence_description = Sequence Description
label.edit_sequence_name_description = Edit Sequence Name/Description
-label.spaces_converted_to_backslashes = Spaces have been converted to _
+label.spaces_converted_to_underscores = Spaces have been converted to _
label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name
label.select_outline_colour = Select Outline Colour
label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences."
label.select_startup_file = Select startup file
label.select_default_browser = Select default web browser
label.save_tree_as_newick = Save tree as newick file
-label.create_eps_from_tree = Create EPS file from tree
-label.create_png_from_tree = Create PNG image from tree
label.save_colour_scheme = Save colour scheme
label.edit_params_for = Edit parameters for {0}
label.choose_filename_for_param_file = Choose a filename for this parameter file
label.cancelled_params = Cancelled {0}
error.implementation_error_cannot_show_view_alignment_frame = Implementation error: cannot show a view from another alignment in an AlignFrame.
error.implementation_error_dont_know_about_threshold_setting = Implementation error: don't know about threshold setting for current AnnotationColourGradient.
-error.eps_generation_not_implemented = EPS Generation not yet implemented
-error.png_generation_not_implemented = PNG Generation not yet implemented
error.try_join_vamsas_session_another = Trying to join a vamsas session when another is already connected
error.invalid_vamsas_session_id = Invalid vamsas session id
label.groovy_support_failed = Jalview Groovy Support Failed
label.marked = Marked
label.containing = containing
label.not_containing = not containing
- label.no_feature_of_type_found = No features of type {0} found.
+ label.no_feature_of_type_found = No features of type {0} found
+ label.no_feature_found_selection = No features of type {0} found in selection
label.submission_params = Submission {0}
label.empty_alignment_job = Empty Alignment Job
label.add_new_sbrs_service = Add a new Simple Bioinformatics Rest Service
label.pca_calculating = Calculating PCA
label.select_foreground_colour = Choose foreground colour
label.select_colour_for_text = Select Colour for Text
-label.adjunst_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold
+label.adjust_foreground_text_colour_threshold = Adjust Foreground Text Colour Threshold
label.select_subtree_colour = Select Sub-Tree Colour
label.create_new_sequence_features = Create New Sequence Feature(s)
label.amend_delete_features = Amend/Delete Features for {0}
exception.jobsubmission_invalid_params_set = Invalid parameter set. Check Jalview implementation
exception.notvaliddata_group_contains_less_than_min_seqs = Group contains less than {0} sequences.
exception.outofmemory_loading_pdb_file = Out of memory loading PDB File
-exception.eps_coudnt_write_output_file = Could not write to the output file: {0}
exception.eps_method_not_supported = Method not currently supported by EpsGraphics2D version {0}
exception.eps_unable_to_get_inverse_matrix = Unable to get inverse of matrix: {0}
warn.job_cannot_be_cancelled_close_window = This job cannot be cancelled.\nJust close the window.
status.finished_searching_for_sequences_from = Finished searching for sequences from {0}
label.eps_file = EPS file
label.png_image = PNG image
-status.saving_file = Saving {0}
-status.export_complete = {0} Export completed.
+status.export_complete = {0} Export completed
status.fetching_pdb = Fetching PDB {0}
status.refreshing_news = Refreshing news
status.importing_vamsas_session_from = Importing VAMSAS session from {0}
label.structure_chooser_no_of_structures = Structure Chooser - {0} Found ({1})
info.no_pdb_entry_found_for = No PDB entry found for {0}
exception.unable_to_detect_internet_connection = Jalview is unable to detect an internet connection
- exception.fts_rest_service_no_longer_available = {0} rest services no longer available!
- exception.resource_not_be_found = The requested resource could not be found
- exception.fts_server_error = There seems to be an error from the {0} server
exception.fts_server_unreachable = Jalview is unable to reach the {0} server. \nPlease ensure that you are connected to the internet and try again.
label.nw_mapping = Needleman & Wunsch Alignment
label.sifts_mapping = SIFTs Mapping
label.mapping_method = Sequence \u27f7 Structure mapping method
-status.waiting_for_user_to_select_output_file = Waiting for user to select {0} file
status.cancelled_image_export_operation = Cancelled {0} export operation
info.error_creating_file = Error creating {0} file
exception.outofmemory_loading_mmcif_file = Out of memory loading mmCIF File
action.prev_page= <<
label.next_page_tooltip=Next Page
label.prev_page_tooltip=Previous Page
- exception.bad_request=Bad request. There is a problem with your input.
- exception.service_not_available=Service not available. The server is being updated, try again later.
status.launching_3d_structure_viewer = Launching 3D Structure viewer...
status.fetching_3d_structures_for_selected_entries = Fetching 3D Structures for selected entries...
status.fetching_dbrefs_for_sequences_without_valid_refs = Fetching db refs for {0} sequence(s) without valid db ref required for SIFTS mapping
label.filter = Filter
label.filters = Filters
label.join_conditions = Join conditions with
+ label.delete_condition = Delete this condition
label.score = Score
label.colour_by_label = Colour by label
label.variable_colour = Variable colour...
-label.select_colour = Select colour
+label.select_colour_for = Select colour for {0}
option.enable_disable_autosearch = When ticked, search is performed automatically
option.autosearch = Autosearch
label.retrieve_ids = Retrieve IDs
label.most_polymer_residues = Most Polymer Residues
label.cached_structures = Cached Structures
label.free_text_search = Free Text Search
+label.annotation_name = Annotation Name
+label.annotation_description = Annotation Description
+label.edit_annotation_name_description = Edit Annotation Name/Description
+label.alignment = alignment
+label.pca = PCA
+label.create_image_of = Create {0} image of {1}
+label.click_to_edit = Click to edit, right-click for menu
label.backupfiles_confirm_delete = Confirm delete
label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options)
label.backupfiles_confirm_save_file = Confirm save file
label.append_to_filename_tooltip = %n in the text will be replaced by the backup number. The text will appear after the filename. See the summary box above.
label.index_digits = Number of digits to use for the backup number (%n)
label.summary_of_backups_scheme = Summary of backup scheme
+ label.scheme_examples = Scheme examples
label.increment_index = Increase appended text numbers - newest file has largest number.
label.reverse_roll = "Roll" appended text numbers - newest backup file is always number 1.
label.keep_files = Deleting old backup files
label.keep_all_backup_files = Do not delete old backup files
label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files
- label.autodelete_old_backup_files = Autodelete old backup files:
+ label.autodelete_old_backup_files = Auto-delete old backup files:
label.always_ask = Always ask
label.auto_delete = Automatically delete
label.filename = filename
label.configure_feature_tooltip = Click to configure variable colour or filters
label.schemes = Schemes
label.customise = Customise
+ label.custom = Custom
label.default = Default
label.single_file = Single backup
label.keep_all_versions = Keep all versions
label.rolled_backups = Rolled backup files
+ label.customise_description = Select Customise, make changes, and click on OK to save your own custom scheme
+ label.custom_description = Your own saved scheme
+ label.default_description = Keep the last three versions of the file
+ label.single_file_description = Keep the last version of the file
+ label.keep_all_versions_description = Keep all previous versions of the file
+ label.rolled_backups_description = Keep the last nine versions of the file from _bak.1 (newest) to _bak.9 (oldest)
+ label.cancel_changes_description = Cancel changes made to your last saved Custom scheme
label.previously_saved_scheme = Previously saved scheme
label.no_backup_files = NO BACKUP FILES
label.include_backup_files = Include backup files
action.save_project = Guardar proyecto
action.save_project_as = Guardar proyecto como...
action.quit = Salir
+ label.quit_jalview = Salir de Jalview?
action.expand_views = Expandir vistas
action.gather_views = Capturar vistas
action.page_setup = Configuración de la página
label.groovy_console = Consola Groovy
label.lineart = Lineart
label.dont_ask_me_again = No volver a preguntar
-label.select_eps_character_rendering_style = Seleccionar el carácter EPS como estilo de visualización
+label.select_character_rendering_style = Estilo de visualización para carácter {0}
+label.select_character_style_title = Opciones de visualización {0}
label.invert_selection = Invertir selección
label.optimise_order = Optimizar orden
label.seq_sort_by_score = Ordenar las secuencias por puntuación
label.check_for_latest_version = Comprobar la última versión
label.url_linkfrom_sequence_id = URL del enlace del ID de la secuencia
label.use_proxy_server = Utilizar un servidor proxy
-label.eps_rendering_style = Estilo de visualización EPS
+label.rendering_style = Estilo de visualización {0}
label.append_start_end = Añadir /inicio-fin (/15-380)
label.full_sequence_id = ID de la secuencia completo
label.smooth_font = Fuente alargada
label.sequence_name = Nombre de la secuencia
label.sequence_description = Descripción de la secuencia
label.edit_sequence_name_description = Editar el nombre/descripción de la secuencia
-label.spaces_converted_to_backslashes = Los espacios se han convertido en _
+label.spaces_converted_to_underscores = Los espacios se han convertido en _
label.no_spaces_allowed_sequence_name = No se permiten espacios en el nombre de la secuencia
label.select_outline_colour = Seleccionar el color del límite
label.web_browser_not_found_unix = Unixers\: No es posible encontrar el navegador web por defecto.\nA\u00F1ada la ruta completa de su navegador en la pesta\u00F1a de Preferencias.
label.select_startup_file = Seleccionar fichero de arranque
label.select_default_browser = Seleccionar navegador web por defecto
label.save_tree_as_newick = Guardar árbol como fichero newick
-label.create_eps_from_tree = Crear un fichero EPS a partir de un árbol
-label.create_png_from_tree = Crear una imagen PNG a partir de un árbol
label.save_colour_scheme = Guardar esquema cromático
label.edit_params_for = Editar los parámetros de {0}
label.choose_filename_for_param_file = Escoja un nombre de fichero para este fichero de parámetros
label.cancelled_params = {0} cancelado
error.implementation_error_cannot_show_view_alignment_frame = Error de implementación: no es posible mostrar una vista de otro alineamiento en un AlignFrame.
error.implementation_error_dont_know_about_threshold_setting = Error de implementación: no se conoce la configuración del umbral para el AnnotationColourGradient actual.
-error.eps_generation_not_implemented = La generación de EPS no se ha implementado todavía
-error.png_generation_not_implemented = La generación de PNG no se ha implementado todavía
error.try_join_vamsas_session_another = Tratando de establecer una sesión VAMSAS cuando ya había otra conectada
error.invalid_vamsas_session_id = Identificador de sesión VAMSAS no válido
label.groovy_support_failed = El soporte Groovy de Jalview ha fallado
label.marked = Marcada
label.containing = conteniendo
label.not_containing = no conteniendo
- label.no_feature_of_type_found = No se han encontrado características del tipo {0}.
+ label.no_feature_of_type_found = No se han encontrado características del tipo {0}
+ label.no_feature_found_selection = No se han encontrado características del tipo {0} en la región seleccionada
label.submission_params = Envío {0}
label.empty_alignment_job = Trabajo de alineamiento vacío
label.add_new_sbrs_service = Añadir un nuevo SBRS
label.pca_calculating = Calculando ACP
label.select_foreground_colour = Escoger color del primer plano
label.select_colour_for_text = Seleccione el color del texto
-label.adjunst_foreground_text_colour_threshold = Ajustar el umbral del color del texto en primer plano
+label.adjust_foreground_text_colour_threshold = Ajustar el umbral del color del texto en primer plano
label.select_subtree_colour = Seleccioanr el color del sub-árbol
label.create_new_sequence_features = Crear nueva(s) característica(s) de secuencia
label.amend_delete_features = Arrelgar/Borrar características de {0}
exception.jobsubmission_invalid_params_set = Conjunto de parámetros no válido. Comprueba la implementación de Jalview
exception.notvaliddata_group_contains_less_than_min_seqs = El grupo contiene menos de {0} secuencias.
exception.outofmemory_loading_pdb_file = Sin memoria al cargar el fichero PDB
-exception.eps_coudnt_write_output_file = No es posible escribir el fichero de salida: {0}
exception.eps_method_not_supported = Método actualmente no suportado por la versión {0} de EpsGraphics2D
exception.eps_unable_to_get_inverse_matrix = Imposible obtener la inversa de la matrix: {0}
warn.job_cannot_be_cancelled_close_window = Este trabajo no se puede cancelar.\nSimplemente, cierre la ventana.
status.finished_searching_for_sequences_from = Finalizada la búsqueda de secuencias en {0}
label.eps_file = Fichero EPS
label.png_image = Imagen PNG
-status.saving_file = Guardando {0}
-status.export_complete = Exportación completada.
+status.export_complete = Exportación completada
status.fetching_pdb = Recuperando PDB {0}
status.refreshing_news = Refrescando noticias
status.importing_vamsas_session_from = Importando sesión VAMSAS de {0}
label.show_selected_annotations=Mostrar anotaciones seleccionadas
status.colouring_chimera=Coloreando Chimera
label.configure_displayed_columns=Configurar Columnas Mostradas
- exception.resource_not_be_found=El recurso solicitado no se ha encontrado
label.aacon_calculations=cálculos AACon
label.pdb_web-service_error=Error de servicio web PDB
exception.unable_to_detect_internet_connection=Jalview no puede detectar una conexión a Internet
exception.outofmemory_loading_mmcif_file=Sin memoria al cargar el fichero mmCIF
label.hide_columns_not_containing=Ocultar las columnas que no contengan
label.pdb_sequence_fetcher=Recuperador de secuencias PDB
- exception.fts_server_error=Parece que hay un error desde el servidor {0}
- exception.service_not_available=Servicio no disponible. El servidor se está actualizando, vuelva a intentarlo más tarde.
+ status.waiting_for_user_to_select_output_file=Esperando que el usuario seleccione el fichero {0}
action.prev_page=<<
status.cancelled_image_export_operation=Operación de exportación {0} cancelada
label.couldnt_run_groovy_script=No se ha podido ejecutar el script Groovy
- exception.bad_request=Solicitud incorrecta. Hay un problema con su entrada.
label.run_groovy=Ejecutar script Groovy desde la consola
action.next_page=>>
label.uniprot_sequence_fetcher=Recuperador de secuencias UniProt
label.sifts_mapping=Mapeado SIFTs
label.mapping_method=Método de mapeo de secuencia \u27F7 estructura
info.error_creating_file=Error al crear fichero {0}
- exception.fts_rest_service_no_longer_available= Servicios Rest {0} ya no están disponibles!
status.launching_3d_structure_viewer=Lanzando visualizador de estructura 3D...
status.obtaining_mapping_with_sifts=Obteniendo mapeo por SIFTS
status.fetching_3d_structures_for=Buscando la estructura 3D para {0}
label.numeric_required = Valor numérico requerido
label.filter = Filtro
label.filters = Filtros
+ label.delete_condition = Borrar esta condición
label.join_conditions = Combinar condiciones con
label.score = Puntuación
label.colour_by_label = Colorear por texto
label.variable_colour = Color variable...
-label.select_colour = Seleccionar color
+label.select_colour_for = Seleccionar color para {0}
option.enable_disable_autosearch = Marcar para buscar automáticamente
option.autosearch = Auto búsqueda
label.retrieve_ids = Recuperar IDs
label.most_polymer_residues = Más Residuos de Polímeros
label.cached_structures = Estructuras en Caché
label.free_text_search = Búsqueda de texto libre
+label.annotation_name = Nombre de la anotación
+label.annotation_description = Descripción de la anotación
+label.edit_annotation_name_description = Editar el nombre/descripción de la anotación
+label.alignment = alineamiento
+label.pca = ACP
+label.create_image_of = Crear imagen {0} de {1}
+label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú
label.backupfiles_confirm_delete = Confirmar borrar
label.backupfiles_confirm_delete_old_files = ¿Borrar los siguientes archivos? (ver la pestaña 'Copias' de la ventana de Preferencias para más opciones)
label.backupfiles_confirm_save_file = Confirmar guardar archivo
label.append_to_filename_tooltip = %n en el texto será reemplazado por el número de respaldo. El texto será después del nombre del archivo. Vea el cuadro de resumen arriba.
label.index_digits = Número de dígitos a utilizar para el número de respaldo.
label.summary_of_backups_scheme = Resumen del esquema de copias de seguridad
+ label.scheme_examples = Ejemplos de esquema
label.increment_index = Aumente los números de texto adjuntos: el archivo más nuevo tiene el número más grande
label.reverse_roll = Ciclos de texto adjuntos: el respaldo más reciente es siempre el número 1
label.keep_files = Borrando los respaldos antiguos
label.configuration = Configuración
label.configure_feature_tooltip = Haga clic para configurar el color o los filtros
label.schemes = Esquemas
- label.customise = Personalizado
+ label.customise = Personalizar
+ label.custom = Personal
label.default = Defecto
label.single_file = Solo uno respaldo
label.keep_all_versions = Mantener todas las versiones
label.rolled_backups = Ciclos respaldos
+ label.customise_description = Seleccione Personalizar, haga cambios y haga clic en OK para guardar su propio esquema personalizado
+ label.custom_description = Tu propio esquema guardado
+ label.default_description = Conserve las últimas tres versiones del archivo
+ label.single_file_description = Conserve la última versión del archivo
+ label.keep_all_versions_description = Mantener todas las versiones anteriores del archivo
+ label.rolled_backups_description = Mantenga las últimas nueve versiones del archivo desde _bak.1 (más reciente) a _bak.9 (más antigua)
+ label.cancel_changes_description = Cancelar los cambios realizados en su último esquema personalizado guardado
label.previously_saved_scheme = Esquema previamente guardado
label.no_backup_files = NO ARCHIVOS DE RESPALDOS
label.include_backup_files = Incluir archivos de respaldos
* contains
*
* <pre>
- * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercent, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value
* </pre>
*
*/
public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
{
- int[] rtnval = new int[64];
ResidueCount counts = profile.getCounts();
if (counts == null)
{
char[] symbols = symbolCounts.symbols;
int[] values = symbolCounts.values;
QuickSort.sort(values, symbols);
- int nextArrayPos = 2;
int totalPercentage = 0;
final int divisor = ignoreGaps ? profile.getNonGapped()
: profile.getHeight();
/*
* traverse the arrays in reverse order (highest counts first)
*/
+ int[] result = new int[3 + 2 * symbols.length];
+ int nextArrayPos = 3;
+ int nonZeroCount = 0;
+
for (int i = symbols.length - 1; i >= 0; i--)
{
int theChar = symbols[i];
int charCount = values[i];
-
- rtnval[nextArrayPos++] = theChar;
final int percentage = (charCount * 100) / divisor;
- rtnval[nextArrayPos++] = percentage;
+ if (percentage == 0)
+ {
+ /*
+ * this count (and any remaining) round down to 0% - discard
+ */
+ break;
+ }
+ nonZeroCount++;
+ result[nextArrayPos++] = theChar;
+ result[nextArrayPos++] = percentage;
totalPercentage += percentage;
}
- rtnval[0] = symbols.length;
- rtnval[1] = totalPercentage;
- int[] result = new int[rtnval.length + 1];
+
+ /*
+ * truncate array if any zero values were discarded
+ */
+ if (nonZeroCount < symbols.length)
+ {
+ int[] tmp = new int[3 + 2 * nonZeroCount];
+ System.arraycopy(result, 0, tmp, 0, tmp.length);
+ result = tmp;
+ }
+
+ /*
+ * fill in 'header' values
+ */
result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
- System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+ result[1] = nonZeroCount;
+ result[2] = totalPercentage;
return result;
}
* contains
*
* <pre>
- * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercentage, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value, where the character values encode codon triplets
* </pre>
*
* @param hashtable
* @return
*/
- public static int[] extractCdnaProfile(Hashtable hashtable,
+ public static int[] extractCdnaProfile(
+ Hashtable<String, Object> hashtable,
boolean ignoreGaps)
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
{
break; // nothing else of interest here
}
+ final int percentage = codonCount * 100 / divisor;
+ if (percentage == 0)
+ {
+ /*
+ * this (and any remaining) values rounded down to 0 - discard
+ */
+ break;
+ }
distinctValuesCount++;
result[j++] = codons[i];
- final int percentage = codonCount * 100 / divisor;
result[j++] = percentage;
totalPercentage += percentage;
}
* the consensus data stores to be populated (one per column)
*/
public static void calculateCdna(AlignmentI alignment,
- Hashtable[] hconsensus)
+ Hashtable<String, Object>[] hconsensus)
{
final char gapCharacter = alignment.getGapCharacter();
List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<>();
+ Hashtable<String, Object> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
+ break;
}
}
}
*/
public static void completeCdnaConsensus(
AlignmentAnnotation consensusAnnotation,
- Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
+ Hashtable<String, Object>[] consensusData, boolean showProfileLogo,
+ int nseqs)
{
if (consensusAnnotation == null
|| consensusAnnotation.annotations == null
consensusAnnotation.scaleColLabel = true;
for (int col = 0; col < consensusData.length; col++)
{
- Hashtable hci = consensusData[col];
+ Hashtable<String, Object> hci = consensusData[col];
if (hci == null)
{
// gapped protein column?
}
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- List<SequenceI> asq;
- synchronized (asq = align.getSequences())
+ List<SequenceI> asq = align.getSequences();
+ synchronized (asq)
{
for (int i = 0; i < len; i++)
{
public static void setOrder(AlignmentI align, SequenceI[] seqs)
{
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- List<SequenceI> algn;
- synchronized (algn = align.getSequences())
+ List<SequenceI> algn = align.getSequences();
+ synchronized (algn)
{
- List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<SequenceI> tmp = new ArrayList<>();
for (int i = 0; i < seqs.length; i++)
{
{
// MAINTAINS ORIGNAL SEQUENCE ORDER,
// ORDERS BY GROUP SIZE
- List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> groups = new ArrayList<>();
if (groups.hashCode() != lastGroupHash)
{
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
for (int i = 0; i < groups.size(); i++)
{
// tmp2 = tmp.retainAll(mask);
// return tmp2.addAll(mask.removeAll(tmp2))
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ ArrayList<SequenceI> seqs = new ArrayList<>();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
{
int nSeq = align.getHeight();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<SequenceI> tmp = new ArrayList<>();
tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
for (int i = 0; i < alignment.length; i++)
{
- ids[i] = (new Float(alignment[i].getName().substring(8)))
+ ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
.floatValue();
}
return false;
}
String name = seq2.getName();
- final DBRefEntry[] xrefs = seq1.getDBRefs();
+ final List<DBRefEntry> xrefs = seq1.getDBRefs();
if (xrefs != null)
{
- for (DBRefEntry xref : xrefs)
+ for (int ix = 0, nx = xrefs.size(); ix < nx; ix++)
{
+ DBRefEntry xref = xrefs.get(ix);
String xrefName = xref.getSource() + "|" + xref.getAccessionId();
// case-insensitive test, consistent with DBRefEntry.equalRef()
if (xrefName.equalsIgnoreCase(name))
// need to
// synthesize an xref.
- for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
+ List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs();
+ for (int ip = 0, np = primrefs.size(); ip < np; ip++)
{
+ DBRefEntry primRef = primrefs.get(ip);
/*
* create a cross-reference from CDS to the source sequence's
* primary reference and vice versa
dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
.getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
-
// problem here is that the cross-reference is synthesized -
// cdsSeq.getName() may be like 'CDS|dnaaccession' or
// 'CDS|emblcdsacc'
.getInverse()));
proteinProduct.addDBRef(proteinToCdsRef);
}
-
/*
* transfer any features on dna that overlap the CDS
*/
return;
}
- MapList newMap = targetToFrom.traverse(fromLoci.getMap());
+ MapList newMap = targetToFrom.traverse(fromLoci.getMapping());
if (newMap != null)
{
List<DBRefEntry> direct = new ArrayList<>();
HashSet<String> directSources = new HashSet<>();
- if (contig.getDBRefs() != null)
+ List<DBRefEntry> refs = contig.getDBRefs();
+ if (refs != null)
{
- for (DBRefEntry dbr : contig.getDBRefs())
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
- if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap())
+ DBRefEntry dbr = refs.get(ib);
+ MapList map;
+ if (dbr.hasMap() && (map = dbr.getMap().getMap()).isTripletMap())
{
- MapList map = dbr.getMap().getMap();
// check if map is the CDS mapping
if (mapping.getMap().equals(map))
{
}
}
}
- DBRefEntry[] onSource = DBRefUtils.selectRefs(
+ List<DBRefEntry> onSource = DBRefUtils.selectRefs(
proteinProduct.getDBRefs(),
directSources.toArray(new String[0]));
List<DBRefEntry> propagated = new ArrayList<>();
// and generate appropriate mappings
- for (DBRefEntry cdsref : direct)
+ for (int ic = 0, nc = direct.size(); ic < nc; ic++)
{
+ DBRefEntry cdsref = direct.get(ic);
+ Mapping m = cdsref.getMap();
// clone maplist and mapping
MapList cdsposmap = new MapList(
Arrays.asList(new int[][]
{ new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }),
- cdsref.getMap().getMap().getToRanges(), 3, 1);
- Mapping cdsmap = new Mapping(cdsref.getMap().getTo(),
- cdsref.getMap().getMap());
+ m.getMap().getToRanges(), 3, 1);
+ Mapping cdsmap = new Mapping(m.getTo(),m.getMap());
// create dbref
DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
int phase = 0;
try
{
- phase = Integer.parseInt(sf.getPhase());
+ String s = sf.getPhase();
+ if (s != null)
+ {
+ phase = Integer.parseInt(s);
+ }
} catch (NumberFormatException e)
{
- // ignore
+ // SwingJS -- need to avoid these.
}
/*
* phase > 0 on first codon means 5' incomplete - skip to the start
/*
* variants in first codon base
*/
- for (DnaVariant var : codonVariants[0])
+ for (DnaVariant dnavar : codonVariants[0])
{
- if (var.variant != null)
+ if (dnavar.variant != null)
{
- String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
+ String alleles = (String) dnavar.variant.getValue(Gff3Helper.ALLELES);
if (alleles != null)
{
for (String base : alleles.split(","))
+ base3.toLowerCase();
String canonical = base1.toUpperCase() + base2.toLowerCase()
+ base3.toLowerCase();
- if (addPeptideVariant(peptide, peptidePos, residue, var,
+ if (addPeptideVariant(peptide, peptidePos, residue, dnavar,
codon, canonical))
{
count++;
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
- for (SequenceI xref : xrefs)
+ // BH 2019.01.25 streamlined this triply nested loop to remove all iterators
+
+ for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
{
- DBRefEntry[] dbrefs = xref.getDBRefs();
+ SequenceI xref = xrefs[ix];
+ List<DBRefEntry> dbrefs = xref.getDBRefs();
if (dbrefs != null)
{
- for (DBRefEntry dbref : dbrefs)
+ for (int ir = 0, nir = dbrefs.size(); ir < nir; ir++)
{
- if (dbref.getMap() == null || dbref.getMap().getTo() == null
- || dbref.getMap().getTo().isProtein() != isProtein)
+ DBRefEntry dbref = dbrefs.get(ir);
+ Mapping map = dbref.getMap();
+ SequenceI mto;
+ if (map == null || (mto = map.getTo()) == null
+ || mto.isProtein() != isProtein)
{
continue;
}
- SequenceI mappedTo = dbref.getMap().getTo();
+ SequenceI mappedTo = mto;
SequenceI match = matcher.findIdMatch(mappedTo);
if (match == null)
{
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
+import jalview.util.Format;
import java.awt.Color;
import java.util.List;
private static final int GAP_INDEX = -1;
+ private static final Format FORMAT_3DP = new Format("%2.5f");
+
SequenceI[] sequences;
int start;
max = Math.max(max, bigtot);
- quality.addElement(new Double(bigtot));
+ quality.addElement(Double.valueOf(bigtot));
}
double newmax = -Double.MAX_VALUE;
tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
// System.out.println(tmp+ " " + j);
- quality.setElementAt(new Double(tmp), j);
+ quality.setElementAt(Double.valueOf(tmp), j);
if (tmp > newmax)
{
value = quality.elementAt(i).floatValue();
float vprop = value - qmin;
vprop /= qmax;
- quality2.annotations[i] = new Annotation(" ", String.valueOf(value),
+ String description = FORMAT_3DP.form(value);
+ quality2.annotations[i] = new Annotation(" ", description,
' ', value, new Color(minR + (maxR * vprop),
minG + (maxG * vprop), minB + (maxB * vprop)));
}
import jalview.util.Comparison;
import jalview.util.Format;
-import java.util.ArrayList;
import java.util.Hashtable;
/**
* @param rnaStruc
*/
public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result, boolean profile,
+ int end, Hashtable<String, Object>[] result, boolean profile,
AlignmentAnnotation rnaStruc)
{
- Hashtable residueHash;
+ Hashtable<String, Object> residueHash;
String maxResidue;
char[] struc = rnaStruc.getRNAStruc().toCharArray();
}
}
- residueHash = new Hashtable();
+ residueHash = new Hashtable<>();
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
maxResidue = "{";
}
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
+ residueHash.put(PID_GAPS, Float.valueOf(percentage));
percentage = ((float) count * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
if (result[i] == null)
{
maxResidue = maxResidue.equals("(") ? ")"
: maxResidue.equals("[") ? "]" : "}";
- residueHash = new Hashtable();
+ residueHash = new Hashtable<>();
if (profile)
{
residueHash.put(PROFILE,
residueHash.put(PAIRPROFILE, pairs);
}
- residueHash.put(MAXCOUNT, new Integer(count));
+ residueHash.put(MAXCOUNT, Integer.valueOf(count));
residueHash.put(MAXRESIDUE, maxResidue);
percentage = ((float) count * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
+ residueHash.put(PID_GAPS, Float.valueOf(percentage));
percentage = ((float) count * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
+ residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
result[bpEnd] = residueHash;
}
* @param includeAllConsSymbols
*/
public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
+ Hashtable<String, Object>[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols, long nseq)
{
for (int i = iStart; i < width; i++)
{
- Hashtable hci;
+ Hashtable<String, Object> hci;
if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
{
// happens if sequences calculated over were shorter than alignment
* @param hconsensus
* @return profile of the given column
*/
- public static int[] extractProfile(Hashtable hconsensus,
+ public static int[] extractProfile(Hashtable<String, Object> hconsensus,
boolean ignoreGapsInConsensusCalculation)
{
int[] rtnval = new int[STRUCTURE_PROFILE_LENGTH]; // 2*(5*5)+2
System.arraycopy(rtnval, 0, result, 1, rtnval.length);
return result;
}
-
- public static void main(String args[])
- {
- // Short test to see if checkBpType works
- ArrayList<String> test = new ArrayList<String>();
- test.add("A");
- test.add("c");
- test.add("g");
- test.add("T");
- test.add("U");
- for (String i : test)
- {
- for (String j : test)
- {
- System.out.println(i + "-" + j + ": "
- + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
- }
- }
- }
}
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
*
* @return
*/
- Hashtable[] getComplementConsensusHash();
+ Hashtable<String, Object>[] getComplementConsensusHash();
- Hashtable[] getRnaStructureConsensusHash();
+ Hashtable<String, Object>[] getRnaStructureConsensusHash();
boolean isIgnoreGapsConsensus();
*
* @param hconsensus
*/
- void setComplementConsensusHash(Hashtable[] hconsensus);
+ void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
/**
*
*
* @param hStrucConsensus
*/
- void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+ void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] hStrucConsensus);
/**
* Sets the colour scheme for the background alignment (as distinct from
*/
void setFollowHighlight(boolean b);
+ /**
+ * configure the feature renderer with predefined feature settings
+ *
+ * @param featureSettings
+ */
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
+ * Apply the given feature settings on top of existing feature settings.
+ */
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
* check if current selection group is defined on the view, or is simply a
* temporary group.
*
@Override
void setProteinFontAsCdna(boolean b);
- public abstract TreeModel getCurrentTree();
+ TreeModel getCurrentTree();
- public abstract void setCurrentTree(TreeModel tree);
+ void setCurrentTree(TreeModel tree);
+
+ /**
+ * Answers a data bean containing data for export as configured by the
+ * supplied options
+ *
+ * @param options
+ * @return
+ */
+ AlignmentExportData getAlignExportData(AlignExportSettingsI options);
/**
* @param update
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.IOException;
+ import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.net.URLEncoder;
import java.util.Arrays;
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true, true);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.getString("label.successfully_added_features_alignment"));
}
return featuresFile;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
try
{
new URL(url);
- url = URLEncoder.encode(url);
+ url = URLEncoder.encode(url, "UTF-8");
}
/*
* When we finally deprecate 1.1 compatibility, we can start to use
{
url = viewport.applet.getCodeBase() + url;
}
+ catch (UnsupportedEncodingException ex)
+ {
+ System.err.println(
+ "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+ + url);
+ ex.printStackTrace();
+ }
return url;
}
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
- viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+ // 2019.04.18
viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
column, al);
}
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new String[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
*/
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText(MessageManager.getString("label.status_bar"));
+ setStatus(MessageManager.getString("label.status_bar"));
this.add(statusBar, BorderLayout.SOUTH);
}
}
else
{
- new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
}
public jalview.bin.JalviewLite applet;
- boolean MAC = false;
-
private AnnotationColumnChooser annotationColumnSelectionState;
public AlignViewport(AlignmentI al, JalviewLite applet)
{
try
{
- widthScale = new Float(param).floatValue();
+ widthScale = Float.valueOf(param).floatValue();
} catch (Exception e)
{
}
{
try
{
- heightScale = new Float(param).floatValue();
+ heightScale = Float.valueOf(param).floatValue();
} catch (Exception e)
{
}
}
setFont(font, true);
- MAC = new jalview.util.Platform().isAMac();
-
if (applet != null)
{
setShowJVSuffix(
public void resetSeqLimits(int height)
{
- ranges.setEndSeq(height / getCharHeight());
+ ranges.setEndSeq(height / getCharHeight() - 1); // BH 2019.04.18
}
boolean centreColumnLabels;
}
/**
- * Applies the supplied feature settings descriptor to currently known
- * features. This supports an 'initial configuration' of feature colouring
- * based on a preset or user favourite. This may then be modified in the usual
- * way using the Feature Settings dialogue.
+ * Applies the supplied feature settings descriptor to currently known features.
+ * This supports an 'initial configuration' of feature colouring based on a
+ * preset or user favourite. This may then be modified in the usual way using
+ * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
// TODO implement for applet
}
+ /**
+ * Merges the supplied feature settings descriptor with existing feature styles.
+ * This supports an 'initial configuration' of feature colouring based on a
+ * preset or user favourite. This may then be modified in the usual way using
+ * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
public static int GRAPH_HEIGHT = 40;
- boolean MAC = false;
+// boolean MAC = false;
public final AnnotationRenderer renderer;
public AnnotationPanel(AlignmentPanel ap)
{
new jalview.util.Platform();
- MAC = Platform.isAMac();
+// MAC = Platform.isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
}
}
- if ((evt.getModifiers()
- & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK
&& activeRow != -1)
{
if (av.getColumnSelection() == null
*/
package jalview.appletgui;
+import jalview.util.Platform;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.FlowLayout;
* @author Jim Procter and Andrew Waterhouse
*
*/
- @SuppressWarnings("serial")
- public class EmbmenuFrame extends Frame implements MouseListener
+ public class EmbmenuFrame extends Frame
+ implements MouseListener, AutoCloseable
{
protected static final Font FONT_ARIAL_PLAIN_11 = new Font("Arial",
Font.PLAIN, 11);
/**
* map from labels to popup menus for the embedded menubar
*/
- protected Map<Label, PopupMenu> embeddedPopup = new HashMap<Label, PopupMenu>();
+ protected Map<Label, PopupMenu> embeddedPopup = new HashMap<>();
/**
* the embedded menu is built on this and should be added to the frame at the
return false;
}
// DEBUG Hint: can test embedded menus by inserting true here.
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMacAndNotJS())
{
// Build the embedded menu panel, allowing override with system font
embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, true, false);
return embeddedMenu;
}
+ @Override
public void mousePressed(MouseEvent evt)
{
PopupMenu popup = null;
return embeddedPopup.get(source);
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
/**
* calls destroyMenus()
*/
- public void finalize() throws Throwable
+ @Override
+ public void close()
{
destroyMenus();
embeddedPopup = null;
embeddedMenu = null;
- super.finalize();
- // no close for Frame
- // super.finalize();
}
}
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
+import javax.swing.SwingUtilities;
+
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener, ViewportListenerI
{
@Override
public void mouseClicked(MouseEvent evt)
{
- if ((evt.getModifiers()
- & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
{
showPopupMenu(evt);
}
@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);
}
@Override
public void mouseDragged(MouseEvent evt)
{
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ if (Platform.isWinRightButton(evt))
{
- if (!Platform.isAMac())
- {
- showPopupMenu(evt);
- }
+ showPopupMenu(evt);
+ return;
}
- else
- {
- if (draggingBox)
- {
- // set the mouse position as a fixed point in the box
- // and drag relative to that position
- od.adjustViewportFromMouse(evt.getX(), evt.getY(),
- av.getAlignment().getHiddenSequences(),
- av.getAlignment().getHiddenColumns());
- }
- else
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(),
- av.getAlignment().getHiddenSequences(),
- av.getAlignment().getHiddenColumns());
- }
- ap.paintAlignment(false, false);
+
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ return;
}
+
+ if (draggingBox)
+ {
+ // set the mouse position as a fixed point in the box
+ // and drag relative to that position
+ od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ ap.paintAlignment(false, false);
}
/**
import jalview.util.Comparison;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
// 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;
}
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers()
- & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
{
List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence,
sequence.findPosition(column + 1));
import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ColorUtils;
+import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly = false;
+ private static boolean propsAreReadOnly = Platform.isJS();
+
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
public static void initLogger()
{
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
- if (propsFile == null)
+ if (propsFile == null && !propsAreReadOnly)
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
propsAreReadOnly = true;
}
- try
+ if (propertiesFile == null)
+ { // BH 2019
+ Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+ applicationProperties);
+ }
+ else
{
- InputStream fis;
try
{
- fis = new java.net.URL(propertiesFile).openStream();
- System.out.println(
- "Loading jalview properties from : " + propertiesFile);
- System.out.println(
- "Disabling Jalview writing to user's local properties file.");
- propsAreReadOnly = true;
+ InputStream fis;
+ try
+ {
+ fis = new java.net.URL(propertiesFile).openStream();
+ System.out.println(
+ "Loading jalview properties from : " + propertiesFile);
+ System.out.println(
+ "Disabling Jalview writing to user's local properties file.");
+ propsAreReadOnly = true;
+
+ } catch (Exception ex)
+ {
+ fis = null;
+ }
+ if (fis == null)
+ {
+ fis = new FileInputStream(propertiesFile);
+ }
+ applicationProperties.clear();
+ applicationProperties.load(fis);
+
+ // remove any old build properties
+ deleteBuildProperties();
+ fis.close();
} catch (Exception ex)
{
- fis = null;
- }
- if (fis == null)
- {
- fis = new FileInputStream(propertiesFile);
+ System.out.println("Error reading properties file: " + ex);
}
- applicationProperties.clear();
- applicationProperties.load(fis);
-
- // remove any old build properties
-
- deleteBuildProperties();
- fis.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading properties file: " + ex);
}
-
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
}
// LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = resolveResourceURLFor("authors.props");
+
try
{
- String authorDetails = "jar:"
- .concat(Cache.class.getProtectionDomain().getCodeSource()
- .getLocation().toString().concat("!/authors.props"));
-
- java.net.URL localJarFileURL = new java.net.URL(authorDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
+ if (authorDetails != null)
+ {
+ java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ }
} 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));
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
-
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
// StructureImportSettings
// .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
- // jnlpVersion will be null if we're using InstallAnywhere
+
+ String jnlpVersion = System.getProperty("jalview.version");
+
+ // jnlpVersion will be null if a latest version check for the channel needs to
+ // be done
// Dont do this check if running in headless mode
+
if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (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");
*/
public static String getProperty(String key)
{
- return applicationProperties.getProperty(key);
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
}
/**
}
/**
- * These methods are used when checking if the saved preference is different
- * to the default setting
+ * Answers the value of the given property, or the supplied default value if
+ * the property is not set
*/
public static String getDefault(String property, String def)
{
- String string = getProperty(property);
- if (string != null)
- {
- return string;
- }
-
- return def;
+ String value = getProperty(property);
+ return value == null ? def : value;
}
/**
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ if (propertiesFile != null && !propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
}
}
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ return "Jalview Version: "
+ + jalview.bin.Cache.getDefault("VERSION", "TEST")
+ + "\n" + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION",
+ "unknown")
+ + "\n" + "Build Date: "
+ + jalview.bin.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")
+ + (jalview.bin.Cache.getDefault("VERSION", "TEST")
+ .equals("DEVELOPMENT")
+ ? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: "
+ + System.getProperty(
+ "java.home")
+ + File.separator + "bin"
+ + File.separator + "java"
+ : "");
+ }
+
+ /**
+ *
+ * @return build details as reported in splashscreen
+ */
+ public static String getBuildDetailsForSplash()
+ {
+ // consider returning more human friendly info
+ // eg 'built from Source' or update channel
+ return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ }
}
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
+ import com.threerings.getdown.util.LaunchUtil;
+
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
*/
public class Jalview
{
- /*
- * singleton instance of this class
- */
+ static
+ {
+ Platform.getURLCommandArguments();
+ }
+
+ // singleton instance of this class
+
private static Jalview instance;
private Desktop desktop;
static
{
- // grab all the rights we can the JVM
- Policy.setPolicy(new Policy()
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- @Override
- public PermissionCollection getPermissions(CodeSource codesource)
- {
- Permissions perms = new Permissions();
- perms.add(new AllPermission());
- return (perms);
- }
-
- @Override
- public void refresh()
- {
- }
- });
+ // grab all the rights we can for the JVM
+ Policy.setPolicy(new Policy()
+ {
+ @Override
+ public PermissionCollection getPermissions(CodeSource codesource)
+ {
+ Permissions perms = new Permissions();
+ perms.add(new AllPermission());
+ return (perms);
+ }
+
+ @Override
+ public void refresh()
+ {
+ }
+ });
+ }
}
/**
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
+ * TODO: generalise to track all jalview events to orchestrate batch processing
+ * events.
*/
private int queued = 0;
* main class for Jalview application
*
* @param args
- * open <em>filename</em>
+ * open <em>filename</em>
*/
public static void main(String[] args)
{
+// setLogging(); // BH - for event debugging in JavaScript
instance = new Jalview();
instance.doMain(args);
+}
+
+ private static void logClass(String name)
+ {
+ // BH - for event debugging in JavaScript
+ ConsoleHandler consoleHandler = new ConsoleHandler();
+ consoleHandler.setLevel(Level.ALL);
+ Logger logger = Logger.getLogger(name);
+ logger.setLevel(Level.ALL);
+ logger.addHandler(consoleHandler);
+ }
+
+ @SuppressWarnings("unused")
+ private static void setLogging()
+ {
+
+ /**
+ * @j2sIgnore
+ *
+ */
+ {
+ System.out.println("not in js");
+ }
+
+ // BH - for event debugging in JavaScript (Java mode only)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Logger.getLogger("").setLevel(Level.ALL);
+ logClass("java.awt.EventDispatchThread");
+ logClass("java.awt.EventQueue");
+ logClass("java.awt.Component");
+ logClass("java.awt.focus.Component");
+ logClass("java.awt.focus.DefaultKeyboardFocusManager");
+ }
+
}
+
+
+
/**
* @param args
*/
void doMain(String[] args)
{
- System.setSecurityManager(null);
+
+ if (!Platform.isJS())
+ {
+ System.setSecurityManager(null);
+ }
+
System.out
.println("Java version: " + System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ // report Jalview version
+ Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
- if (aparser.contains("help") || aparser.contains("h"))
- {
- showUsage();
- System.exit(0);
- }
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
- {
- System.setProperty("java.awt.headless", "true");
- headless = true;
- }
String usrPropsFile = aparser.getValue("props");
Cache.loadProperties(usrPropsFile); // must do this before
if (usrPropsFile != null)
"CMD [-props " + usrPropsFile + "] executed successfully!");
}
- // anything else!
-
- final String jabawsUrl = aparser.getValue("jabaws");
- if (jabawsUrl != null)
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- try
+ if (aparser.contains("help") || aparser.contains("h"))
{
- Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println(
- "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
- } catch (MalformedURLException e)
+ showUsage();
+ System.exit(0);
+ }
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
- System.err.println(
- "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ System.setProperty("java.awt.headless", "true");
+ headless = true;
+ }
+ // anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+ }
}
- }
+ }
String defs = aparser.getValue("setprop");
while (defs != null)
{
else
{
System.out.println("Executing setprop argument: " + defs);
- // DISABLED FOR SECURITY REASONS
- // TODO: add a property to allow properties to be overriden by cli args
- // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ if (Platform.isJS())
+ {
+ Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ }
}
defs = aparser.getValue("setprop");
}
System.err.println("Unexpected Look and Feel Exception");
ex.printStackTrace();
}
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
"Failed to set QuaQua look and feel: " + e.toString());
}
}
- if (lookAndFeel == null || !(lookAndFeel.getClass()
- .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
|| !UIManager.getLookAndFeel().getClass().toString()
.toLowerCase().contains("quaqua"))
{
}
/*
- * configure 'full' SO model if preferences say to,
- * else use the default (SO Lite)
+ * configure 'full' SO model if preferences say to, else use the default (SO
+ * Lite)
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault("USE_FULL_SO", true))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
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
{
- if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
+ if (!aparser.contains("noquestionnaire"))
+ {
+ String url = aparser.getValue("questionnaire");
+ if (url != 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);
+ 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;
System.out.println("No files to open!");
System.exit(1);
}
- String vamsasImport = aparser.getValue("vdoc");
- String vamsasSession = aparser.getValue("vsess");
- if (vamsasImport != null || vamsasSession != null)
- {
- if (desktop == null || headless)
- {
- System.out.println(
- "Headless vamsas sessions not yet supported. Sorry.");
- System.exit(1);
- }
- // if we have a file, start a new session and import it.
- boolean inSession = false;
- if (vamsasImport != null)
- {
- try
- {
- DataSourceType viprotocol = AppletFormatAdapter
- .checkProtocol(vamsasImport);
- if (viprotocol == DataSourceType.FILE)
- {
- inSession = desktop.vamsasImport(new File(vamsasImport));
- }
- else if (viprotocol == DataSourceType.URL)
- {
- inSession = desktop.vamsasImport(new URL(vamsasImport));
- }
-
- } catch (Exception e)
- {
- System.err.println("Exeption when importing " + vamsasImport
- + " as a vamsas document.");
- e.printStackTrace();
- }
- if (!inSession)
- {
- System.err.println("Failed to import " + vamsasImport
- + " as a vamsas document.");
- }
- else
- {
- System.out.println("Imported Successfully into new session "
- + desktop.getVamsasApplication().getCurrentSession());
- }
- }
- if (vamsasSession != null)
- {
- if (vamsasImport != null)
- {
- // close the newly imported session and import the Jalview specific
- // remnants into the new session later on.
- desktop.vamsasStop_actionPerformed(null);
- }
- // now join the new session
- try
- {
- if (desktop.joinVamsasSession(vamsasSession))
- {
- System.out.println(
- "Successfully joined vamsas session " + vamsasSession);
- }
- else
- {
- System.err.println("WARNING: Failed to join vamsas session "
- + vamsasSession);
- }
- } catch (Exception e)
- {
- System.err.println(
- "ERROR: Failed to join vamsas session " + vamsasSession);
- e.printStackTrace();
- }
- if (vamsasImport != null)
- {
- // the Jalview specific remnants can now be imported into the new
- // session at the user's leisure.
- Cache.log.info(
- "Skipping Push for import of data into existing vamsas session."); // TODO:
- // enable
- // this
- // when
- // debugged
- // desktop.getVamsasApplication().push_update();
- }
- }
- }
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
}
System.out.println("CMD [-open " + file + "] executed successfully!");
- if (!file.startsWith("http://"))
+ if (!Platform.isJS())
+ /**
+ * ignore in JavaScript -- can't just file existence - could load it?
+ *
+ * @j2sIgnore
+ */
{
- if (!(new File(file)).exists())
+ if (!file.startsWith("http://") && !file.startsWith("https://"))
+ // BH 2019 added https check for Java
{
- System.out.println("Can't find " + file);
- if (headless)
+ if (!(new File(file)).exists())
{
- System.exit(1);
+ System.out.println("Can't find " + file);
+ if (headless)
+ {
+ System.exit(1);
+ }
}
}
}
- protocol = AppletFormatAdapter.checkProtocol(file);
+ protocol = AppletFormatAdapter.checkProtocol(file);
try
{
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport(),
- af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
if (cs != null)
{
continue;
}
- if (af.saveAlignment(file, format))
+ af.saveAlignment(file, format);
+ if (af.isSaveAlignmentSuccessful())
{
System.out.println("Written alignment in " + format
+ " format to " + file);
// 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;
// passed in correctly)"
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
- // +
- // "-vdoc vamsas-document\tImport vamsas document into new
- // session or join existing session with same URN\n"
- // + "-vses vamsas-session\tJoin session with given URN\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
}
* Locate the given string as a file and pass it to the groovy interpreter.
*
* @param groovyscript
- * the script to execute
+ * the script to execute
* @param jalviewContext
- * the Jalview Desktop object passed in to the groovy binding as the
- * 'Jalview' object.
+ * the Jalview Desktop object passed in to the groovy
+ * binding as the 'Jalview' object.
*/
private void executeGroovyScript(String groovyscript, AlignFrame af)
{
}
try
{
- Map<String, Object> vbinding = new HashMap<>();
+ Map<String, java.lang.Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode
- * when it just ends the JVM
+ * Quit method delegates to Desktop.quit - unless running in headless mode when
+ * it just ends the JVM
*/
public void quit()
{
int apos = -1;
try
{
- apos = new Integer(position).intValue();
+ apos = Integer.valueOf(position).intValue();
apos--;
} catch (NumberFormatException ex)
{
int from = -1, to = -1;
try
{
- from = new Integer(cl.substring(0, p)).intValue();
+ from = Integer.valueOf(cl.substring(0, p)).intValue();
from--;
} catch (NumberFormatException ex)
{
}
try
{
- to = new Integer(cl.substring(p + 1)).intValue();
+ to = Integer.valueOf(cl.substring(p + 1)).intValue();
to--;
} catch (NumberFormatException ex)
{
int r = -1;
try
{
- r = new Integer(cl).intValue();
+ r = Integer.valueOf(cl).intValue();
r--;
} catch (NumberFormatException ex)
{
try
{
StructureSelectionManager.getStructureSelectionManager(me)
- .mouseOverStructure(new Integer(pdbResNum).intValue(),
+ .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
chain, pdbfile);
if (debug)
{
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(),
- new Integer(leftHandColumn).intValue());
+ alf.scrollTo(Integer.valueOf(topRow).intValue(),
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
{
try
{
- alf.scrollToRow(new Integer(topRow).intValue());
+ alf.scrollToRow(Integer.valueOf(topRow).intValue());
} catch (Exception ex)
{
{
try
{
- alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+ alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
private boolean alignPdbStructures = false;
/**
- * use an external structure viewer exclusively (no jmols or MCViews will be
+ * use an external structure viewer exclusively (no jmols or mc_views will be
* opened by JalviewLite itself)
*/
public boolean useXtrnalSviewer = false;
if (!jmolAvailable)
{
System.out.println(
- "Jmol not available - Using MCview for structures");
+ "Jmol not available - Using mc_view for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
if (debug)
{
System.err.println(
- "Skipping Jmol check. Will use MCView (probably)");
+ "Skipping Jmol check. Will use mc_view (probably)");
}
}
checkedForJmol = true;
*/
if (command.alIndex[i] < command.al.getHeight())
{
- List<SequenceI> sequences;
- synchronized (sequences = command.al.getSequences())
+ List<SequenceI> sequences = command.al.getSequences();
+ synchronized (sequences)
{
if (!(command.alIndex[i] < 0))
{
// old ds and edited ds are different, so
// create the new dataset sequence
SequenceI newds = new Sequence(oldds);
- newds.setSequence(fullseq);
+ newds.setSequence(fullseq.toUpperCase());
if (command.oldds == null)
{
public class Edit
{
- private SequenceI[] oldds;
+ SequenceI[] oldds;
/**
* start and end of sequence prior to edit
*/
- private Range[] oldStartEnd;
+ Range[] oldStartEnd;
- private boolean fullAlignmentHeight = false;
+ boolean fullAlignmentHeight = false;
- private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+ Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- private Map<String, Annotation[]> deletedAnnotations;
+ Map<String, Annotation[]> deletedAnnotations;
/*
* features deleted by the cut (re-add on Undo)
* (including the original of any shortened features)
*/
- private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
+ Map<SequenceI, List<SequenceFeature>> deletedFeatures;
/*
* shortened features added by the cut (delete on Undo)
*/
- private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
+ Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
- private AlignmentI al;
+ AlignmentI al;
- final private Action command;
+ final Action command;
char[][] string;
SequenceI[] seqs;
- private int[] alIndex;
+ int[] alIndex;
- private int position;
+ int position;
- private int number;
+ int number;
- private char gapChar;
+ char gapChar;
/*
* flag that identifies edits inserted to balance
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
- || extendCurrent) ? viewport.getAlignment()
- : viewport.getSelectionGroup();
+ boolean searchSelection = viewport.getSelectionGroup() != null
+ && !extendCurrent;
+ SequenceCollectionI sqcol = searchSelection ? viewport
+ .getSelectionGroup() : viewport.getAlignment();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
}
else
{
- avcg.setStatus(MessageManager
- .formatMessage("label.no_feature_of_type_found", new String[]
- { featureType }));
+ String key = searchSelection ? "label.no_feature_found_selection"
+ : "label.no_feature_of_type_found";
+ avcg.setStatus(MessageManager.formatMessage(key,
+ new String[] { featureType }));
if (!extendCurrent)
{
cs.clear();
}
@Override
- public boolean parseFeaturesFile(String file, DataSourceType protocol,
+ public boolean parseFeaturesFile(Object file, DataSourceType protocol,
boolean relaxedIdMatching)
{
boolean featuresAdded = false;
* @author JimP
*
*/
- public class Alignment implements AlignmentI
+ public class Alignment implements AlignmentI, AutoCloseable
{
private Alignment dataset;
{
synchronized (sequences)
{
+
if (i > -1 && i < sequences.size())
{
return sequences.get(i);
}
@Override
- public void finalize() throws Throwable
+ public void close()
{
if (getDataset() != null)
{
- getDataset().removeAlignmentRef();
+ try
+ {
+ getDataset().removeAlignmentRef();
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
}
nullReferences();
- super.finalize();
}
/**
int i = 0;
SequenceI sq = null;
String sqname = null;
+ int nseq = sequences.size();
if (startAfter != null)
{
// try to find the sequence in the alignment
boolean matched = false;
- while (i < sequences.size())
+ while (i < nseq)
{
if (getSequenceAt(i++) == startAfter)
{
i = 0;
}
}
- while (i < sequences.size())
+ while (i < nseq)
{
sq = getSequenceAt(i);
sqname = sq.getName();
int maxLength = -1;
SequenceI current;
- for (int i = 0; i < sequences.size(); i++)
+ int nseq = sequences.size();
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size(); i++)
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
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);
/**
*
* @param source
- * canonical source (uppercase only)
+ * canonical source (turned to uppercase; cannot be null)
* @param version
- * (source dependent version string)
+ * (source dependent version string or null)
* @param accessionId
- * (source dependent accession number string)
+ * (source dependent accession number string or null)
* @param map
* (mapping from local sequence numbering to source accession
- * numbering)
+ * numbering or null)
*/
public DBRefEntry(String source, String version, String accessionId,
Mapping map)
{
+
this.source = source.toUpperCase();
- this.version = version;
+ setVersion(version);
this.accessionId = accessionId;
this.map = map;
}
+ /**
+ * Clone an entry, this time not allowing any null fields except map.
+ *
+ */
public DBRefEntry(DBRefEntryI entry)
{
this((entry.getSource() == null ? "" : new String(entry.getSource())),
{
// TODO should also override hashCode to ensure equal objects have equal
// hashcodes
- if (o == null || !(o instanceof DBRefEntry))
- {
- return false;
- }
- DBRefEntry entry = (DBRefEntry) o;
- if (entry == this)
- {
- return true;
- }
- if (equalRef(entry) && ((map == null && entry.map == null)
- || (map != null && entry.map != null && map.equals(entry.map))))
- {
- return true;
- }
- return false;
+
+
+// if (o == null || !(o instanceof DBRefEntry))
+// {
+// return false;
+// }
+// DBRefEntry entry = (DBRefEntry) o;
+// if (entry == this)
+// {
+// return true;
+// }
+ Mapping em;
+ return (o != null && o instanceof DBRefEntry
+ && (o == this
+ || equalRef((DBRefEntry) o)
+ && (map == null) == ((em = ((DBRefEntry) o).map) == null)
+ && (map == null || map.equals(em))));
+//
+// {
+// return true;
+// }
+// return false;
}
/**
{
return true;
}
- if (entry != null
+
+ // BH 2019.01.25/2019.02.04 source cannot/should not be null.
+ // for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
+
+ return (entry != null
&& (source != null && entry.getSource() != null
&& source.equalsIgnoreCase(entry.getSource()))
&& (accessionId != null && entry.getAccessionId() != null
&& accessionId.equalsIgnoreCase(entry.getAccessionId()))
&& (version != null && entry.getVersion() != null
- && version.equalsIgnoreCase(entry.getVersion())))
- {
- return true;
- }
- return false;
+ && version.equalsIgnoreCase(entry.getVersion())));
}
@Override
return source;
}
+ public int getSourceKey()
+ {
+ return (sourceKey == Integer.MIN_VALUE ? (sourceKey = DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey);
+ }
+
+ /**
+ * can be null
+ */
@Override
public String getVersion()
{
return version;
}
+ /**
+ * can be null
+ */
@Override
public String getAccessionId()
{
@Override
public void setAccessionId(String accessionId)
{
- this.accessionId = accessionId;
+ this.accessionId = accessionId;
+// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
}
+ /**
+ * CAUTION! allows setting source null or not uppercase!
+ */
@Override
public void setSource(String source)
{
- this.source = source;
+ this.source = source;
+
+// this.source = (source == null ? "" : source).toUpperCase();
+// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
@Override
public void setVersion(String version)
{
this.version = version;
+ this.ucversion = (version == null ? null : version.toUpperCase());
}
@Override
*/
if (map != null)
{
- if (map.getTo() != null)
+ SequenceI mto = map.getTo();
+ if (mto != null)
{
return false;
}
- if (map.getMap().getFromRatio() != map.getMap().getToRatio()
- || map.getMap().getFromRatio() != 1)
+ MapList ml = map.getMap();
+ if (ml.getFromRatio() != ml.getToRatio()
+ || ml.getFromRatio() != 1)
{
return false;
}
// check map is between identical single contiguous ranges
- List<int[]> fromRanges = map.getMap().getFromRanges();
- List<int[]> toRanges = map.getMap().getToRanges();
- if (fromRanges.size() != 1 || toRanges.size() != 1)
+ List<int[]> fromRanges, toRanges;
+ if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
{
return false;
}
// 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);
}
-
-
}
package jalview.datamodel;
import jalview.analysis.AlignSeq;
-import jalview.api.DBRefEntryI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.datamodel.features.SequenceFeaturesI;
import jalview.util.Comparison;
*/
public class Sequence extends ASequence implements SequenceI
{
+
+ /**
+ * A subclass that gives us access to modCount, which tracks whether there
+ * have been any changes. We use this to update
+ *
+ * @author hansonr
+ *
+ * @param <T>
+ */
+ @SuppressWarnings("serial")
+ public class DBModList<T> extends ArrayList<DBRefEntry>
+ {
+
+ protected int getModCount()
+ {
+ return modCount;
+ }
+
+ }
+
SequenceI datasetSequence;
- String name;
+ private String name;
private char[] sequence;
- String description;
+ private String description;
+
+ private int start;
- int start;
+ private int end;
- int end;
+ private Vector<PDBEntry> pdbIds;
- Vector<PDBEntry> pdbIds;
+ private String vamsasId;
- String vamsasId;
+ private DBModList<DBRefEntry> dbrefs; // controlled access
- DBRefEntry[] dbrefs;
+ /**
+ * a flag to let us know that elements have changed in dbrefs
+ *
+ * @author Bob Hanson
+ */
+ private int refModCount = 0;
- RNA rna;
+ private RNA rna;
/**
* This annotation is displayed below the alignment but the positions are tied
*
* TODO: change to List<>
*/
- Vector<AlignmentAnnotation> annotation;
+ private Vector<AlignmentAnnotation> annotation;
private SequenceFeaturesI sequenceFeatureStore;
{
setDatasetSequence(seq.getDatasetSequence());
}
-
+
/*
* only copy DBRefs and seqfeatures if we really are a dataset sequence
*/
if (datasetSequence == null)
{
- if (seq.getDBRefs() != null)
+ List<DBRefEntry> dbr = seq.getDBRefs();
+ if (dbr != null)
{
- DBRefEntry[] dbr = seq.getDBRefs();
- for (int i = 0; i < dbr.length; i++)
+ for (int i = 0, n = dbr.size(); i < n; i++)
{
- addDBRef(new DBRefEntry(dbr[i]));
+ addDBRef(new DBRefEntry(dbr.get(i)));
}
}
{
if (sf.getType() == null)
{
- System.err.println("SequenceFeature type may not be null: "
- + sf.toString());
+ System.err.println(
+ "SequenceFeature type may not be null: " + sf.toString());
return false;
}
public char[] getSequence()
{
// return sequence;
- return sequence == null ? null : Arrays.copyOf(sequence,
- sequence.length);
+ return sequence == null ? null
+ : Arrays.copyOf(sequence, sequence.length);
}
/*
public void setGeneLoci(String speciesId, String assemblyId,
String chromosomeId, MapList map)
{
- addDBRef(new DBRefEntry(speciesId, assemblyId,
- DBRefEntry.CHROMOSOME + ":" + chromosomeId, new Mapping(map)));
+ addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+ new Mapping(map)));
}
/**
@Override
public GeneLociI getGeneLoci()
{
- DBRefEntry[] refs = getDBRefs();
+ List<DBRefEntry> refs = getDBRefs();
if (refs != null)
{
for (final DBRefEntry ref : refs)
{
- if (ref.isChromosome())
+ if (ref instanceof GeneLociI)
{
- return new GeneLociI()
- {
- @Override
- public String getSpeciesId()
- {
- return ref.getSource();
- }
-
- @Override
- public String getAssemblyId()
- {
- // DEV NOTE: DBRefEntry is reused here to hold chromosomal locus
- // of a gene sequence.
- // source=species, version=assemblyId, accession=chromosome, map =
- // positions.
-
- return ref.getVersion();
- }
-
- @Override
- public String getChromosomeId()
- {
- // strip off "chromosome:" prefix to chrId
- return ref.getAccessionId()
- .substring(DBRefEntry.CHROMOSOME.length() + 1);
- }
-
- @Override
- public MapList getMap()
- {
- return ref.getMap().getMap();
- }
- };
+ return (GeneLociI) ref;
}
}
}
{
return findPosition(column + 1, cursor);
}
-
+
// TODO recode this more naturally i.e. count residues only
// as they are found, not 'in anticipation'
{
ArrayList<int[]> map = new ArrayList<>();
int lastj = -1, j = 0;
- int pos = start;
+ // int pos = start;
int seqlen = sequence.length;
while ((j < seqlen))
{
{
BitSet map = new BitSet();
int lastj = -1, j = 0;
- int pos = start;
+ // int pos = start;
int seqlen = sequence.length;
while ((j < seqlen))
{
vamsasId = id;
}
+ @Deprecated
@Override
- public void setDBRefs(DBRefEntry[] dbref)
+ public void setDBRefs(DBModList<DBRefEntry> newDBrefs)
{
if (dbrefs == null && datasetSequence != null
&& this != datasetSequence)
{
- datasetSequence.setDBRefs(dbref);
+ datasetSequence.setDBRefs(newDBrefs);
return;
}
- dbrefs = dbref;
- if (dbrefs != null)
- {
- DBRefUtils.ensurePrimaries(this);
- }
+ dbrefs = newDBrefs;
+ refModCount = 0;
}
@Override
- public DBRefEntry[] getDBRefs()
+ public DBModList<DBRefEntry> getDBRefs()
{
if (dbrefs == null && datasetSequence != null
&& this != datasetSequence)
if (dbrefs == null)
{
- dbrefs = new DBRefEntry[0];
+ dbrefs = new DBModList<>();
}
- for (DBRefEntryI dbr : dbrefs)
+ for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
{
- if (dbr.updateFrom(entry))
+ if (dbrefs.get(ib).updateFrom(entry))
{
/*
* found a dbref that either matched, or could be
}
}
- /*
- * extend the array to make room for one more
- */
- // TODO use an ArrayList instead
- int j = dbrefs.length;
- DBRefEntry[] temp = new DBRefEntry[j + 1];
- System.arraycopy(dbrefs, 0, temp, 0, j);
- temp[temp.length - 1] = entry;
-
- dbrefs = temp;
+ // /// BH OUCH!
+ // /*
+ // * extend the array to make room for one more
+ // */
+ // // TODO use an ArrayList instead
+ // int j = dbrefs.length;
+ // List<DBRefEntry> temp = new DBRefEntry[j + 1];
+ // System.arraycopy(dbrefs, 0, temp, 0, j);
+ // temp[temp.length - 1] = entry;
+ //
+ // dbrefs = temp;
- DBRefUtils.ensurePrimaries(this);
+ dbrefs.add(entry);
}
@Override
private int _seqhash = 0;
+ private List<DBRefEntry> primaryRefs;
+
/**
* Answers false if the sequence is more than 85% nucleotide (ACGTU), else
* true
_isNa = Comparison.isNucleotide(this);
}
return !_isNa;
-- };
++ }
/*
* (non-Javadoc)
// TODO: could merge DBRefs
return datasetSequence.updatePDBIds();
}
- if (dbrefs == null || dbrefs.length == 0)
+ if (dbrefs == null || dbrefs.size() == 0)
{
return false;
}
boolean added = false;
- for (DBRefEntry dbr : dbrefs)
+ for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
{
+ DBRefEntry dbr = dbrefs.get(ib);
if (DBRefSource.PDB.equals(dbr.getSource()))
{
/*
List<SequenceFeature> sfs = entry.getSequenceFeatures();
for (SequenceFeature feature : sfs)
{
- SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
- : new SequenceFeature[] { new SequenceFeature(feature) };
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+ : new SequenceFeature[]
+ { new SequenceFeature(feature) };
if (sf != null)
{
for (int sfi = 0; sfi < sf.length; sfi++)
}
}
// transfer database references
- DBRefEntry[] entryRefs = entry.getDBRefs();
+ List<DBRefEntry> entryRefs = entry.getDBRefs();
if (entryRefs != null)
{
- for (int r = 0; r < entryRefs.length; r++)
+ for (int r = 0, n = entryRefs.size(); r < n; r++)
{
- DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+ DBRefEntry newref = new DBRefEntry(entryRefs.get(r));
if (newref.getMap() != null && mp != null)
{
// remap ref using our local mapping
return null;
}
+ private List<DBRefEntry> tmpList;
+
@Override
public List<DBRefEntry> getPrimaryDBRefs()
{
{
return datasetSequence.getPrimaryDBRefs();
}
- if (dbrefs == null || dbrefs.length == 0)
+ if (dbrefs == null || dbrefs.size() == 0)
{
return Collections.emptyList();
}
synchronized (dbrefs)
{
- List<DBRefEntry> primaries = new ArrayList<>();
- DBRefEntry[] tmp = new DBRefEntry[1];
- for (DBRefEntry ref : dbrefs)
+ if (refModCount == dbrefs.getModCount() && primaryRefs != null)
+ {
+ return primaryRefs; // no changes
+ }
+ refModCount = dbrefs.getModCount();
+ List<DBRefEntry> primaries = (primaryRefs == null
+ ? (primaryRefs = new ArrayList<>())
+ : primaryRefs);
+ primaries.clear();
+ if (tmpList == null)
{
+ tmpList = new ArrayList<>();
+ tmpList.add(null); // for replacement
+ }
+ for (int i = 0, n = dbrefs.size(); i < n; i++)
+ {
+ DBRefEntry ref = dbrefs.get(i);
if (!ref.isPrimaryCandidate())
{
continue;
}
}
// whilst it looks like it is a primary ref, we also sanity check type
- if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
- .equals(DBRefUtils.getCanonicalName(ref.getSource())))
+ if (DBRefSource.PDB_CANONICAL_NAME
+ .equals(ref.getCanonicalSourceName()))
{
// PDB dbrefs imply there should be a PDBEntry associated
// TODO: tighten PDB dbrefs
// handle on the PDBEntry, and a real mapping between sequence and
// extracted sequence from PDB file
PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
- if (pdbentry != null && pdbentry.getFile() != null)
+ if (pdbentry == null || pdbentry.getFile() == null)
{
- primaries.add(ref);
+ continue;
}
- continue;
}
- // check standard protein or dna sources
- tmp[0] = ref;
- DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
- if (res != null && res[0] == tmp[0])
+ else
{
- primaries.add(ref);
- continue;
+ // check standard protein or dna sources
+ tmpList.set(0, ref);
+ List<DBRefEntry> res = DBRefUtils.selectDbRefs(!isProtein(),
+ tmpList);
+ if (res == null || res.get(0) != tmpList.get(0))
+ {
+ continue;
+ }
}
+ primaries.add(ref);
}
+
+ // version must be not null, as otherwise it will not be a candidate,
+ // above
+ DBRefUtils.ensurePrimaries(this, primaries);
return primaries;
}
}
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.JSONUtils;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
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;
/**
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
+
List<String> queries = new ArrayList<>();
queries.add(query);
- BufferedReader fp = getSequenceReader(queries);
- if (fp == null)
- {
- return null;
- }
-
- SequenceI seq = parseFeaturesJson(fp);
+ SequenceI seq = parseFeaturesJson(queries);
+ if (seq == null)
+ return null;
return new Alignment(new SequenceI[] { seq });
+
}
/**
* @param br
* @return
*/
- private SequenceI parseFeaturesJson(BufferedReader br)
+ @SuppressWarnings("unchecked")
+ private SequenceI parseFeaturesJson(List<String> queries)
{
SequenceI seq = new Sequence("Dummy", "");
-
- JSONParser jp = new JSONParser();
try
{
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
- while (rvals.hasNext())
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+ if (rvals == null)
{
+ return null;
+ }
+ while (rvals.hasNext())
+ {
try
{
- JSONObject obj = (JSONObject) rvals.next();
+ Map<String, Object> obj = (Map<String, Object>) rvals.next();
String type = obj.get("feature_type").toString();
int start = Integer.parseInt(obj.get("start").toString());
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'
{
type = SequenceOntologyI.CDS;
}
-
+
String desc = getFirstNotNull(obj, "alleles", "external_name",
JSON_ID);
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
source);
sf.setStrand("1".equals(strand) ? "+" : "-");
+ if (phase != null)
+ {
+ sf.setPhase(phase.toString());
+ }
setFeatureAttribute(sf, obj, "id");
setFeatureAttribute(sf, obj, "Parent");
setFeatureAttribute(sf, obj, "consequence_type");
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
+
} catch (Throwable t)
{
// ignore - keep trying other features
}
} catch (ParseException | IOException e)
{
+ e.printStackTrace();
// ignore
}
* @param keys
* @return
*/
- protected String getFirstNotNull(JSONObject obj, String... keys)
+ @SuppressWarnings("unchecked")
+ protected String getFirstNotNull(Map<String, Object> obj, String... keys)
{
- String desc = null;
-
for (String key : keys)
{
Object val = obj.get(key);
if (val != null)
{
- String s = val instanceof JSONArray
- ? JSONUtils.arrayToList((JSONArray) val)
+ String s = val instanceof List<?>
+ ? JSONUtils.arrayToStringList((List<Object>) val)
: val.toString();
if (!s.isEmpty())
{
}
}
}
- return desc;
+ return null;
}
/**
* @param obj
* @param key
*/
- protected void setFeatureAttribute(SequenceFeature sf, JSONObject obj,
+ protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
String key)
{
Object object = obj.get(key);
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
- import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
+import jalview.util.Platform;
import java.awt.Color;
import java.io.UnsupportedEncodingException;
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ private static final String CHROMOSOME = "chromosome";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
* convert to a non-duplicated list of gene identifiers
*/
List<String> geneIds = getGeneIds(query);
-
AlignmentI al = null;
for (String geneId : geneIds)
{
{
// ensure id has 'correct' case for the Ensembl identifier
geneId = geneAlignment.getSequenceAt(0).getName();
-
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
-
getTranscripts(geneAlignment, geneId);
}
if (al == null)
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), geneLoci.getMapping());
}
else
{
return false;
}
String[] tokens = description.split(":");
- if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+ if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
{
String ref = tokens[1];
String chrom = tokens[2];
return;
}
- MapList geneMapping = loci.getMap();
+ MapList geneMapping = loci.getMapping();
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
@Override
public String getTestQuery()
{
- return "ENSG00000157764"; // BRAF, 5 transcripts, reverse strand
+ return Platform.isJS() ? "ENSG00000123569" : "ENSG00000157764";
+ // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
+ // ENSG00000157764 // BRAF, 5 transcripts, reverse strand
// ENSG00000090266 // NDUFB2, 15 transcripts, forward strand
// ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand
- // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
}
/**
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 java.util.Arrays;
import java.util.Collections;
import java.util.List;
+import java.util.Map;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
/**
* @param br
* @return
*/
- protected String parseGeneId(JSONObject val)
+ protected String parseGeneId(Map<String, Object> val)
{
if (val == null)
{
public String getSpecies(String identifier)
{
String species = null;
- JSONObject json = getResult(identifier, null);
+ Map<String, Object> json = getResult(identifier, null);
if (json != null)
{
Object o = json.get(SPECIES);
}
/**
- * Calls the /lookup/id rest service and returns the response as a JSONObject,
+ * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
* or null if any error
*
* @param identifier
* (optional)
* @return
*/
- protected JSONObject getResult(String identifier, String objectType)
+ @SuppressWarnings("unchecked")
+ protected Map<String, Object> getResult(String identifier, String objectType)
{
List<String> ids = Arrays.asList(new String[] { identifier });
- BufferedReader br = null;
try
{
- URL url = getUrl(identifier, objectType);
-
- if (url != null)
- {
- br = getHttpResponse(url, ids);
- }
- return br == null ? null : (JSONObject) (new JSONParser().parse(br));
- } catch (IOException | ParseException e)
+ return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
+ }
+ catch (IOException | ParseException e)
{
System.err.println("Error parsing " + identifier + " lookup response "
+ e.getMessage());
return null;
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
}
}
* @param json
* @return
*/
- GeneLociI parseGeneLoci(JSONObject json)
+ GeneLociI parseGeneLoci(Map<String, Object> json)
{
if (json == null)
{
fromEnd });
List<int[]> toRange = Collections.singletonList(new int[] { toStart,
toEnd });
- final MapList map = new MapList(fromRange, toRange, 1, 1);
- return new GeneLociI()
- {
-
- @Override
- public String getSpeciesId()
- {
- return species == null ? "" : species;
- }
-
- @Override
- public String getAssemblyId()
- {
- return assembly;
- }
-
- @Override
- public String getChromosomeId()
- {
- return chromosome;
- }
-
- @Override
- public MapList getMap()
- {
- return map;
- }
- };
+ final Mapping map = new Mapping(
+ new MapList(fromRange, toRange, 1, 1));
+ return new GeneLocus(species == null ? "" : species, assembly,
+ chromosome, map);
} catch (NullPointerException | NumberFormatException e)
{
Cache.log.error("Error looking up gene loci: " + e.getMessage());
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";
String fromRef, String toRef, int[] queryRange)
{
URL url = null;
- BufferedReader br = null;
-
try
{
url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
queryRange[1]);
- br = getHttpResponse(url, null);
- return (parseAssemblyMappingResponse(br));
+ return (parseAssemblyMappingResponse(url));
} catch (Throwable t)
{
System.out.println("Error calling " + url + ": " + t.getMessage());
return null;
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
}
}
* @param br
* @return
*/
- protected int[] parseAssemblyMappingResponse(BufferedReader br)
+ @SuppressWarnings("unchecked")
+ protected int[] parseAssemblyMappingResponse(URL url)
{
int[] result = null;
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"
- JSONObject val = (JSONObject) rvals.next();
- JSONObject mapped = (JSONObject) val.get(MAPPED);
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
+ Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
int start = Integer.parseInt(mapped.get("start").toString());
int end = Integer.parseInt(mapped.get("end").toString());
String strand = mapped.get("strand").toString();
int end, String cdsOrCdna)
{
URL url = null;
- BufferedReader br = null;
-
try
{
String domain = new EnsemblInfo().getDomain(division);
if (domain != null)
{
url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
- br = getHttpResponse(url, null);
- if (br != null)
- {
- return (parseIdMappingResponse(br, accession, domain));
- }
+ return (parseIdMappingResponse(url, accession, domain));
}
return null;
} catch (Throwable t)
{
System.out.println("Error calling " + url + ": " + t.getMessage());
return null;
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
}
}
* @param domain
* @return
*/
- GeneLociI parseIdMappingResponse(BufferedReader br, String accession,
+ @SuppressWarnings("unchecked")
+GeneLociI parseIdMappingResponse(URL url, String accession,
String domain)
{
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;
while (rvals.hasNext())
{
- JSONObject val = (JSONObject) rvals.next();
- JSONObject original = (JSONObject) val.get("original");
+ Map<String, Object> val = (Map<String, Object>) rvals.next();
+ Map<String, Object> original = (Map<String, Object>) val.get("original");
fromEnd = Integer.parseInt(original.get("end").toString());
- JSONObject mapped = (JSONObject) val.get(MAPPED);
+ Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
int start = Integer.parseInt(mapped.get("start").toString());
int end = Integer.parseInt(mapped.get("end").toString());
String ass = mapped.get("assembly_name").toString();
final String chr = chromosome;
List<int[]> fromRange = Collections.singletonList(new int[] { 1,
fromEnd });
- final MapList map = new MapList(fromRange, regions, 1, 1);
- return new GeneLociI()
- {
-
- @Override
- public String getSpeciesId()
- {
- return species == null ? "" : species;
- }
-
- @Override
- public String getAssemblyId()
- {
- return as;
- }
-
- @Override
- public String getChromosomeId()
- {
- return chr;
- }
-
- @Override
- public MapList getMap()
- {
- return map;
- }
- };
+ Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
+ return new GeneLocus(species == null ? "" : species, as, chr,
+ mapping);
} catch (IOException | ParseException | NumberFormatException e)
{
// ignore
import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
- import java.security.AccessControlException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Hashtable;
{
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getStructureFiles());
- viewer.dispose();
+ if (viewer != null)
+ {
+ viewer.dispose();
+ }
lastCommand = null;
viewer = null;
releaseUIResources();
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
- viewer.evalStringQuiet(command + "\n");
+ jmolScript(command + "\n");
}
jmolHistory(true);
lastCommand = command;
}
Thread colourby = null;
+
/**
* Sends a set of colour commands to the structure viewer
*
colourby.interrupt();
colourby = null;
}
- colourby = new Thread(new Runnable()
+ Thread colourby = new Thread(new Runnable()
{
@Override
public void run()
}
});
colourby.start();
+ this.colourby = colourby;
}
/**
*/
private int _modelFileNameMap[];
- // ////////////////////////////////
- // /StructureListener
- // @Override
- public synchronized String[] getPdbFilex()
- {
- if (viewer == null)
- {
- return new String[0];
- }
- if (modelFileNames == null)
- {
- List<String> mset = new ArrayList<>();
- _modelFileNameMap = new int[viewer.ms.mc];
- String m = viewer.ms.getModelFileName(0);
- if (m != null)
- {
- String filePath = m;
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet
- System.err.println(
- "jmolBinding: Using local file string from Jmol: " + m);
- }
- if (filePath.indexOf("/file:") != -1)
- {
- // applet path with docroot - discard as format won't match pdbfile
- filePath = m;
- }
- mset.add(filePath);
- _modelFileNameMap[0] = 0; // filename index for first model is always 0.
- }
- int j = 1;
- for (int i = 1; i < viewer.ms.mc; i++)
- {
- m = viewer.ms.getModelFileName(i);
- String filePath = m;
- if (m != null)
- {
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet, so keep raw handle
- // System.err.println("jmolBinding: Using local file string from
- // Jmol: "+m);
- }
- }
-
- /*
- * add this model unless it is read from a structure file we have
- * already seen (example: 2MJW is an NMR structure with 10 models)
- */
- if (!mset.contains(filePath))
- {
- mset.add(filePath);
- _modelFileNameMap[j] = i; // record the model index for the filename
- j++;
- }
- }
- modelFileNames = mset.toArray(new String[mset.size()]);
- }
- return modelFileNames;
- }
-
@Override
public synchronized String[] getStructureFiles()
{
{
if (resetLastRes.length() > 0)
{
- viewer.evalStringQuiet(resetLastRes.toString());
+ jmolScript(resetLastRes.toString());
resetLastRes.setLength(0);
}
for (AtomSpec atom : atoms)
cmd.append("spacefill 200;select none");
- viewer.evalStringQuiet(cmd.toString());
+ jmolScript(cmd.toString());
jmolHistory(true);
}
private void jmolHistory(boolean enable)
{
- viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+ jmolScript("History " + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)
try
{
// recover PDB filename for the model hovered over.
- int mnumber = new Integer(mdlId).intValue() - 1;
+ int mnumber = Integer.valueOf(mdlId).intValue() - 1;
if (_modelFileNameMap != null)
{
int _mp = _modelFileNameMap.length - 1;
{
/**
* this implements the toggle label behaviour copied from the original
- * structure viewer, MCView
+ * structure viewer, mc_view
*/
if (strData != null)
{
if (!atomsPicked.contains(picked))
{
- viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+ jmolScript("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE,
- getIProgressIndicator());
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
// }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet(
+ jmolScript(
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
public void showHelp()
{
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ showUrl("http://wiki.jmol.org"
+ // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+ , "jmolHelp");
}
/**
*/
public abstract void showConsole(boolean show);
+ public static Viewer getJmolData(JmolParser jmolParser)
+ {
+ return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
+ "-x -o -n", jmolParser);
+ }
+
/**
+ *
+ *
+ *
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* @param consolePanel
* - panel to contain Jmol console
* @param buttonsToShow
- * - buttons to show on the console, in ordr
+ * - buttons to show on the console, in order
*/
public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions, final Container consolePanel,
String buttonsToShow)
{
+
+ System.err.println("Allocating Jmol Viewer: " + commandOptions);
+
if (commandOptions == null)
{
commandOptions = "";
viewer.setJmolStatusListener(this); // extends JmolCallbackListener
- console = createJmolConsole(consolePanel, buttonsToShow);
+ try
+ {
+ console = createJmolConsole(consolePanel, buttonsToShow);
+ } catch (Throwable e)
+ {
+ System.err.println("Could not create Jmol application console. "
+ + e.getMessage());
+ e.printStackTrace();
+ }
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
protected abstract JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow);
+ // BH 2018 -- Jmol console is not working due to problems with styled
+ // documents.
+
protected org.jmol.api.JmolAppConsoleInterface console = null;
@Override
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
+ jmolScript("background [" + col.getRed() + "," + col.getGreen() + ","
+ + col.getBlue() + "];");
jmolHistory(true);
}
+ private String jmolScript(String script)
+ {
+
+ System.err.println(">>Jmol>> " + script);
+
+ String s = viewer.scriptWait(script);
+
+ System.err.println("<<Jmol<< " + s);
+
+ return s;
+ }
+
@Override
public int[] resizeInnerPanel(String data)
{
{
showConsole(false);
}
+
}
*/
package jalview.ext.paradise;
+import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import org.apache.http.NameValuePair;
import org.apache.http.message.BasicNameValuePair;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
import org.json.simple.parser.ContentHandler;
import org.json.simple.parser.ParseException;
public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
throws Exception
{
- List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ List<NameValuePair> vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("data", pdbfile));
vals.add(new BasicNameValuePair("output", "rnaml"));
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
- ArrayList<Reader> readers = new ArrayList<Reader>();
+ ArrayList<Reader> readers = new ArrayList<>();
final BufferedReader postResponse = HttpClientUtils
.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
readers.add(postResponse);
}
+ /**
+ * @param respons
+ * @return
+ * @throws Exception
+ */
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)
throws Exception
{
- List<NameValuePair> vals = new ArrayList<NameValuePair>();
+ List<NameValuePair> vals = new ArrayList<>();
vals.add(new BasicNameValuePair("tool", "rnaview"));
vals.add(new BasicNameValuePair("pdbid", pdbid));
vals.add(new BasicNameValuePair("output", "rnaml"));
+ pdbid + "&output=rnaml");
// return processJsonResponseFor(new
// InputStreamReader(geturl.openStream()));
- ArrayList<Reader> readers = new ArrayList<Reader>();
+ ArrayList<Reader> readers = new ArrayList<>();
readers.add(new InputStreamReader(geturl.openStream()));
return readers.iterator();
}
}
-
-class RvalsIterator implements Iterator, AutoCloseable
-{
- private Iterator rvals;
-
- protected RvalsIterator(JSONArray responses)
- {
- this.rvals = responses.iterator();
- }
-
- @Override
- public boolean hasNext()
- {
- return rvals.hasNext();
- }
-
- @Override
- public Reader next()
- {
- JSONObject val = (JSONObject) 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 instanceof JSONObject) ? ((JSONObject) sval).toString()
- : 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
- public void close()
- {
- while (rvals.hasNext())
- {
- rvals.next();
- }
- }
-}
*/
public abstract class FTSRestClient implements FTSRestClientI
{
- protected Collection<FTSDataColumnI> dataColumns = new ArrayList<FTSDataColumnI>();
+ protected Collection<FTSDataColumnI> dataColumns = new ArrayList<>();
- protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<FTSDataColumnGroupI>();
+ protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<>();
- protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<FTSDataColumnI>();
+ protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<>();
- protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<FTSDataColumnI>();
+ protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<>();
protected FTSDataColumnI primaryKeyColumn;
InputStream in = getClass().getResourceAsStream(fileName);
- try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
+ try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
{
String line;
while ((line = br.readLine()) != null)
throw new Exception("Couldn't find data column group with id : " + id);
}
- public String getMessageByHTTPStatusCode(int code, String service)
+ public static String getMessageByHTTPStatusCode(int code, String service)
{
String message = "";
switch (code)
{
case 400:
- message = MessageManager.getString("exception.bad_request");
+ message = "Bad request. There is a problem with your input.";
break;
case 410:
message = MessageManager.formatMessage(
- "exception.fts_rest_service_no_longer_available", service);
+ service + " rest services no longer available!");
break;
case 403:
case 404:
- message = MessageManager.getString("exception.resource_not_be_found");
+ message = "The requested resource could not be found";
break;
case 408:
case 409:
case 502:
case 504:
case 505:
- message = MessageManager.formatMessage("exception.fts_server_error",
- service);
+ message = "There seems to be an error from the " + service
+ + " server";
break;
case 503:
- message = MessageManager.getString("exception.service_not_available");
+ message = "Service not available. The server is being updated, try again later.";
break;
default:
break;
}
- return message;
+ return String.valueOf(code) + " " + message;
}
protected String getResourceFile(String fileName)
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.util.JSONUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import java.net.URI;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Objects;
import javax.ws.rs.core.MediaType;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
-import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
/**
* A rest client for querying the Search endpoint of the PDB API
*
* @author tcnofoegbu
- *
*/
public class PDBFTSRestClient extends FTSRestClient
{
* @return the pdbResponse object for the given request
* @throws Exception
*/
+ @SuppressWarnings({ "unused", "unchecked" })
@Override
public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest)
throws Exception
{
try
{
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
pdbRestRequest.getWantedFields());
int responseSize = (pdbRestRequest.getResponseSize() == 0)
: " AND status:REL");
// Build request parameters for the REST Request
- WebResource webResource = null;
+
+ // BH 2018 the trick here is to coerce the classes in Javascript to be
+ // different from the ones in Java yet still allow this to be correct for Java
+ Client client;
+ Class<ClientResponse> clientResponseClass;
+ if (Platform.isJS())
+ {
+ // JavaScript only -- coerce types to Java types for Java
+ client = (Client) (Object) new jalview.javascript.web.Client();
+ clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
+ }
+
+ WebResource webResource;
if (pdbRestRequest.isFacet())
{
webResource = client.resource(PDB_SEARCH_ENDPOINT)
.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();
* the JSON string containing error message from the server
* @return the processed error message from the JSON string
*/
- public static String parseJsonExceptionString(String jsonErrorResponse)
+ @SuppressWarnings("unchecked")
+public static String parseJsonExceptionString(String jsonErrorResponse)
{
StringBuilder errorMessage = new StringBuilder(
"\n============= PDB Rest Client RunTime error =============\n");
+
+// {
+// "responseHeader":{
+// "status":0,
+// "QTime":0,
+// "params":{
+// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
+// "fl":"pdb_id,title,experimental_method,resolution",
+// "start":"0",
+// "sort":"overall_quality desc",
+// "rows":"500",
+// "wt":"json"}},
+// "response":{"numFound":1,"start":0,"docs":[
+// {
+// "experimental_method":["X-ray diffraction"],
+// "pdb_id":"4zhp",
+// "resolution":2.46,
+// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
+// }}
+//
try
{
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
- JSONObject errorResponse = (JSONObject) jsonObj.get("error");
+ Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils.parse(jsonErrorResponse);
+ Map<String, Object> errorResponse = (Map<String, Object>) jsonObj.get("error");
- JSONObject responseHeader = (JSONObject) jsonObj
+ Map<String, Object> responseHeader = (Map<String, Object>) jsonObj
.get("responseHeader");
- JSONObject paramsObj = (JSONObject) responseHeader.get("params");
+ Map<String, Object> paramsObj = (Map<String, Object>) responseHeader.get("params");
String status = responseHeader.get("status").toString();
String message = errorResponse.get("msg").toString();
String query = paramsObj.get("q").toString();
* JSON string
* @return
*/
public static FTSRestResponse parsePDBJsonResponse(
String pdbJsonResponseString, FTSRestRequest pdbRestRequest)
{
+ return parsePDBJsonResponse(pdbJsonResponseString,
+ (Map<String, Object>) null, pdbRestRequest);
+ }
+
+ @SuppressWarnings("unchecked")
+ public static FTSRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString, Map<String, Object> jsonObj,
+ FTSRestRequest pdbRestRequest)
+ {
FTSRestResponse searchResult = new FTSRestResponse();
List<FTSData> result = null;
try
{
- JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser
- .parse(pdbJsonResponseString);
-
- JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
- String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
+ if (jsonObj == null)
+ {
+ jsonObj = (Map<String, Object>) JSONUtils.parse(pdbJsonResponseString);
+ }
+ Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj.get("response");
+ String queryTime = ((Map<String, Object>) jsonObj.get("responseHeader"))
.get("QTime").toString();
int numFound = Integer
.valueOf(pdbResponse.get("numFound").toString());
if (numFound > 0)
{
- result = new ArrayList<FTSData>();
- JSONArray docs = (JSONArray) pdbResponse.get("docs");
- for (Iterator<JSONObject> docIter = docs.iterator(); docIter
+ result = new ArrayList<>();
+ List<Object> docs = (List<Object>) pdbResponse.get("docs");
+ for (Iterator<Object> docIter = docs.iterator(); docIter
.hasNext();)
{
- JSONObject doc = docIter.next();
+ Map<String, Object> doc = (Map<String, Object>) docIter.next();
result.add(getFTSData(doc, pdbRestRequest));
}
searchResult.setNumberOfItemsFound(numFound);
return searchResult;
}
- public static FTSData getFTSData(JSONObject pdbJsonDoc,
+ public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,
FTSRestRequest request)
{
if (allDefaultDisplayedStructureDataColumns == null
|| allDefaultDisplayedStructureDataColumns.isEmpty())
{
- allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
+ allDefaultDisplayedStructureDataColumns = new ArrayList<>();
allDefaultDisplayedStructureDataColumns
.addAll(super.getAllDefaultDisplayedFTSDataColumns());
}
return allDefaultDisplayedStructureDataColumns;
}
+
+
}
--- /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.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+ import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignExportSettingsAdapter;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.io.TCoffeeScoreFile;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
+import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Component;
import java.awt.Rectangle;
import java.awt.Toolkit;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
+import ext.vamsas.ServiceHandle;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
*/
String fileName = null;
+ File fileObject;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
*/
void init()
{
+// setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
+ if (!Platform.isJS())
+ {
+ addServiceListeners();
+ }
setGUINucleotide();
}
}
/**
+ * JavaScript will have this, maybe others. More dependable than a file name
+ * and maintains a reference to the actual bytes loaded.
+ *
+ * @param file
+ */
+ public void setFileObject(File file)
+ {
+ this.fileObject = file;
+ }
+
+ /**
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
* events
*/
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
{
- cut_actionPerformed(null);
+ cut_actionPerformed();
}
else
{
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
- };
+ }
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
}
@Override
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
@Override
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
- protocol, currentFileFormat);
+
+ AlignFrame newframe = null;
+
+ if (fileObject == null)
+ {
+
+ DataSourceType protocol = (fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE);
+ newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ newframe = loader.LoadFileWaitTillLoaded(fileObject,
+ DataSourceType.FILE, currentFileFormat);
+ }
newframe.setBounds(bounds);
if (featureSettings != null && featureSettings.isShowing())
if (fileName == null || (currentFileFormat == null)
|| fileName.startsWith("http"))
{
- saveAs_actionPerformed(null);
+ saveAs_actionPerformed();
}
else
{
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Saves the alignment to a file with a name chosen by the user, if necessary
+ * warning if a file would be overwritten
*/
@Override
- public void saveAs_actionPerformed(ActionEvent e)
+ public void saveAs_actionPerformed()
{
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
+ return;
+ }
+ currentFileFormat = chooser.getSelectedFormat();
+ // todo is this (2005) test now obsolete - value is never null?
+ while (currentFileFormat == null)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"),
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
- while (currentFileFormat == null)
+ value = chooser.showSaveDialog(this);
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"),
- JvOptionPane.WARNING_MESSAGE);
- currentFileFormat = chooser.getSelectedFormat();
- value = chooser.showSaveDialog(this);
- if (value != JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ return;
}
+ }
- fileName = chooser.getSelectedFile().getPath();
+ fileName = chooser.getSelectedFile().getPath();
- Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
+ boolean lastSaveSuccessful = false;
+
+ FileFormatI lastFormatSaved;
+
+ String lastFilenameSaved;
+
+ /**
+ * Raise a dialog or status message for the last call to saveAlignment.
+ *
+ * @return true if last call to saveAlignment(file, format) was successful.
+ */
+ public boolean isSaveAlignmentSuccessful()
+ {
+
+ if (!lastSaveSuccessful)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
}
+ else
+ {
+
+ setStatus(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { lastFilenameSaved, lastFormatSaved }));
+
+ }
+ return lastSaveSuccessful;
}
- public boolean saveAlignment(String file, FileFormatI format)
+ /**
+ * Saves the alignment to the specified file path, in the specified format,
+ * which may be an alignment format, or Jalview project format. If the
+ * alignment has hidden regions, or the format is one capable of including
+ * non-sequence data (features, annotations, groups), then the user may be
+ * prompted to specify what to include in the output.
+ *
+ * @param file
+ * @param format
+ */
+ public void saveAlignment(String file, FileFormatI format)
{
- boolean success = true;
+ lastSaveSuccessful = true;
+ lastFilenameSaved = file;
+ lastFormatSaved = format;
if (FileFormat.Jalview.equals(format))
{
String shortName = title;
-
- if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ if (shortName.indexOf(File.separatorChar) > -1)
{
shortName = shortName.substring(
- shortName.lastIndexOf(java.io.File.separatorChar) + 1);
+ shortName.lastIndexOf(File.separatorChar) + 1);
}
-
- success = new jalview.project.Jalview2XML().saveAlignment(this, file,
- shortName);
-
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
+
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ fileName, format }));
-
+
+ return;
}
- else
+
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable cancelAction = new Runnable()
{
- AlignmentExportData exportData = getAlignmentForExport(format,
- viewport, null);
- if (exportData.getSettings().isCancelled())
- {
- return false;
- }
- FormatAdapter f = new FormatAdapter(alignPanel,
- exportData.getSettings());
- String output = f.formatSequences(format, exportData.getAlignment(), // class
- // cast
- // exceptions
- // will
- // occur in the distant future
- exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format),
- viewport.getAlignment().getHiddenColumns());
-
- if (output == null)
+ @Override
+ public void run()
{
- success = false;
+ lastSaveSuccessful = false;
}
- else
+ };
+ Runnable outputAction = new Runnable()
+ {
+ @Override
+ public void run()
{
- // create backupfiles object and get new temp filename destination
- BackupFiles backupfiles = new BackupFiles(file);
-
- try
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ String output = new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns());
+ if (output == null)
+ {
+ lastSaveSuccessful = false;
+ }
+ else
{
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+ try
+ {
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
+ PrintWriter out = new PrintWriter(
+ new FileWriter(tempFilePath));
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
+ out.print(output);
+ out.close();
+ AlignFrame.this.setTitle(file);
+ statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ fileName, format.getName() }));
- } catch (Exception ex)
- {
- success = false;
- ex.printStackTrace();
- }
-
- backupfiles.setWriteSuccess(success);
- // do the backup file roll and rename the temp file to actual file
- success = backupfiles.rollBackupsAndRenameTempFile();
+ lastSaveSuccessful = true;
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ ex.printStackTrace();
+ }
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ }
+ }
}
- }
-
- if (!success)
- {
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
-
- return success;
- }
+ };
- private void warningMessage(String warning, String title)
- {
- if (new jalview.util.Platform().isHeadless())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, format))
{
- System.err.println("Warning: " + title + "\nWarning: " + warning);
-
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), format, options);
+ choices.setResponseAction(0, outputAction);
+ choices.setResponseAction(1, cancelAction);
+ choices.showDialog();
}
else
{
- JvOptionPane.showInternalMessageDialog(this, warning, title,
- JvOptionPane.WARNING_MESSAGE);
+ outputAction.run();
}
}
/**
- * DOCUMENT ME!
+ * Outputs the alignment to textbox in the requested format, if necessary
+ * first prompting the user for whether to include hidden regions or
+ * non-sequence data
*
- * @param e
- * DOCUMENT ME!
+ * @param fileFormatName
*/
@Override
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String fileFormatName)
{
FileFormatI fileFormat = FileFormats.getInstance()
- .forName(e.getActionCommand());
- AlignmentExportData exportData = getAlignmentForExport(fileFormat,
- viewport, null);
- if (exportData.getSettings().isCancelled())
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- return;
- }
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
- try
- {
- FileFormatI format = fileFormat;
- cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns()));
- Desktop.addInternalFrame(cap, MessageManager
- .formatMessage("label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + e.getActionCommand(),
- oom);
- cap.dispose();
- }
-
- }
-
- public static AlignmentExportData getAlignmentForExport(
- FileFormatI format, AlignViewportI viewport,
- AlignExportSettingI exportSettings)
- {
- AlignmentI alignmentToExport = null;
- AlignExportSettingI settings = exportSettings;
- String[] omitHidden = null;
-
- HiddenSequences hiddenSeqs = viewport.getAlignment()
- .getHiddenSequences();
-
- alignmentToExport = viewport.getAlignment();
-
- boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
- if (settings == null)
- {
- settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), format);
- }
- // settings.isExportAnnotations();
-
- if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
- {
- omitHidden = viewport.getViewAsString(false,
- settings.isExportHiddenSequences());
- }
+ @Override
+ public void run()
+ {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
+ {
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { fileFormat.getName() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+ oom);
+ cap.dispose();
+ }
+ }
+ };
- int[] alignmentStartEnd = new int[2];
- if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, fileFormat))
{
- alignmentToExport = hiddenSeqs.getFullAlignment();
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), fileFormat, options);
+ choices.setResponseAction(0, outputAction);
+ choices.showDialog();
}
else
{
- alignmentToExport = viewport.getAlignment();
+ outputAction.run();
}
- alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
- .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
- AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
- omitHidden, alignmentStartEnd, settings);
- return ed;
}
/**
}
/**
- * DOCUMENT ME!
+ * Creates a PNG image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
*
- * @param e
- * DOCUMENT ME!
+ * @param f
*/
@Override
public void createPNG(File f)
{
- alignPanel.makePNG(f);
+ alignPanel.makeAlignmentImage(TYPE.PNG, f);
}
/**
- * DOCUMENT ME!
+ * Creates an EPS image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
*
- * @param e
- * DOCUMENT ME!
+ * @param f
*/
@Override
public void createEPS(File f)
{
- alignPanel.makeEPS(f);
+ alignPanel.makeAlignmentImage(TYPE.EPS, f);
}
+ /**
+ * Creates an SVG image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
+ *
+ * @param f
+ */
@Override
public void createSVG(File f)
{
- alignPanel.makeSVG(f);
+ alignPanel.makeAlignmentImage(TYPE.SVG, f);
}
@Override
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(
+ final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_jalview_annotations"));
chooser.setToolTipText(
MessageManager.getString("label.load_jalview_annotations"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice, null, null, null);
- }
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+ }
+ });
+ chooser.showOpenDialog(this);
}
/**
* DOCUMENT ME!
*/
@Override
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
{ Integer.valueOf(seqs.length).toString() }));
}
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action Cut (delete and copy) the selected region
*/
@Override
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
- copy_actionPerformed(null);
- delete_actionPerformed(null);
+ copy_actionPerformed();
+ delete_actionPerformed();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Performs menu option to Delete the currently selected region
*/
@Override
- protected void delete_actionPerformed(ActionEvent evt)
+ protected void delete_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
return;
}
+ Runnable okAction = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }};
+
/*
- * If the cut affects all sequences, warn, remove highlighted columns
+ * If the cut affects all sequences, prompt for confirmation
*/
- if (sg.getSize() == viewport.getAlignment().getHeight())
- {
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
- + 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (isEntireAlignWidth)
- {
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JvOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
- {
- return;
- }
- }
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
+ boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ } else
+ {
+ okAction.run();
+ }
}
/**
column, viewport.getAlignment());
}
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
@Override
public void alignmentProperties()
{
- JEditorPane editPane = new JEditorPane("text/html", "");
- editPane.setEditable(false);
+ JComponent pane;
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+
.formatAsHtml();
- editPane.setText(
- MessageManager.formatMessage("label.html_content", new Object[]
- { contents.toString() }));
+ String content = MessageManager.formatMessage("label.html_content",
+ new Object[]
+ { contents.toString() });
+ contents = null;
+
+ if (Platform.isJS())
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(content);
+ textLabel.setBackground(Color.WHITE);
+
+ pane = new JPanel(new BorderLayout());
+ ((JPanel) pane).setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JEditorPane editPane = new JEditorPane("text/html", "");
+ editPane.setEditable(false);
+ editPane.setText(content);
+ pane = editPane;
+ }
+
JInternalFrame frame = new JInternalFrame();
- frame.getContentPane().add(new JScrollPane(editPane));
+
+ frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.alignment_properties", new Object[]
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
+ Hashtable<String, String> scoreSorts = new Hashtable<>();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
}
}
}
- Enumeration labels = scoreSorts.keys();
+ Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
+ labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0,new Runnable()
{
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(filePath, DataSourceType.FILE);
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
- } catch (Exception ex)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- if (fin != null && fin.hasWarningMessage())
+ @Override
+ public void run()
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
+ try
+ {
+ fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
+ DataSourceType.FILE));
+ viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager.getString(
+ "label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
- }
+ });
+ chooser.showOpenDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
+ Vector<ServiceHandle> secstrpr = Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ final ext.vamsas.ServiceHandle sh = secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file or a File object
* @param sourceType
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
- public boolean parseFeaturesFile(String file, DataSourceType sourceType)
+ public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
+ // BH 2018
return avc.parseFeaturesFile(file, sourceType,
Cache.getDefault("RELAXEDSEQIDMATCHING", false));
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
+
final AlignFrame thisaf = this;
- final List<String> files = new ArrayList<>();
+ final List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
* Object[] { String,SequenceI}
*/
ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<String> filesnotmatched = new ArrayList<>();
+ ArrayList<Object> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018
+ Object file = files.get(i);
+ String fileName = file.toString();
String pdbfn = "";
- DataSourceType protocol = FormatAdapter.checkProtocol(file);
+ DataSourceType protocol = (file instanceof File
+ ? DataSourceType.FILE
+ : FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = new File(file);
+ File fl;
+ if (file instanceof File) {
+ fl = (File) file;
+ Platform.cacheFileData(fl);
+ } else {
+ fl = new File(fileName);
+ }
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
{
- URL url = new URL(file);
+ URL url = new URL(fileName);
pdbfn = url.getFile();
}
if (pdbfn.length() > 0)
}
if (mtch != null)
{
- FileFormatI type = null;
+ FileFormatI type;
try
{
type = new IdentifyFile().identify(file, protocol);
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
+ .associatePdbWithSeq(fm[0].toString(),
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
+ + (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
}
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add((String) o[0]);
+ filesnotmatched.add(o[0]);
}
}
}
{
return;
}
- for (String fn : filesnotmatched)
+ for (Object fn : filesnotmatched)
{
loadJalviewDataFile(fn, null, null, null);
}
* @param file
* either a filename or a URL string.
*/
- public void loadJalviewDataFile(String file, DataSourceType sourceType,
+ public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
+ // BH 2018 was String file
try
{
if (sourceType == null)
changeColour(
new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar.setText(MessageManager.getString(
+ setStatus(MessageManager.getString(
"label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_loaded_matrix",
sm.getMatrixName()));
}
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
- JvOptionPane.QUESTION_MESSAGE);
+ String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
+ String reply = JvOptionPane.showInputDialog(msg, ttl);
if (reply != null)
{
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
});
rfetch.add(fetchr);
- final AlignFrame me = this;
new Thread(new Runnable()
{
@Override
public void run()
{
final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(me);
+ .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
+ String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
{
continue;
}
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // for (DbSourceProxy db:dbs)
- // {
- // if (!db.isA(DBRefSource.ALIGNMENTDB)
- // }
if (mname == null)
{
mname = "From " + dbclass;
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ final AlignFrame us = this;
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ }
+ });
+ chooser.showOpenDialog(null);
}
+
}
class PrintThread extends Thread
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+ import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
+ import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
{
if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(toAdd, title))
- {
- return;
- }
+ openLinkedAlignment(toAdd, title);
+ return;
}
}
+ addDataToAlignment(toAdd);
+ }
- /*
- * No mappings, or offer declined - add sequences to this alignment
- */
+ /**
+ * adds sequences to this alignment
+ *
+ * @param toAdd
+ */
+ void addDataToAlignment(AlignmentI toAdd)
+ {
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
}
}
- ranges.setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}
* @param al
* @param title
*/
- protected boolean openLinkedAlignment(AlignmentI al, String title)
+ protected void openLinkedAlignment(AlignmentI al, String title)
{
String[] options = new String[] { MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+ final AlignViewport us = this;
+
+ /*
+ * options No, Split Window, New Window correspond to
+ * dialog responses 0, 1, 2 (even though JOptionPane shows them
+ * in reverse order)
+ */
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+ .setResponseHandler(0, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ addDataToAlignment(al);
+ }
+ }).setResponseHandler(1, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ us.openLinkedAlignmentAs(al, title, true);
+ }
+ }).setResponseHandler(2, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ us.openLinkedAlignmentAs(al, title, false);
+ }
+ });
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
+ }
- if (response != 1 && response != 2)
+ protected void openLinkedAlignmentAs(AlignmentI al, String title,
+ boolean newWindowOrSplitPane)
{
- return false;
- }
- final boolean openSplitPane = (response == 1);
- final boolean openInNewWindow = (response == 2);
-
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
*/
- AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ AlignmentI thisAlignment = newWindowOrSplitPane
+ ? new Alignment(getAlignment())
: getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
// alignFrame.setFileName(file, format);
// }
- if (openInNewWindow)
+ if (!newWindowOrSplitPane)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
{
}
- if (openSplitPane)
+ if (newWindowOrSplitPane)
{
al.alignAs(thisAlignment);
protein = openSplitFrame(newAlignFrame, thisAlignment);
}
-
- return true;
}
/**
@Override
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
+ transferFeaturesStyles(featureSettings, false);
+ }
+
+ /**
+ * Applies the supplied feature settings descriptor to currently known features.
+ * This supports an 'initial configuration' of feature colouring based on a
+ * preset or user favourite. This may then be modified in the usual way using
+ * the Feature Settings dialogue.
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ transferFeaturesStyles(featureSettings, true);
+ }
+
+ /**
+ * when mergeOnly is set, then group and feature visibility or feature colours
+ * are not modified for features and groups already known to the feature
+ * renderer. Feature ordering is always adjusted, and transparency is always set
+ * regardless.
+ *
+ * @param featureSettings
+ * @param mergeOnly
+ */
+ private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+ boolean mergeOnly)
+ {
if (featureSettings == null)
{
return;
}
-
+
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
+ List<String> origRenderOrder = new ArrayList(),
+ origGroups = new ArrayList();
+ // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+ origRenderOrder.addAll(fr.getRenderOrder());
+ origGroups.addAll(fr.getFeatureGroups());
+
fr.findAllFeatures(true);
List<String> renderOrder = fr.getRenderOrder();
FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
- displayed.clear();
+ if (!mergeOnly)
+ {
+ // only clear displayed features if we are mergeing
+ displayed.clear();
+ }
// TODO this clears displayed.featuresRegistered - do we care?
-
+ //
+ // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
+ // feature visibility has already been configured is not very friendly
/*
* set feature colour if specified by feature settings
* set visibility of all features
{
FeatureColourI preferredColour = featureSettings
.getFeatureColour(type);
- if (preferredColour != null)
- {
- fr.setColour(type, preferredColour);
- }
- if (featureSettings.isFeatureDisplayed(type))
+ FeatureColourI origColour = fr.getFeatureStyle(type);
+ if (!mergeOnly || (!origRenderOrder.contains(type)
+ || origColour == null
+ || (!origColour.isGraduatedColour()
+ && origColour.getColour() != null
+ && origColour.getColour().equals(
+ ColorUtils.createColourFromName(type)))))
{
- displayed.setVisible(type);
+ // if we are merging, only update if there wasn't already a colour defined for
+ // this type
+ if (preferredColour != null)
+ {
+ fr.setColour(type, preferredColour);
+ }
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
}
}
*/
for (String group : fr.getFeatureGroups())
{
- fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+ if (!mergeOnly || !origGroups.contains(group))
+ {
+ // when merging, display groups only if the aren't already marked as not visible
+ fr.setGroupVisibility(group,
+ featureSettings.isGroupDisplayed(group));
+ }
}
/*
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
for (String s : files)
{
fileList.append(SPACE).append(QUOTE)
- .append(Platform.escapeString(s)).append(QUOTE);
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
String filesString = fileList.toString();
} catch (Exception ex)
{
Cache.log.error("Couldn't open Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
}
else
new OOMWarning("When trying to add structures to the Jmol viewer!",
oomerror);
Cache.log.debug("File locations are " + filesString);
+ return;
} catch (Exception ex)
{
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
}
addingStructures = true; // already files loaded.
for (int c = 0; c < filesInViewer.length; c++)
{
- if (filesInViewer[c].equals(file))
+ if (Platform.pathEquals(filesInViewer[c], file))
{
file = null;
break;
return files;
}
- @Override
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
- }
-
- @Override
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
- }
-
- void makePDBImage(jalview.util.ImageMaker.TYPE type)
+ /**
+ * Outputs the Jmol viewer image as an image file, after prompting the user to
+ * choose a file and (for EPS) choice of Text or Lineart character rendering
+ * (unless a preference for this is set)
+ *
+ * @param type
+ */
+ public void makePDBImage(ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.TYPE.PNG)
+ ImageWriterI writer = new ImageWriterI()
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
- width, height, null, null, null, 0, false);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
-
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
-
- if (im.getGraphics() != null)
- {
- jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
- im.writeImage();
- }
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ jmb.viewer.renderScreenImage(g, width, height);
+ }
+ };
+ String view = MessageManager.getString("action.view").toLowerCase();
+ ImageExporter exporter = new ImageExporter(writer,
+ jmb.getIProgressIndicator(), type, getTitle());
+ exporter.doExport(null, this, width, height, view);
}
@Override
{
try
{
- BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ BrowserLauncher // BH 2018
+ .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
}
}
};
- };
+ }
private JLabel lblChannels = new JLabel();
} catch (Exception x)
{
}
- ;
if (chan != null && chan.getItems() != null)
{
Cache.log.debug("Scanning news items: newsnew=" + newsnew
public LaunchJvBrowserOnItem(JList listItems)
{
super("Open in Browser");
- this.putValue(MNEMONIC_KEY, new Integer(KeyEvent.VK_O));
+ this.putValue(MNEMONIC_KEY, Integer.valueOf(KeyEvent.VK_O));
this.putValue(Action.LONG_DESCRIPTION, "Open in Browser");
_listItems = listItems;
}
}
}
+ /**
+ * @j2sIgnore
+ * @param args
+ */
public static void main(String args[])
{
// this tests the detection of new news based on the last read date stored
} catch (InterruptedException x)
{
}
- ;
} while (me.isVisible());
if (me.isNewsNew())
import jalview.io.StructureFile;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
{
filePDB.add(thePdbEntry);
filePDBpos.add(Integer.valueOf(pi));
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.append(" \"" + Platform.escapeBackslashes(file) + "\"");
}
}
} catch (OutOfMemoryError oomerror)
}
@Override
- public void eps_actionPerformed(ActionEvent e)
+ public void makePDBImage(TYPE imageType)
{
- throw new Error(MessageManager
- .getString("error.eps_generation_not_implemented"));
- }
-
- @Override
- public void png_actionPerformed(ActionEvent e)
- {
- throw new Error(MessageManager
- .getString("error.png_generation_not_implemented"));
+ throw new UnsupportedOperationException(
+ "Image export for Chimera is not implemented");
}
@Override
FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(source);
+ if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
+ {
+ // override default featureColourScheme so products have Ensembl variant colours
+ featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(DBRefSource.ENSEMBL);
+ }
+
AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
xrefs);
if (!dna)
/*
* apply 'database source' feature configuration
- * if any was found
+ * if any - first to the new splitframe view about to be displayed
*/
- // TODO is this the feature colouring for the original
- // alignment or the fetched xrefs? either could be Ensembl
+
newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
+ /*
+ * and for JAL-3330 also to original alignFrame view(s)
+ * this currently trashes any original settings.
+ */
+ for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+ origpanel.getAlignViewport()
+ .mergeFeaturesStyle(featureColourScheme);
+ }
+
SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
dna ? newFrame : copyThis);
+
newFrame.setVisible(true);
copyThis.setVisible(true);
String linkedTitle = MessageManager
*/
String[] divisionsArray = ensemblDivisions
.toArray(new String[ensemblDivisions.size()]);
- DBRefEntry[] seqRefs = seq.getDBRefs();
- DBRefEntry[] directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
+ List<DBRefEntry> seqRefs = seq.getDBRefs();
+ List<DBRefEntry> directEnsemblRefs = DBRefUtils.selectRefs(seqRefs,
divisionsArray);
if (directEnsemblRefs != null)
{
{
if (dbref.getMap() != null && dbref.getMap().getTo() != null)
{
- DBRefEntry[] dbrefs = dbref.getMap().getTo().getDBRefs();
- DBRefEntry[] indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
+ List<DBRefEntry> dbrefs = dbref.getMap().getTo().getDBRefs();
+ List<DBRefEntry> indirectEnsemblRefs = DBRefUtils.selectRefs(dbrefs,
divisionsArray);
if (indirectEnsemblRefs != null)
{
seq.getLength());
if (geneLoci != null)
{
- MapList map = geneLoci.getMap();
+ MapList map = geneLoci.getMapping();
int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
if (mappedFromLength == seq.getLength())
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), map);
retrievedLoci.put(dbref, geneLoci);
return true;
}
seq.getLength());
if (geneLoci != null)
{
- MapList map = geneLoci.getMap();
+ MapList map = geneLoci.getMapping();
int mappedFromLength = MappingUtils.getLength(map.getFromRanges());
if (mappedFromLength == seq.getLength())
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), map);
retrievedLoci.put(dbref, geneLoci);
return true;
}
*/
package jalview.gui;
- import static jalview.util.UrlConstants.SEQUENCE_ID;
-
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.gui.ImageExporter.ImageWriterI;
import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
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;
import java.awt.event.WindowEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
- import java.io.BufferedInputStream;
import java.io.File;
- import java.io.FileOutputStream;
+ import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
+ import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.ListIterator;
-import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
- import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
- import javax.swing.event.MenuEvent;
- import javax.swing.event.MenuListener;
import org.stackoverflowusers.file.WindowsShortcut;
private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+ protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+
+ public static HashMap<String, FileWriter> savingFiles = new HashMap<>();
+
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
/**
public static MyDesktopPane desktop;
+ public static MyDesktopPane getDesktop()
+ {
+ // BH 2018 could use currentThread() here as a reference to a
+ // Hashtable<Thread, MyDesktopPane> in JavaScript
+ return desktop;
+ }
+
static int openFrameCount = 0;
static final int xOffset = 30;
*/
public Desktop()
{
+ super();
/**
* A note to implementors. It is ESSENTIAL that any activities that might
* block are spawned off as threads rather than waited for during this
* 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();
// sp.getViewport().setView(desktop);
// getContentPane().add(sp, BorderLayout.CENTER);
+
+ // BH 2018 - just an experiment to try unclipped JInternalFrames.
+ if (Platform.isJS())
+ {
+ getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+ }
+
getContentPane().add(desktop, BorderLayout.CENTER);
desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindows() ? new DefaultDesktopManager()
- : Platform.isAMac()
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
? new AquaInternalFrameManager(
desktop.getDesktopManager())
: desktop.getDesktopManager())));
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()
{
});
desktop.addMouseListener(ma);
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- // 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);
- }
-
- });
}
/**
// 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("Starting news thread.");
-
jvnews = new BlogReader(me);
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
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
void showNews(boolean visible)
{
+ Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
- showNews.setSelected(visible);
- if (visible && !jvnews.isVisible())
+ new Thread(new Runnable()
{
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"),
- now);
- jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
- jvnews.showNews();
- }
- }).start();
- }
+ long now = System.currentTimeMillis();
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, now);
+ jvnews.showNews();
+ }
+ }).start();
}
}
{
// 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);
}
return null;
}
- private void doVamsasClientCheck()
- {
- if (Cache.vamsasJarsPresent())
- {
- setupVamsasDisconnectedGui();
- VamsasMenu.setVisible(true);
- final Desktop us = this;
- VamsasMenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- if (refresh)
- {
- us.buildVamsasStMenu();
- refresh = false;
- }
- }
- });
- vamsasStart.setVisible(true);
- }
- }
-
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setOpaque(false);
+ frame.setOpaque(Platform.isJS());
if (frame.getX() < 1 && frame.getY() < 1)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
-- };
++ }
});
menuItem.addActionListener(new ActionListener()
frame.setIcon(false);
} catch (java.beans.PropertyVetoException ex)
{
-
+ // System.err.println(ex.toString());
}
}
});
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
- * the window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
+ * window
*
* @param frame
*/
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);
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- List<String> files = new ArrayList<>();
+ List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
{
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018 File or String
+ Object file = files.get(i);
+ String fileName = file.toString();
DataSourceType protocol = (protocols == null)
? DataSourceType.FILE
: protocols.get(i);
FileFormatI format = null;
- if (file.endsWith(".jar"))
+ if (fileName.endsWith(".jar"))
{
format = FileFormat.Jalview;
{
format = new IdentifyFile().identify(file, protocol);
}
-
- new FileLoader().LoadFile(file, protocol, format);
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
+ new FileLoader().LoadFile(null, file, protocol, format);
}
} catch (Exception ex)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true);
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ @Override
+ public void run()
+ {
+ File selectedFile = chooser.getSelectedFile();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- FileFormatI format = chooser.getSelectedFormat();
+ FileFormatI format = chooser.getSelectedFormat();
- /*
- * Call IdentifyFile to verify the file contains what its extension implies.
- * Skip this step for dynamically added file formats, because
- * IdentifyFile does not know how to recognise them.
- */
- if (FileFormats.getInstance().isIdentifiable(format))
- {
- try
- {
- format = new IdentifyFile().identify(choice, DataSourceType.FILE);
- } catch (FileFormatException e)
+ /*
+ * Call IdentifyFile to verify the file contains what its extension implies.
+ * Skip this step for dynamically added file formats, because
+ * IdentifyFile does not know how to recognise them.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
{
- // format = null; //??
+ try
+ {
+ format = new IdentifyFile().identify(selectedFile,
+ DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ // format = null; //??
+ }
}
- }
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
- format);
- }
- else
- {
- new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
+ new FileLoader().LoadFile(viewport, selectedFile,
+ DataSourceType.FILE, format);
}
- }
+ });
+ chooser.showOpenDialog(this);
}
/**
- * DOCUMENT ME!
+ * Shows a dialog for input of a URL at which to retrieve alignment data
*
- * @param e
- * DOCUMENT ME!
+ * @param viewport
*/
@Override
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
// for viewing
JLabel label = new JLabel(
MessageManager.getString("label.input_file_url"));
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
- panel.add(history);
- history.setPreferredSize(new Dimension(400, 20));
- history.setEditable(true);
- history.addItem("http://www.");
-
- String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
-
- StringTokenizer st;
-
- if (historyItems != null)
- {
- st = new StringTokenizer(historyItems, "\t");
-
- while (st.hasMoreTokens())
- {
- history.addItem(st.nextElement());
- }
- }
-
- int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString("label.input_alignment_from_url"),
- JvOptionPane.OK_CANCEL_OPTION);
- if (reply != JvOptionPane.OK_OPTION)
+ /*
+ * the URL to fetch is
+ * Java: an editable combobox with history
+ * JS: (pending JAL-3038) a plain text field
+ */
+ JComponent history;
+ String urlBase = "http://www.";
+ if (Platform.isJS())
{
- return;
+ history = new JTextField(urlBase, 35);
}
-
- String url = history.getSelectedItem().toString();
-
- if (url.toLowerCase().endsWith(".jar"))
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
+ JComboBox<String> asCombo = new JComboBox<>();
+ asCombo.setPreferredSize(new Dimension(400, 20));
+ asCombo.setEditable(true);
+ asCombo.addItem(urlBase);
+ String historyItems = Cache.getProperty("RECENT_URL");
+ if (historyItems != null)
{
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
+ for (String token : historyItems.split("\\t"))
+ {
+ asCombo.addItem(token);
+ }
}
+ history = asCombo;
}
- else
+ panel.add(history);
+
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ Runnable action = new Runnable()
{
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
+ @Override
+ public void run()
{
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getSelectedItem()
+ .toString());
- if (format == null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate",
- new Object[]
- { url }),
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
- return;
- }
+ if (format == null)
+ {
+ String msg = MessageManager
+ .formatMessage("label.couldnt_locate", url);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
+ return;
+ }
+
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL, format);
+ }
+ }
}
- }
+ };
+ String dialogOption = MessageManager
+ .getString("label.input_alignment_from_url");
+ JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
+ .showInternalDialog(panel, dialogOption,
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
}
/**
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>"
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ public void documentationMenuItem_actionPerformed()
{
try
{
- Help.showHelpWindow();
+ if (Platform.isJS())
+ {
+ BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Help.showHelpWindow();
+ }
} catch (Exception ex)
{
+ System.err.println("Error opening help: " + ex.getMessage());
}
}
}
Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
- if (v_client != null)
- {
- // TODO clear binding to vamsas document objects on close_all
- }
/*
* reset state of singleton objects as appropriate (clear down session state
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.");
}
/*
*/
void showConsole(boolean selected)
{
- showConsole.setSelected(selected);
// TODO: decide if we should update properties file
- Cache.setProperty("SHOW_JAVA_CONSOLE",
- Boolean.valueOf(selected).toString());
- jconsole.setVisible(selected);
+ if (jconsole != null) // BH 2018
+ {
+ showConsole.setSelected(selected);
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
+ jconsole.setVisible(selected);
+ }
}
void reorderAssociatedWindows(boolean minimize, boolean close)
}
/**
- * Shows a file chooser dialog and writes out the current session as a Jalview
- * project file
+ * Prompts the user to choose a file and then saves the Jalview state as a
+ * Jalview project file
*/
@Override
public void saveState_actionPerformed()
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
try
{
- BackupFiles backupfiles = new BackupFiles(chosenFile);
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
- new Jalview2XML().saveState(backupfiles.getTempFile());
+ new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
- backupfiles.setWriteSuccess(true);
- backupfiles.rollBackupsAndRenameTempFile();
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(true);
+ backupfiles.rollBackupsAndRenameTempFile();
+ }
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst saving current state to "
setProgressBar(null, chosenFile.hashCode());
}
}).start();
- }
+ }
}
@Override
"Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, true); // last two booleans: allFiles,
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- final File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
- try
- {
- new Jalview2XML().loadJalviewAlign(choice);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
+ @Override
+ public void run()
{
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(choice);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
- setProgressBar(null, choice.hashCode());
- }
- }).start();
- }
+ }).start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
- public void startLoading(final String fileName)
+ public void startLoading(final Object fileName)
{
if (fileLoadingCount == 0)
{
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the
- * expanded views. Note the expanded frames may themselves have multiple
- * views. We take the lot.
+ * identifier back in to this frame as additional views, and close the expanded
+ * views. Note the expanded frames may themselves have multiple views. We take
+ * the lot.
*
* @param source
*/
}
}
}
--
- }
-
- 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()
while (li.hasNext())
{
String link = li.next();
- if (link.contains(SEQUENCE_ID)
+ if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
&& !UrlConstants.isDefaultString(link))
{
check = true;
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs
- * low.
+ * usage and highlights the desktop area with a red bar if free memory runs low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane implements Runnable
+ public class MyDesktopPane extends JDesktopPane
+ implements Runnable
{
-
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
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"),
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
- * binding when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
+ * when opened
*/
protected void addQuitHandler()
{
getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
.put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
public void setProgressBar(String message, long id)
{
+ Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
+
if (progressBars == null)
{
progressBars = new Hashtable<>();
progressBarHandlers = new Hashtable<>();
}
- if (progressBars.get(new Long(id)) != null)
+ if (progressBars.get(Long.valueOf(id)) != null)
{
- JPanel panel = progressBars.remove(new Long(id));
- if (progressBarHandlers.contains(new Long(id)))
+ JPanel panel = progressBars.remove(Long.valueOf(id));
+ if (progressBarHandlers.contains(Long.valueOf(id)))
{
- progressBarHandlers.remove(new Long(id));
+ progressBarHandlers.remove(Long.valueOf(id));
}
removeProgressPanel(panel);
}
else
{
- progressBars.put(new Long(id), addProgressPanel(message));
+ progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
final IProgressIndicatorHandler handler)
{
if (progressBarHandlers == null
- || !progressBars.containsKey(new Long(id)))
+ || !progressBars.containsKey(Long.valueOf(id)))
{
throw new Error(MessageManager.getString(
"error.call_setprogressbar_before_registering_handler"));
}
- progressBarHandlers.put(new Long(id), handler);
- final JPanel progressPanel = progressBars.get(new Long(id));
+ progressBarHandlers.put(Long.valueOf(id), handler);
+ final JPanel progressPanel = progressBars.get(Long.valueOf(id));
if (handler.canCancel())
{
JButton cancel = new JButton(
}
/**
- * This will return the first AlignFrame holding the given viewport instance.
- * It will break if there are more than one AlignFrames viewing a particular
- * av.
+ * This will return the first AlignFrame holding the given viewport instance. It
+ * will break if there are more than one AlignFrames viewing a particular av.
*
* @param viewport
* @return alignFrame for viewport
public VamsasApplication getVamsasApplication()
{
- return v_client;
+ // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+ return null;
}
} catch (InterruptedException x)
{
}
-- ;
}
if (instance == null)
{
block.release();
}
+ /**
+ * Outputs an image of the desktop to file in EPS format, after prompting the
+ * user for choice of Text or Lineart character rendering (unless a preference
+ * has been set). The file name is generated as
+ *
+ * <pre>
+ * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+ * </pre>
+ */
@Override
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
+ // currently the menu option to do this is not shown
invalidate();
- File of;
- ImageMaker im = new jalview.util.ImageMaker(
- this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
- getHeight(), of = new File("Jalview_snapshot"
- + System.currentTimeMillis() + ".eps"),
- "View of desktop", null, 0, false);
- try
- {
- paintAll(im.getGraphics());
- im.writeImage();
- } catch (Exception q)
+
+ int width = getWidth();
+ int height = getHeight();
+ File of = new File(
+ "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI()
{
- Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
- q);
- return;
- }
- Cache.log.info("Successfully written snapshot to file "
- + of.getAbsolutePath());
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ paintAll(g);
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+ };
+ String title = "View of desktop";
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+ title);
+ exporter.doExport(of, this, width, height, title);
}
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size
- * and location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size and
+ * location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
* - the payload from the drop event
* @throws Exception
*/
- public static void transferFromDropTarget(List<String> files,
+ public static void transferFromDropTarget(List<Object> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
+ // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
+
+ // DataFlavor[] flavors = t.getTransferDataFlavors();
+ // for (int i = 0; i < flavors.length; i++) {
+ // if (flavors[i].isFlavorJavaFileListType()) {
+ // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ // List<File> list = (List<File>) t.getTransferData(flavors[i]);
+ // for (int j = 0; j < list.size(); j++) {
+ // File file = (File) list.get(j);
+ // byte[] data = getDroppedFileBytes(file);
+ // fileName.setText(file.getName() + " - " + data.length + " " +
+ // evt.getLocation());
+ // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
+ // target.setText(new String(data));
+ // }
+ // dtde.dropComplete(true);
+ // return;
+ // }
+ //
+
DataFlavor uriListFlavor = new DataFlavor(
"text/uri-list;class=java.lang.String"), urlFlavour = null;
try
}
else
{
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
System.err.println(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
-- ;
}
} catch (Throwable ex)
{
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
- files.add(((File) file).toString());
+ files.add(file);
protocols.add(DataSourceType.FILE);
}
}
}
}
}
- if (Platform.isWindows())
-
+ if (Platform.isWindowsAndNotJS())
{
Cache.log.debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++)
{
- String source = files.get(f).toLowerCase();
+ String source = files.get(f).toString().toLowerCase();
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url")
|| source.endsWith(".site")))
{
try
{
- File lf = new File(files.get(f));
+ Object obj = files.get(f);
+ File lf = (obj instanceof File ? (File) obj
+ : new File((String) obj));
// process link file to get a URL
Cache.log.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
}
/**
- * Answers a (possibly empty) list of any structure viewer frames (currently
- * for either Jmol or Chimera) which are currently open. This may optionally
- * be restricted to viewers of a specified class, or viewers linked to a
- * specified alignment panel.
+ * Answers a (possibly empty) list of any structure viewer frames (currently for
+ * either Jmol or Chimera) which are currently open. This may optionally be
+ * restricted to viewers of a specified class, or viewers linked to a specified
+ * alignment panel.
*
* @param apanel
* if not null, only return viewers linked to this panel
*/
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;
/**
transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
}
}
-
- FeatureColourI oldcol, fcol;
-
- int featureIndex = 0;
-
- /**
- * Presents a dialog allowing the user to add new features, or amend or delete
- * existing features. Currently this can be on
- * <ul>
- * <li>double-click on a sequence - Amend/Delete features at position</li>
- * <li>Create sequence feature from pop-up menu on selected region</li>
- * <li>Create features for pattern matches from Find</li>
- * </ul>
- * If the supplied feature type is null, show (and update on confirm) the type
- * and group of the last new feature created (with initial defaults of
- * "feature_1" and "Jalview").
- *
- * @param sequences
- * the sequences features are to be created on (if creating
- * features), or a single sequence (if amending features)
- * @param features
- * the current features at the position (if amending), or template
- * new feature(s) with start/end position set (if creating)
- * @param create
- * true to create features, false to amend or delete
- * @param alignPanel
- * @return
- */
- protected boolean amendFeatures(final List<SequenceI> sequences,
- final List<SequenceFeature> features, boolean create,
- final AlignmentPanel alignPanel)
- {
- featureIndex = 0;
-
- final JPanel mainPanel = new JPanel(new BorderLayout());
-
- final JTextField name = new JTextField(25);
- name.getDocument().addDocumentListener(new DocumentListener()
- {
- @Override
- public void insertUpdate(DocumentEvent e)
- {
- warnIfTypeHidden(mainPanel, name.getText());
- }
-
- @Override
- public void removeUpdate(DocumentEvent e)
- {
- warnIfTypeHidden(mainPanel, name.getText());
- }
-
- @Override
- public void changedUpdate(DocumentEvent e)
- {
- warnIfTypeHidden(mainPanel, name.getText());
- }
- });
-
- final JTextField group = new JTextField(25);
- group.getDocument().addDocumentListener(new DocumentListener()
- {
- @Override
- public void insertUpdate(DocumentEvent e)
- {
- warnIfGroupHidden(mainPanel, group.getText());
- }
-
- @Override
- public void removeUpdate(DocumentEvent e)
- {
- warnIfGroupHidden(mainPanel, group.getText());
- }
-
- @Override
- public void changedUpdate(DocumentEvent e)
- {
- warnIfGroupHidden(mainPanel, group.getText());
- }
- });
-
- final JTextArea description = new JTextArea(3, 25);
- final JSpinner start = new JSpinner();
- final JSpinner end = new JSpinner();
- start.setPreferredSize(new Dimension(80, 20));
- end.setPreferredSize(new Dimension(80, 20));
- final JLabel colour = new JLabel();
- colour.setOpaque(true);
- // colour.setBorder(BorderFactory.createEtchedBorder());
- colour.setMaximumSize(new Dimension(30, 16));
- colour.addMouseListener(new MouseAdapter()
- {
- /*
- * open colour chooser on click in colour panel
- */
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (fcol.isSimpleColour())
- {
- Color col = JColorChooser.showDialog(Desktop.desktop,
- MessageManager.getString("label.select_feature_colour"),
- fcol.getColour());
- if (col != null)
- {
- fcol = new FeatureColour(col);
- updateColourButton(mainPanel, colour, fcol);
- }
- }
- else
- {
- /*
- * variable colour dialog - on OK, refetch the updated
- * feature colour and update this display
- */
- final String ft = features.get(featureIndex).getType();
- final String type = ft == null ? lastFeatureAdded : ft;
- FeatureTypeSettings fcc = new FeatureTypeSettings(
- FeatureRenderer.this, type);
- fcc.setRequestFocusEnabled(true);
- fcc.requestFocus();
- fcc.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fcol = FeatureRenderer.this.getFeatureStyle(ft);
- setColour(type, fcol);
- updateColourButton(mainPanel, colour, fcol);
- }
- });
- }
- }
- });
- JPanel gridPanel = new JPanel(new GridLayout(3, 1));
-
- if (!create && features.size() > 1)
- {
- /*
- * more than one feature at selected position -
- * add a drop-down to choose the feature to amend
- * space pad text if necessary to make entries distinct
- */
- gridPanel = new JPanel(new GridLayout(4, 1));
- JPanel choosePanel = new JPanel();
- choosePanel.add(new JLabel(
- MessageManager.getString("label.select_feature") + ":"));
- final JComboBox<String> overlaps = new JComboBox<>();
- List<String> added = new ArrayList<>();
- for (SequenceFeature sf : features)
- {
- String text = String.format("%s/%d-%d (%s)", sf.getType(),
- sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
- while (added.contains(text))
- {
- text += " ";
- }
- overlaps.addItem(text);
- added.add(text);
- }
- choosePanel.add(overlaps);
-
- overlaps.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- int index = overlaps.getSelectedIndex();
- if (index != -1)
- {
- featureIndex = index;
- SequenceFeature sf = features.get(index);
- name.setText(sf.getType());
- description.setText(sf.getDescription());
- group.setText(sf.getFeatureGroup());
- start.setValue(Integer.valueOf(sf.getBegin()));
- end.setValue(Integer.valueOf(sf.getEnd()));
-
- SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequences.get(0), sf.getBegin(),
- sf.getEnd());
-
- alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
- highlight, false);
- }
- FeatureColourI col = getFeatureStyle(name.getText());
- if (col == null)
- {
- col = new FeatureColour(
- ColorUtils.createColourFromName(name.getText()));
- }
- oldcol = fcol = col;
- updateColourButton(mainPanel, colour, col);
- }
- });
-
- gridPanel.add(choosePanel);
- }
-
- JPanel namePanel = new JPanel();
- gridPanel.add(namePanel);
- namePanel.add(new JLabel(MessageManager.getString("label.name:"),
- JLabel.RIGHT));
- namePanel.add(name);
-
- JPanel groupPanel = new JPanel();
- gridPanel.add(groupPanel);
- groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
- JLabel.RIGHT));
- groupPanel.add(group);
-
- JPanel colourPanel = new JPanel();
- gridPanel.add(colourPanel);
- colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
- JLabel.RIGHT));
- colourPanel.add(colour);
- colour.setPreferredSize(new Dimension(150, 15));
- colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
- colour.setForeground(Color.black);
- colour.setHorizontalAlignment(SwingConstants.CENTER);
- colour.setVerticalAlignment(SwingConstants.CENTER);
- colour.setHorizontalTextPosition(SwingConstants.CENTER);
- colour.setVerticalTextPosition(SwingConstants.CENTER);
- mainPanel.add(gridPanel, BorderLayout.NORTH);
-
- JPanel descriptionPanel = new JPanel();
- descriptionPanel.add(new JLabel(
- MessageManager.getString("label.description:"), JLabel.RIGHT));
- description.setFont(JvSwingUtils.getTextAreaFont());
- description.setLineWrap(true);
- descriptionPanel.add(new JScrollPane(description));
-
- if (!create)
- {
- mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
-
- JPanel startEndPanel = new JPanel();
- startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
- JLabel.RIGHT));
- startEndPanel.add(start);
- startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
- JLabel.RIGHT));
- startEndPanel.add(end);
- mainPanel.add(startEndPanel, BorderLayout.CENTER);
- }
- else
- {
- mainPanel.add(descriptionPanel, BorderLayout.CENTER);
- }
-
- /*
- * default feature type and group to that of the first feature supplied,
- * or to the last feature created if not supplied (null value)
- */
- SequenceFeature firstFeature = features.get(0);
- boolean useLastDefaults = firstFeature.getType() == null;
- final String featureType = useLastDefaults ? lastFeatureAdded
- : firstFeature.getType();
- final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
- : firstFeature.getFeatureGroup();
- name.setText(featureType);
- group.setText(featureGroup);
-
- start.setValue(Integer.valueOf(firstFeature.getBegin()));
- end.setValue(Integer.valueOf(firstFeature.getEnd()));
- description.setText(firstFeature.getDescription());
- updateColourButton(mainPanel, colour,
- (oldcol = fcol = getFeatureStyle(featureType)));
- Object[] options;
- if (!create)
- {
- options = new Object[] { MessageManager.getString("label.amend"),
- MessageManager.getString("action.delete"),
- MessageManager.getString("action.cancel") };
- }
- else
- {
- options = new Object[] { MessageManager.getString("action.ok"),
- MessageManager.getString("action.cancel") };
- }
-
- String title = create
- ? MessageManager.getString("label.create_new_sequence_features")
- : MessageManager.formatMessage("label.amend_delete_features",
- new String[]
- { sequences.get(0).getName() });
-
- /*
- * show the dialog
- */
- int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
- mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
- JvOptionPane.QUESTION_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
-
- FeaturesFile ffile = new FeaturesFile();
-
- final String enteredType = name.getText().trim();
- final String enteredGroup = group.getText().trim();
- final String enteredDescription = description.getText().replaceAll("\n", " ");
-
- if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
- {
- /*
- * update default values only if creating using default values
- */
- if (useLastDefaults)
- {
- lastFeatureAdded = enteredType;
- lastFeatureGroupAdded = enteredGroup;
- // TODO: determine if the null feature group is valid
- if (lastFeatureGroupAdded.length() < 1)
- {
- lastFeatureGroupAdded = null;
- }
- }
- }
-
- if (!create)
- {
- SequenceFeature sf = features.get(featureIndex);
-
- if (reply == JvOptionPane.NO_OPTION)
- {
- /*
- * NO_OPTION corresponds to the Delete button
- */
- sequences.get(0).getDatasetSequence().deleteFeature(sf);
- // update Feature Settings for removal of feature / group
- featuresAdded();
- }
- else if (reply == JvOptionPane.YES_OPTION)
- {
- /*
- * YES_OPTION corresponds to the Amend button
- * need to refresh Feature Settings if type, group or colour changed;
- * note we don't force the feature to be visible - the user has been
- * warned if a hidden feature type or group was entered
- */
- boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
- .equals(enteredGroup));
- refreshSettings |= (fcol != oldcol);
- setColour(enteredType, fcol);
- int newBegin = sf.begin;
- int newEnd = sf.end;
- try
- {
- newBegin = ((Integer) start.getValue()).intValue();
- newEnd = ((Integer) end.getValue()).intValue();
- } catch (NumberFormatException ex)
- {
- // JSpinner doesn't accept invalid format data :-)
- }
-
- /*
- * replace the feature by deleting it and adding a new one
- * (to ensure integrity of SequenceFeatures data store)
- */
- sequences.get(0).deleteFeature(sf);
- SequenceFeature newSf = new SequenceFeature(sf, enteredType,
- newBegin, newEnd, enteredGroup, sf.getScore());
- newSf.setDescription(enteredDescription);
- ffile.parseDescriptionHTML(newSf, false);
- // amend features dialog only updates one sequence at a time
- sequences.get(0).addSequenceFeature(newSf);
-
- if (refreshSettings)
- {
- featuresAdded();
- }
- }
- }
- else
- // NEW FEATURES ADDED
- {
- if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
- {
- for (int i = 0; i < sequences.size(); i++)
- {
- SequenceFeature sf = features.get(i);
- SequenceFeature sf2 = new SequenceFeature(enteredType,
- enteredDescription, sf.getBegin(), sf.getEnd(),
- enteredGroup);
- ffile.parseDescriptionHTML(sf2, false);
- sequences.get(i).addSequenceFeature(sf2);
- }
-
- setColour(enteredType, fcol);
-
- featuresAdded();
-
- alignPanel.paintAlignment(true, true);
-
- return true;
- }
- else
- {
- return false;
- }
- }
-
- alignPanel.paintAlignment(true, true);
-
- return true;
- }
-
- /**
- * Show a warning message if the entered type is one that is currently hidden
- *
- * @param panel
- * @param type
- */
- protected void warnIfTypeHidden(JPanel panel, String type)
- {
- if (getRenderOrder().contains(type))
- {
- if (!showFeatureOfType(type))
- {
- String msg = MessageManager.formatMessage("label.warning_hidden",
- MessageManager.getString("label.feature_type"), type);
- JvOptionPane.showMessageDialog(panel, msg, "",
- JvOptionPane.OK_OPTION);
- }
- }
- }
-
- /**
- * Show a warning message if the entered group is one that is currently hidden
- *
- * @param panel
- * @param group
- */
- protected void warnIfGroupHidden(JPanel panel, String group)
- {
- if (featureGroups.containsKey(group) && !featureGroups.get(group))
- {
- String msg = MessageManager.formatMessage("label.warning_hidden",
- MessageManager.getString("label.group"), group);
- JvOptionPane.showMessageDialog(panel, msg, "",
- JvOptionPane.OK_OPTION);
- }
- }
-
- /**
- * update the amend feature button dependent on the given style
- *
- * @param bigPanel
- * @param col
- * @param col
- */
- protected void updateColourButton(JPanel bigPanel, JLabel colour,
- FeatureColourI col)
- {
- colour.removeAll();
- colour.setIcon(null);
- colour.setToolTipText(null);
- colour.setText("");
-
- if (col.isSimpleColour())
- {
- colour.setBackground(col.getColour());
- }
- else
- {
- colour.setBackground(bigPanel.getBackground());
- colour.setForeground(Color.black);
- FeatureSettings.renderGraduatedColor(colour, col);
- }
- }
-
- /**
- * Orders features in render precedence (last in order is last to render, so
- * displayed on top of other features)
- *
- * @param order
- */
- public void orderFeatures(Comparator<String> order)
- {
- Arrays.sort(renderOrder, order);
- }
}
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.Help.HelpId;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.FeatureColour;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JColorChooser;
-import javax.swing.JDialog;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
+import javax.swing.ToolTipManager;
import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
private static final int MIN_HEIGHT = 400;
- private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+ private final static String BASE_TOOLTIP = MessageManager
+ .getString("label.click_to_edit");
final FeatureRenderer fr;
*/
Object[][] originalData;
- private float originalTransparency;
+ float originalTransparency;
- private Map<String, FeatureMatcherSetI> originalFilters;
+ Map<String, FeatureMatcherSetI> originalFilters;
final JInternalFrame frame;
/*
* true when Feature Settings are updating from feature renderer
*/
- private boolean handlingUpdate = false;
+ boolean handlingUpdate = false;
/*
* holds {featureCount, totalExtent} for each feature type
default:
break;
}
-
+
return tip;
}
tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
tableHeader.setReorderingAllowed(false);
table.setFont(new Font("Verdana", Font.PLAIN, 12));
-
- table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
+ ToolTipManager.sharedInstance().registerComponent(table);
+ table.setDefaultEditor(FeatureColour.class, new ColorEditor());
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
- table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor(this));
+ table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor());
table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
- new ColorRenderer(), new ColorEditor(this));
+ new ColorRenderer(), new ColorEditor());
table.addColumn(colourColumn);
TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
- new FilterRenderer(), new FilterEditor(this));
+ new FilterRenderer(), new FilterEditor());
table.addColumn(filterColumn);
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
if (evt.isPopupTrigger())
{
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
else if (evt.getClickCount() == 2)
{
{
String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
- popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
- evt.getY());
+ showPopupMenu(selectedRow, type, colour, evt.getPoint());
}
}
});
frame = new JInternalFrame();
frame.setContentPane(this);
- if (Platform.isAMac())
- {
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 480);
- }
- else
- {
- Desktop.addInternalFrame(frame,
- MessageManager.getString("label.sequence_feature_settings"),
- 600, 450);
- }
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.sequence_feature_settings"),
+ 600, Platform.isAMacAndNotJS() ? 480 : 450);
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
frame.addInternalFrameListener(
inConstruction = false;
}
- protected void popupSort(final int rowSelected, final String type,
- final Object typeCol, final Map<String, float[][]> minmax, int x,
- int y)
+ /**
+ * Constructs and shows a popup menu of possible actions on the selected row
+ * and feature type
+ *
+ * @param rowSelected
+ * @param type
+ * @param typeCol
+ * @param pt
+ */
+ protected void showPopupMenu(final int rowSelected, final String type,
+ final Object typeCol, final Point pt)
{
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
{ type }));
+ final FeatureColourI featureColour = (FeatureColourI) typeCol;
+
+ /*
+ * menu option to select (or deselect) variable colour
+ */
+ final JCheckBoxMenuItem variableColourCB = new JCheckBoxMenuItem(
+ MessageManager.getString("label.variable_colour"));
+ variableColourCB.setSelected(!featureColour.isSimpleColour());
+ men.add(variableColourCB);
+
+ /*
+ * checkbox action listener doubles up as listener to OK
+ * from the variable colour / filters dialog
+ */
+ variableColourCB.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (e.getSource() == variableColourCB)
+ {
+ men.setVisible(true); // BH 2018 for JavaScript because this is a
+ // checkbox
+ men.setVisible(false); // BH 2018 for JavaScript because this is a
+ // checkbox
+ if (featureColour.isSimpleColour())
+ {
+ /*
+ * toggle simple colour to variable colour - show dialog
+ */
+ FeatureTypeSettings fc = new FeatureTypeSettings(fr, type);
+ fc.addActionListener(this);
+ }
+ else
+ {
+ /*
+ * toggle variable to simple colour - show colour chooser
+ */
+ String title = MessageManager
+ .formatMessage("label.select_colour_for", type);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ table.setValueAt(new FeatureColour(c), rowSelected,
+ COLOUR_COLUMN);
+ table.validate();
+ updateFeatureRenderer(
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
+ }
+ };
+ JalviewColourChooser.showColourChooser(FeatureSettings.this,
+ title, featureColour.getMaxColour(), listener);
+ }
+ }
+ else
+ {
+ if (e.getSource() instanceof FeatureTypeSettings)
+ {
+ /*
+ * update after OK in feature colour dialog; the updated
+ * colour will have already been set in the FeatureRenderer
+ */
+ FeatureColourI fci = fr.getFeatureColours().get(type);
+ table.setValueAt(fci, rowSelected, COLOUR_COLUMN);
+ // BH 2018 setting a table value does not invalidate it.
+ // System.out.println("FeatureSettings is valied" +
+ // table.validate();
+ }
+ }
+ }
+ });
+
+ men.addSeparator();
+
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
- final FeatureSettings me = this;
scr.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc
- .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ af.avc.sortAlignmentByFeatureScore(Arrays.asList(new String[]
{ type }));
}
-
});
JMenuItem dens = new JMenuItem(
MessageManager.getString("label.sort_by_density"));
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc
- .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ af.avc.sortAlignmentByFeatureDensity(Arrays.asList(new String[]
{ type }));
}
-
});
men.add(dens);
men.add(clearCols);
men.add(hideCols);
men.add(hideOtherCols);
- men.show(table, x, y);
+ men.show(table, pt.x, pt.y);
}
@Override
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
- data[dataIndex][SHOW_COLUMN] = new Boolean(
+ data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(
af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
displayableTypes.remove(type);
data[dataIndex][FILTER_COLUMN] = featureFilter == null
? new FeatureMatcherSet()
: featureFilter;
- data[dataIndex][SHOW_COLUMN] = new Boolean(true);
+ data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true);
dataIndex++;
displayableTypes.remove(type);
}
}
/**
- * Updates 'originalData' (used for restore on Cancel) if we detect that changes
- * have been made outwith this dialog
+ * Updates 'originalData' (used for restore on Cancel) if we detect that
+ * changes have been made outwith this dialog
* <ul>
* <li>a new feature type added (and made visible)</li>
* <li>a feature colour changed (in the Amend Features dialog)</li>
/**
* Remove from the groups panel any checkboxes for groups that are not in the
- * foundGroups set. This enables removing a group from the display when the last
- * feature in that group is deleted.
+ * foundGroups set. This enables removing a group from the display when the
+ * last feature in that group is deleted.
*
* @param foundGroups
*/
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- File file = chooser.getSelectedFile();
- load(file);
- }
+ @Override
+ public void run()
+ {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }
+ });
+ chooser.showOpenDialog(this);
}
/**
if (table != null)
{
resetTable(null);
- Object[][] data = ((FeatureTableModel) table.getModel())
- .getData();
+ Object[][] data = ((FeatureTableModel) table.getModel()).getData();
ensureOrder(data);
updateFeatureRenderer(data, false);
table.repaint();
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
{
- save(chooser.getSelectedFile());
+ File file = chooser.getSelectedFile();
+ save(file);
}
}
ucs.setSchemeName("Sequence Features");
try
{
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(file), "UTF-8"));
+ PrintWriter out = new PrintWriter(
+ new OutputStreamWriter(new FileOutputStream(file), "UTF-8"));
/*
* sort feature types by colour order, from 0 (highest)
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
if (filter != null && !filter.isEmpty())
{
- Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+ Iterator<FeatureMatcherI> iterator = filter.getMatchers()
+ .iterator();
FeatureMatcherI firstMatcher = iterator.next();
jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
- .marshalFilter(firstMatcher, iterator,
- filter.isAnded());
+ .marshalFilter(firstMatcher, iterator, filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
else
{
width[i] /= max; // normalize
- fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
+ fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for
+ // later
}
if (i > 0)
{
}
/**
- * Update the priority order of features; only repaint if this changed the order
- * of visible features
+ * Update the priority order of features; only repaint if this changed the
+ * order of visible features
*
* @param data
* @param visibleNew
*/
- private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
+ void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
FeatureSettingsBean[] rowData = getTableAsBeans(data);
{
boolean thr = false;
StringBuilder tx = new StringBuilder();
-
+
if (gcol.isColourByAttribute())
{
tx.append(FeatureMatcher
renderGraduatedColor(comp, gcol, w, h);
}
+ @SuppressWarnings("serial")
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
- FeatureSettings me;
-
FeatureColourI currentColor;
FeatureTypeSettings chooser;
JButton button;
- JColorChooser colorChooser;
-
- JDialog dialog;
-
protected static final String EDIT = "edit";
int rowSelected = 0;
- public ColorEditor(FeatureSettings me)
+ public ColorEditor()
{
- this.me = me;
// Set up the editor (from the table's point of view),
// which is a button.
// This button brings up the color chooser dialog,
button.setActionCommand(EDIT);
button.addActionListener(this);
button.setBorderPainted(false);
}
/**
- * Handles events from the editor button and from the dialog's OK button.
+ * Handles events from the editor button, and from the colour/filters
+ * dialog's OK button
*/
@Override
public void actionPerformed(ActionEvent e)
{
- // todo test e.getSource() instead here
- if (EDIT.equals(e.getActionCommand()))
+ if (button == e.getSource())
{
- // The user has clicked the cell, so
- // bring up the dialog.
if (currentColor.isSimpleColour())
{
- // bring up simple color chooser
- button.setBackground(currentColor.getColour());
- colorChooser.setColor(currentColor.getColour());
- dialog.setVisible(true);
+ /*
+ * simple colour chooser
+ */
+ String ttl = MessageManager
+ .formatMessage("label.select_colour_for", type);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ currentColor = new FeatureColour(c);
+ table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ fireEditingStopped();
+ }
+
+ @Override
+ public void cancel()
+ {
+ fireEditingStopped();
+ }
+ };
+ JalviewColourChooser.showColourChooser(button, ttl,
+ currentColor.getColour(), listener);
}
else
{
- // bring up graduated chooser.
- chooser = new FeatureTypeSettings(me.fr, type);
+ /*
+ * variable colour and filters dialog
+ */
+ chooser = new FeatureTypeSettings(fr, type);
+ if (!Platform.isJS())
/**
- * @j2sNative
+ * Java only
+ *
+ * @j2sIgnore
*/
{
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
}
chooser.addActionListener(this);
- // Make the renderer reappear.
fireEditingStopped();
}
}
else
{
- if (currentColor.isSimpleColour())
- {
- /*
- * read off colour picked in colour chooser after OK pressed
- */
- currentColor = new FeatureColour(colorChooser.getColor());
- me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
- }
- else
+ /*
+ * after OK in variable colour dialog, any changes to colour
+ * (or filters!) are already set in FeatureRenderer, so just
+ * update table data without triggering updateFeatureRenderer
+ */
+ currentColor = fr.getFeatureColours().get(type);
+ FeatureMatcherSetI currentFilter = fr.getFeatureFilter(type);
+ if (currentFilter == null)
{
- /*
- * after OK in variable colour dialog, any changes to colour
- * (or filters!) are already set in FeatureRenderer, so just
- * update table data without triggering updateFeatureRenderer
- */
- currentColor = fr.getFeatureColours().get(type);
- FeatureMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
- if (currentFilter == null)
- {
- currentFilter = new FeatureMatcherSet();
- }
- Object[] data = ((FeatureTableModel) table.getModel())
- .getData()[rowSelected];
- data[COLOUR_COLUMN] = currentColor;
- data[FILTER_COLUMN] = currentFilter;
+ currentFilter = new FeatureMatcherSet();
}
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
fireEditingStopped();
- me.table.validate();
+ // SwingJS needs an explicit repaint() here,
+ // rather than relying upon no validation having
+ // occurred since the stopEditing call was made.
+ // Its laying out has not been stopped by the modal frame
+ table.validate();
+ table.repaint();
}
}
+ /**
+ * Override allows access to this method from anonymous inner classes
+ */
+ @Override
+ protected void fireEditingStopped()
+ {
+ super.fireEditingStopped();
+ }
+
// Implement the one CellEditor method that AbstractCellEditor doesn't.
@Override
public Object getCellEditorValue()
// Implement the one method defined by TableCellEditor.
@Override
- public Component getTableCellEditorComponent(JTable theTable, Object value,
- boolean isSelected, int row, int column)
+ public Component getTableCellEditorComponent(JTable theTable,
+ Object value, boolean isSelected, int row, int column)
{
currentColor = (FeatureColourI) value;
this.rowSelected = row;
- type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
- button.setBackground(me.getBackground());
+ button.setBackground(FeatureSettings.this.getBackground());
if (!currentColor.isSimpleColour())
{
JLabel btn = new JLabel();
/**
* The cell editor for the Filter column. It displays the text of any filters
- * for the feature type in that row (in full as a tooltip, possible abbreviated
- * as display text). On click in the cell, opens the Feature Display Settings
- * dialog at the Filters tab.
+ * for the feature type in that row (in full as a tooltip, possible
+ * abbreviated as display text). On click in the cell, opens the Feature
+ * Display Settings dialog at the Filters tab.
*/
+ @SuppressWarnings("serial")
class FilterEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
- FeatureSettings me;
FeatureMatcherSetI currentFilter;
int rowSelected = 0;
- public FilterEditor(FeatureSettings me)
+ public FilterEditor()
{
- this.me = me;
button = new JButton();
button.setActionCommand(EDIT);
button.addActionListener(this);
{
if (button == e.getSource())
{
- FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
+ FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type);
chooser.addActionListener(this);
chooser.setRequestFocusEnabled(true);
chooser.requestFocus();
* update table data without triggering updateFeatureRenderer
*/
FeatureColourI currentColor = fr.getFeatureColours().get(type);
- currentFilter = me.fr.getFeatureFilter(type);
+ currentFilter = fr.getFeatureFilter(type);
if (currentFilter == null)
{
currentFilter = new FeatureMatcherSet();
}
+
Object[] data = ((FeatureTableModel) table.getModel())
.getData()[rowSelected];
data[COLOUR_COLUMN] = currentColor;
data[FILTER_COLUMN] = currentFilter;
fireEditingStopped();
- me.table.validate();
+ // SwingJS needs an explicit repaint() here,
+ // rather than relying upon no validation having
+ // occurred since the stopEditing call was made.
+ // Its laying out has not been stopped by the modal frame
+ table.validate();
+ table.repaint();
}
}
}
@Override
- public Component getTableCellEditorComponent(JTable theTable, Object value,
- boolean isSelected, int row, int column)
+ public Component getTableCellEditorComponent(JTable theTable,
+ Object value, boolean isSelected, int row, int column)
{
currentFilter = (FeatureMatcherSetI) value;
this.rowSelected = row;
- type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ type = table.getValueAt(row, TYPE_COLUMN).toString();
button.setOpaque(true);
- button.setBackground(me.getBackground());
+ button.setBackground(FeatureSettings.this.getBackground());
button.setText(currentFilter.toString());
button.setIcon(null);
return button;
g.fillRect(s1, 0, e1 - s1, height);
}
g.setColor(gcol.getMaxColour());
- g.fillRect(0, e1, width - e1, height);
+ // g.fillRect(0, e1, width - e1, height); // BH 2018
+ g.fillRect(e1, 0, width - e1, height);
}
}
}
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
+ import jalview.bin.Cache;
import jalview.datamodel.GraphLine;
import jalview.datamodel.features.FeatureAttributes;
import jalview.datamodel.features.FeatureAttributes.Datatype;
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.schemes.FeatureColour;
import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JColorChooser;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
/*
* the view panel to update when settings change
*/
- private final AlignmentViewPanel ap;
+ final AlignmentViewPanel ap;
- private final String featureType;
+ final String featureType;
/*
* the colour and filters to reset to on Cancel
* set flag to true when setting values programmatically,
* to avoid invocation of action handlers
*/
- private boolean adjusting = false;
+ boolean adjusting = false;
/*
* minimum of the value range for graduated colour
/*
* scale factor for conversion between absolute min-max and slider
*/
- private float scaleFactor;
+ float scaleFactor;
/*
* radio button group, to select what to colour by:
* simple colour, by category (text), or graduated
*/
- private JRadioButton simpleColour = new JRadioButton();
+ JRadioButton simpleColour = new JRadioButton();
- private JRadioButton byCategory = new JRadioButton();
+ JRadioButton byCategory = new JRadioButton();
- private JRadioButton graduatedColour = new JRadioButton();
+ JRadioButton graduatedColour = new JRadioButton();
- /**
- * colours and filters are shown in tabbed view or single content pane
- */
- JPanel coloursPanel, filtersPanel;
+ JPanel coloursPanel;
+
+ JPanel filtersPanel;
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();
/*
* choice of option for 'colour for no value'
*/
- private JComboBox<String> noValueCombo;
+ private JComboBox<Object> noValueCombo;
/*
* choice of what to colour by text (Label or attribute)
*/
- private JComboBox<String> colourByTextCombo;
+ private JComboBox<Object> colourByTextCombo;
/*
* choice of what to colour by range (Score or attribute)
*/
- private JComboBox<String> colourByRangeCombo;
+ private JComboBox<Object> colourByRangeCombo;
private JRadioButton andFilters;
/*
* filters for the currently selected feature type
*/
- private List<FeatureMatcherI> filters;
+ List<FeatureMatcherI> filters;
private JPanel chooseFiltersPanel;
return;
}
- updateColoursTab();
+ updateColoursPanel();
- updateFiltersTab();
+ updateFiltersPanel();
adjusting = false;
}
/**
- * Configures the widgets on the Colours tab according to the current feature
+ * Configures the widgets on the Colours panel according to the current feature
* colour scheme
*/
- private void updateColoursTab()
+ private void updateColoursPanel()
{
FeatureColourI fc = fr.getFeatureColours().get(featureType);
};
/*
- * first panel/tab: colour options
+ * first panel: colour options
*/
JPanel coloursPanel = initialiseColoursPanel();
this.add(coloursPanel, BorderLayout.NORTH);
/*
- * second panel/tab: filter options
+ * second panel: filter options
*/
JPanel filtersPanel = initialiseFiltersPanel();
this.add(filtersPanel, BorderLayout.CENTER);
graduatedColour = new JRadioButton(
MessageManager.getString("label.by_range_of") + COLON);
graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ graduatedColour.setOpaque(false);
graduatedColour.addItemListener(new ItemListener()
{
@Override
{
if (minColour.isEnabled())
{
- showColourChooser(minColour, "label.select_colour_minimum_value");
+ String ttl = MessageManager.getString("label.select_colour_minimum_value");
+ showColourChooser(minColour, ttl);
}
}
});
{
if (maxColour.isEnabled())
{
- showColourChooser(maxColour, "label.select_colour_maximum_value");
+ String ttl = MessageManager.getString("label.select_colour_maximum_value");
+ showColourChooser(maxColour, ttl);
}
}
});
simpleColour = new JRadioButton(
MessageManager.getString("label.simple_colour"));
simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ simpleColour.setOpaque(false);
simpleColour.addItemListener(new ItemListener()
{
@Override
{
if (simpleColour.isSelected())
{
- showColourChooser(singleColour, "label.select_colour");
+ String ttl = MessageManager.formatMessage("label.select_colour_for", featureType);
+ showColourChooser(singleColour, ttl);
}
}
});
byCategory = new JRadioButton(
MessageManager.getString("label.by_text_of") + COLON);
byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ byCategory.setOpaque(false);
byCategory.addItemListener(new ItemListener()
{
@Override
return colourByPanel;
}
- private void showColourChooser(JPanel colourPanel, String key)
+ /**
+ * Shows a colour chooser dialog, and if a selection is made, updates the
+ * colour of the given panel
+ *
+ * @param colourPanel
+ * the panel whose background colour is being picked
+ * @param title
+ */
+ void showColourChooser(JPanel colourPanel, String title)
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString(key), colourPanel.getBackground());
- if (col != null)
+ ColourChooserListener listener = new ColourChooserListener()
{
- colourPanel.setBackground(col);
- colourPanel.setForeground(col);
- }
- colourPanel.repaint();
- colourChanged(true);
+ @Override
+ public void colourSelected(Color col)
+ {
+ colourPanel.setBackground(col);
+ colourPanel.setForeground(col);
+ colourPanel.repaint();
+ colourChanged(true);
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, title,
+ colourPanel.getBackground(), listener);
}
/**
fr.setColour(featureType, acg);
ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
- updateColoursTab();
+ updateColoursPanel();
}
/**
}
float minValue = min;
float maxValue = max;
- final int thresholdOption = threshold.getSelectedIndex();
+ int thresholdOption = threshold.getSelectedIndex();
if (thresholdIsMin.isSelected()
&& thresholdOption == ABOVE_THRESHOLD_OPTION)
{
* @param withRange
* @param withText
*/
- protected JComboBox<String> populateAttributesDropdown(
+ protected JComboBox<Object> populateAttributesDropdown(
List<String[]> attNames, boolean withRange, boolean withText)
{
List<String> displayAtts = new ArrayList<>();
tooltips.add(desc == null ? "" : desc);
}
- JComboBox<String> attCombo = JvSwingUtils
- .buildComboWithTooltips(displayAtts, tooltips);
-
+ // now convert String List to Object List for buildComboWithTooltips
+ List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
+ JComboBox<Object> attCombo = JvSwingUtils
+ .buildComboWithTooltips(displayAttsObjects, tooltips);
+
return attCombo;
}
andOrPanel.setBackground(Color.white);
andFilters = new JRadioButton(MessageManager.getString("label.and"));
orFilters = new JRadioButton(MessageManager.getString("label.or"));
+ andFilters.setOpaque(false);
+ orFilters.setOpaque(false);
ActionListener actionListener = new ActionListener()
{
@Override
* for adding a condition. This should be called after a filter has been
* removed, added or amended.
*/
- private void updateFiltersTab()
+ private void updateFiltersPanel()
{
/*
* clear the panel and list of filter conditions
{
orFilters.setSelected(true);
}
- featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
+ // avoid use of lambda expression to keep SwingJS happy
+ // featureFilters.getMatchers().forEach(item -> filters.add(item));
+ for (FeatureMatcherI matcher : featureFilters.getMatchers())
+ {
+ filters.add(matcher);
+ }
}
/*
* drop-down choice of attribute, with description as a tooltip
* if we can obtain it
*/
- JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
- true);
+ final JComboBox<Object> attCombo = populateAttributesDropdown(attNames,
+ true, true);
String filterBy = setSelectedAttribute(attCombo, filter);
JComboBox<Condition> condCombo = new JComboBox<>();
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
* @param attCombo
* @param filter
*/
- private String setSelectedAttribute(JComboBox<String> attCombo,
+ private String setSelectedAttribute(JComboBox<Object> attCombo,
FeatureMatcherI filter)
{
String item = null;
* @param condCombo
* @param patternField
*/
- private void populateConditions(String attName, Condition cond,
+ void populateConditions(String attName, Condition cond,
JComboBox<Condition> condCombo, JTextField patternField)
{
Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
* @param valueField
* @param filterIndex
*/
- protected boolean updateFilter(JComboBox<String> attCombo,
+ protected boolean updateFilter(JComboBox<Object> attCombo,
JComboBox<Condition> condCombo, JTextField valueField,
int filterIndex)
{
- String attName = (String) attCombo.getSelectedItem();
+ String attName;
+ try
+ {
+ attName = (String) attCombo.getSelectedItem();
+ } catch (Exception e)
+ {
+ Cache.log.error("Problem casting Combo box entry to String");
+ attName = attCombo.getSelectedItem().toString();
+ }
Condition cond = (Condition) condCombo.getSelectedItem();
String pattern = valueField.getText().trim();
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
ap.paintAlignment(true, true);
- updateFiltersTab();
+ updateFiltersPanel();
}
}
}
return (enclose ? "<html>" : "")
- + "<style> p.ttip {width: 350; text-align: justify; word-wrap: break-word;}</style><p class=\"ttip\">"
- + ttext + "</p>" + ((enclose ? "</html>" : ""));
+
+ // BH 2018
+
+ + "<style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style><div class=\"ttip\">"
+
+// + "<style> p.ttip {width:350px;margin:-14px 0px -14px 0px;padding:2px;overflow-wrap:break-word;}"
+// + "</style><p class=\"ttip\">"
+
+ + ttext
+
+ + " </div>"
+// + "</p>"
+ + ((enclose ? "</html>" : ""));
}
* @param entries
* @param tooltips
*/
- public static JComboBox<String> buildComboWithTooltips(
- List<String> entries, List<String> tooltips)
+ public static JComboBox<Object> buildComboWithTooltips(
+ List<Object> entries, List<String> tooltips)
{
- JComboBox<String> combo = new JComboBox<>();
+ JComboBox<Object> combo = new JComboBox<>();
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
combo.setRenderer(renderer);
- for (String attName : entries)
+ for (Object attName : entries)
{
combo.addItem(attName);
}
import jalview.datamodel.AlignmentView;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.jbgui.GPCAPanel;
import jalview.math.RotatableMatrix.Axis;
import jalview.util.ImageMaker;
import java.awt.print.PrinterJob;
import javax.swing.ButtonGroup;
-import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.InternalFrameAdapter;
addKeyListener(getRotatableCanvas());
validate();
-
- this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
/**
@Override
protected void bgcolour_actionPerformed()
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_background_colour"),
- getRotatableCanvas().getBgColour());
-
- if (col != null)
+ String ttl = MessageManager.getString("label.select_background_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- getRotatableCanvas().setBgColour(col);
- }
- getRotatableCanvas().repaint();
+ @Override
+ public void colourSelected(Color c)
+ {
+ rc.setBgColour(c);
+ rc.repaint();
+ }
+ };
+ JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
+ listener);
}
/**
MessageManager.formatMessage("label.calc_title", "PCA",
getPcaModel().getScoreModelName()),
475, 450);
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
working = false;
}
}
}
- /**
- * Handler for 'Save as EPS' option
- */
- @Override
- protected void eps_actionPerformed()
- {
- makePCAImage(ImageMaker.TYPE.EPS);
- }
-
- /**
- * Handler for 'Save as PNG' option
- */
- @Override
- protected void png_actionPerformed()
- {
- makePCAImage(ImageMaker.TYPE.PNG);
- }
-
- void makePCAImage(ImageMaker.TYPE type)
+ public void makePCAImage(ImageMaker.TYPE type)
{
int width = getRotatableCanvas().getWidth();
int height = getRotatableCanvas().getHeight();
-
- ImageMaker im;
-
- switch (type)
+ ImageWriterI writer = new ImageWriterI()
{
- case PNG:
- im = new ImageMaker(this, ImageMaker.TYPE.PNG,
- "Make PNG image from PCA", width, height, null, null, null, 0,
- false);
- break;
- case EPS:
- im = new ImageMaker(this, ImageMaker.TYPE.EPS,
- "Make EPS file from PCA", width, height, null,
- this.getTitle(), null, 0, false);
- break;
- default:
- im = new ImageMaker(this, ImageMaker.TYPE.SVG,
- "Make SVG file from PCA", width, height, null,
- this.getTitle(), null, 0, false);
- }
-
- if (im.getGraphics() != null)
- {
- getRotatableCanvas().drawBackground(im.getGraphics());
- getRotatableCanvas().drawScene(im.getGraphics());
- if (getRotatableCanvas().drawAxes)
+ @Override
+ public void exportImage(Graphics g) throws Exception
{
- getRotatableCanvas().drawAxes(im.getGraphics());
+ RotatableCanvas canvas = getRotatableCanvas();
+ canvas.drawBackground(g);
+ canvas.drawScene(g);
+ if (canvas.drawAxes)
+ {
+ canvas.drawAxes(g);
+ }
}
- im.writeImage();
- }
+ };
+ String pca = MessageManager.getString("label.pca");
+ ImageExporter exporter = new ImageExporter(writer, null, type, pca);
+ exporter.doExport(null, this, width, height, pca);
}
@Override
// }
//
// JPanel progressPanel;
- // Long lId = new Long(id);
+ // Long lId = Long.valueOf(id);
// GridLayout layout = (GridLayout) statusPanel.getLayout();
// if (progressBars.get(lId) != null)
// {
- // progressPanel = (JPanel) progressBars.get(new Long(id));
+ // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
// statusPanel.remove(progressPanel);
// progressBars.remove(lId);
// progressPanel = null;
final IProgressIndicatorHandler handler)
{
progressBar.registerHandler(id, handler);
- // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
// {
// throw new
// Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
// }
- // progressBarHandlers.put(new Long(id), handler);
- // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ // progressBarHandlers.put(Long.valueOf(id), handler);
+ // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
// if (handler.canCancel())
// {
// JButton cancel = new JButton(
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.BackupFiles;
+ import jalview.io.BackupFilesPresetEntry;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.util.List;
import javax.help.HelpSetException;
-import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JPanel;
super();
frame = new JInternalFrame();
frame.setContentPane(this);
- wsPrefs = new WsPreferences();
- wsTab.add(wsPrefs, BorderLayout.CENTER);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ }
int width = 500, height = 450;
- new jalview.util.Platform();
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
width = 570;
height = 480;
new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
sorter.setSortKeys(sortKeys);
- sorter.sort();
+ // BH 2018 setSortKeys will do the sort
+ // sorter.sort();
// set up filtering
ActionListener onReset;
/*
* Set Output tab defaults
*/
- epsRendering.addItem(promptEachTimeOpt);
- epsRendering.addItem(lineArtOpt);
- epsRendering.addItem(textOpt);
- String defaultEPS = Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
- if (defaultEPS.equalsIgnoreCase("Text"))
- {
- epsRendering.setSelectedItem(textOpt);
- }
- else if (defaultEPS.equalsIgnoreCase("Lineart"))
- {
- epsRendering.setSelectedItem(lineArtOpt);
- }
- else
- {
- epsRendering.setSelectedItem(promptEachTimeOpt);
- }
+ setupOutputCombo(epsRendering, "EPS_RENDERING");
+ setupOutputCombo(htmlRendering, "HTML_RENDERING");
+ setupOutputCombo(svgRendering, "SVG_RENDERING");
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
}
/**
+ * A helper method that sets the items and initial selection in a character
+ * rendering option list (Prompt each time/Lineart/Text)
+ *
+ * @param comboBox
+ * @param propertyKey
+ */
+ protected void setupOutputCombo(JComboBox<Object> comboBox,
+ String propertyKey)
+ {
+ comboBox.addItem(promptEachTimeOpt);
+ comboBox.addItem(lineArtOpt);
+ comboBox.addItem(textOpt);
+
+ /*
+ * JalviewJS doesn't support Lineart so force it to Text
+ */
+ String defaultOption = Platform.isJS() ? "Text"
+ : Cache.getDefault(propertyKey, "Prompt each time");
+ if (defaultOption.equalsIgnoreCase("Text"))
+ {
+ comboBox.setSelectedItem(textOpt);
+ }
+ else if (defaultOption.equalsIgnoreCase("Lineart"))
+ {
+ comboBox.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ comboBox.setSelectedItem(promptEachTimeOpt);
+ }
+ }
+
+ /**
* Save user selections on the Preferences tabs to the Cache and write out to
* file.
*
*/
Cache.applicationProperties.setProperty("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
+ Cache.applicationProperties.setProperty("HTML_RENDERING",
+ ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
+ Cache.applicationProperties.setProperty("SVG_RENDERING",
+ ((OptionsParam) svgRendering.getSelectedItem()).getCode());
/*
* Save Connections settings
Cache.applicationProperties.setProperty("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
- wsPrefs.updateAndRefreshWsMenuConfig(false);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateAndRefreshWsMenuConfig(false);
+ }
/*
* Save Backups settings
*/
- Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
- Boolean.toString(backupfilesConfirmDelete.isSelected()));
Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
- Boolean.toString(backupfilesKeepAll.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
- Boolean.toString(suffixReverse.isSelected()));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
- suffixTemplate.getText());
- Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
- Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
- Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
- Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
- Cache.applicationProperties.setProperty(BackupFiles.NS+"_PRESET",
- Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+ int preset = getComboIntStringKey(backupfilesPresetsCombo);
+ Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+
+ if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+ Cache.applicationProperties
+ .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+ customBFPE.toString());
+ }
+
+ BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(preset);
+ Cache.applicationProperties.setProperty(
+ BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
@Override
public void startupFileTextfield_mouseClicked()
{
+ // TODO: JAL-3048 not needed for Jalview-JS
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
{
try
{
- wsPrefs.updateWsMenuConfig(true);
- wsPrefs.refreshWs_actionPerformed(e);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ }
frame.setClosed(true);
} catch (Exception ex)
{
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
- JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(
- MessageManager.getString("label.select_default_browser"));
+ // TODO: JAL-3048 not needed for j2s
+ if (!Platform.isJS()) // BH 2019
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JFileChooser chooser = new JFileChooser(".");
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_default_browser"));
- int value = chooser.showOpenDialog(this);
+ int value = chooser.showOpenDialog(this);
- if (value == JFileChooser.APPROVE_OPTION)
- {
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ }
}
-
}
/*
@Override
public void minColour_actionPerformed(JPanel panel)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_colour_minimum_value"),
- minColour.getBackground());
- if (col != null)
- {
- panel.setBackground(col);
- }
- panel.repaint();
+ panel);
}
@Override
public void maxColour_actionPerformed(JPanel panel)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_colour_maximum_value"),
- maxColour.getBackground());
- if (col != null)
- {
- panel.setBackground(col);
- }
- panel.repaint();
+ panel);
}
@Override
{
if (!useLegacyGap.isSelected())
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_gap_colour"),
- gapColour.getBackground());
- if (col != null)
- {
- gap.setBackground(col);
- }
- gap.repaint();
+ gap);
}
}
@Override
public void hiddenColour_actionPerformed(JPanel hidden)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_hidden_colour"),
- hiddenColour.getBackground());
- if (col != null)
- {
- hidden.setBackground(col);
- }
- hidden.repaint();
+ hidden);
}
@Override
}
} catch (NumberFormatException x)
{
+ userIdWidth.setText("");
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
JvOptionPane.WARNING_MESSAGE);
- userIdWidth.setText("");
}
}
import jalview.viewmodel.AlignmentViewport;
import java.awt.Component;
- import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyAdapter;
import javax.swing.AbstractAction;
import javax.swing.InputMap;
import javax.swing.JComponent;
+ import javax.swing.JDesktopPane;
+ import javax.swing.JInternalFrame;
import javax.swing.JMenuItem;
import javax.swing.KeyStroke;
import javax.swing.event.InternalFrameAdapter;
* estimate width and height of SplitFrame; this.getInsets() doesn't seem to
* give the full additional size (a few pixels short)
*/
- int widthFudge = Platform.isAMac() ? MAC_INSETS_WIDTH
+ int widthFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_WIDTH
: WINDOWS_INSETS_WIDTH;
- int heightFudge = Platform.isAMac() ? MAC_INSETS_HEIGHT
+ int heightFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
: WINDOWS_INSETS_HEIGHT;
int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
int height = ((AlignFrame) getTopFrame()).getHeight()
/*
* estimate ratio of (topFrameContent / bottomFrameContent)
*/
- int insets = Platform.isAMac() ? MAC_INSETS_HEIGHT
+ int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
: WINDOWS_INSETS_HEIGHT;
// allow 3 'rows' for scale, scrollbar, status bar
int topHeight = insets + (3 + topCount) * topCharHeight
* Ctrl-W / Cmd-W - close view or window
*/
KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
action = new AbstractAction()
{
@Override
* Ctrl-T / Cmd-T open new view
*/
KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
AbstractAction action = new AbstractAction()
{
@Override
* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
*/
KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
AbstractAction action = new AbstractAction()
{
@Override
};
overrideKeyBinding(key_cmdF, action);
}
+
+ /**
+ * Override to do nothing if triggered from one of the child frames
+ */
+ @Override
+ public void setSelected(boolean selected) throws PropertyVetoException
+ {
+ JDesktopPane desktopPane = getDesktopPane();
+ JInternalFrame fr = desktopPane == null ? null
+ : desktopPane.getSelectedFrame();
+ if (fr == getTopFrame() || fr == getBottomFrame())
+ {
+ /*
+ * patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
+ * it may be possible to remove this method in future
+ * if the underlying Java behaviour changes
+ */
+ if (selected)
+ {
+ moveToFront();
+ }
+ return;
+ }
+ super.setSelected(selected);
+ }
}
private FTSRestRequest lastPdbRequest;
- private FTSRestClientI pdbRestCleint;
+ private FTSRestClientI pdbRestClient;
private String selectedPdbFileName;
void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
+ pdbRestClient = PDBFTSRestClient.getInstance();
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
e.printStackTrace();
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<>();
+
+ /*
+ * note PDBs as DBRefEntry so they are not duplicated in query
+ */
+ Set<String> pdbids = new HashSet<>();
if (seq.getAllPDBEntries() != null
&& queryBuilder.length() < MAX_QLENGTH)
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
- .append(" OR ");
+ String id = entry.getId().toLowerCase();
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
isPDBRefsFound = true;
+ pdbids.add(id);
}
}
}
- if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
+ List<DBRefEntry> refs = seq.getDBRefs();
+ if (refs != null && refs.size() != 0)
{
- for (DBRefEntry dbRef : seq.getDBRefs())
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
+ DBRefEntry dbRef = refs.get(ib);
if (isValidSeqName(getDBRefId(dbRef))
&& queryBuilder.length() < MAX_QLENGTH)
{
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id:")
- .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
- isPDBRefsFound = true;
+ String id = getDBRefId(dbRef).toLowerCase();
+ if (!pdbids.contains(id))
+ {
+ queryBuilder.append("pdb_id:").append(id).append(" OR ");
+ isPDBRefsFound = true;
+ pdbids.add(id);
+ }
}
else
{
public void run()
{
long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
+ pdbRestClient = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
e.printStackTrace();
@Override
protected void pdbFromFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+ // works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
&& !discoveredStructuresSet.isEmpty();
}
+ protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this.
+ // Doing a search for "1" or "1c" is valuable?
+ // Those work but are enormously slow.
+
@Override
protected void txt_search_ActionPerformed()
{
+ String text = txt_search.getText().trim();
+ if (text.length() >= PDB_ID_MIN)
new Thread()
{
- @Override
+
+ @Override
public void run()
{
errorWarning.setLength(0);
isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
+ if (text.length() > 0)
{
- String searchTerm = txt_search.getText().toLowerCase();
+ String searchTerm = text.toLowerCase();
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<>();
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
errorWarning.append(e.getMessage());
import java.awt.BorderLayout;
import java.awt.Color;
- import java.awt.Font;
+ import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridLayout;
import java.awt.Image;
import java.awt.MediaTracker;
+ import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.image.BufferedImage;
import java.util.Vector;
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;
Image image;
- int angle = 0;
+ float angle = 0f;
String title = "";
{
super.setVisible(aFlag);
frame.setVisible(aFlag);
-- };
++ }
JTabbedPane subjobs = null;
setInfoText(info);
java.net.URL url = getClass()
- .getResource("/images/Jalview_Logo_small.png");
+ .getResource("/images/Jalview_Logo_small_with_border.png");
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
MediaTracker mt = new MediaTracker(this);
}
AnimatedPanel ap = new AnimatedPanel();
- titlePanel.add(ap, BorderLayout.CENTER);
+ ap.setPreferredSize(new Dimension(60, 60));
+ titlePanel.add(ap, BorderLayout.WEST);
+ titlePanel.add(titleText, BorderLayout.CENTER);
+ setStatus(currentStatus);
Thread thread = new Thread(ap);
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 void setStatus(int status)
{
currentStatus = status;
+
+ String message = null;
+ switch (currentStatus)
+ {
+ case STATE_QUEUING:
+ message = MessageManager.getString("label.state_queueing");
+ break;
+
+ case STATE_RUNNING:
+ message = MessageManager.getString("label.state_running");
+ break;
+
+ case STATE_STOPPED_OK:
+ message = MessageManager.getString("label.state_completed");
+ break;
+
+ case STATE_CANCELLED_OK:
+ message = MessageManager.getString("label.state_job_cancelled");
+ break;
+
+ case STATE_STOPPED_ERROR:
+ message = MessageManager.getString("label.state_job_error");
+ break;
+
+ case STATE_STOPPED_SERVERERROR:
+ message = MessageManager.getString("label.server_error_try_later");
+ break;
+ }
+ titleText.setText(title + (message == null ? "" : " - " + message));
+ titleText.repaint();
}
/**
* DOCUMENT ME!
*/
@Override
-protected void cancel_actionPerformed(ActionEvent e)
+ protected void cancel_actionPerformed(ActionEvent e)
{
if (!serviceIsCancellable)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
- public void run()
+ public void run()
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
title, JvOptionPane.WARNING_MESSAGE);
{
startTime = System.currentTimeMillis();
+ float invSpeed = 15f;
+ float factor = 1f;
while (currentStatus < STATE_STOPPED_OK)
{
+ if (currentStatus == STATE_QUEUING)
+ {
+ invSpeed = 25f;
+ factor = 1f;
+ }
+ else if (currentStatus == STATE_RUNNING)
+ {
+ invSpeed = 10f;
+ factor = (float) (0.5 + 1.5
+ * (0.5 - (0.5 * Math.sin(3.14159 / 180 * (angle + 45)))));
+ }
try
{
Thread.sleep(50);
- int units = (int) ((System.currentTimeMillis() - startTime)
- / 10f);
- angle += units;
+ float delta = (System.currentTimeMillis() - startTime) / invSpeed;
+ angle += delta * factor;
angle %= 360;
startTime = System.currentTimeMillis();
if (currentStatus >= STATE_STOPPED_OK)
{
+ park();
angle = 0;
}
cancel.setEnabled(false);
}
+ public void park()
+ {
+ startTime = System.currentTimeMillis();
+
+ while (angle < 360)
+ {
+ float invSpeed = 5f;
+ float factor = 1f;
+ try
+ {
+ Thread.sleep(25);
+
+ float delta = (System.currentTimeMillis() - startTime) / invSpeed;
+ angle += delta * factor;
+ startTime = System.currentTimeMillis();
+
+ if (angle >= 360)
+ {
+ angle = 360;
+ }
+
+ repaint();
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ }
+
void drawPanel()
{
if (offscreen == null || offscreen.getWidth(this) != getWidth()
|| offscreen.getHeight(this) != getHeight())
{
offscreen = new BufferedImage(getWidth(), getHeight(),
- BufferedImage.TYPE_INT_ARGB);
+ BufferedImage.TYPE_INT_RGB);
}
Graphics2D g = (Graphics2D) offscreen.getGraphics();
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ g.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
+ RenderingHints.VALUE_INTERPOLATION_BICUBIC);
+ g.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
if (image != null)
{
int x = image.getWidth(this) / 2, y = image.getHeight(this) / 2;
- g.rotate(Math.toRadians(angle), 10 + x, 10 + y);
- g.drawImage(image, 10, 10, this);
- g.rotate(-Math.toRadians(angle), 10 + x, 10 + y);
+ g.rotate(3.14159 / 180 * (angle), x, y);
+ g.drawImage(image, 0, 0, this);
+ g.rotate(-3.14159 / 180 * (angle), x, y);
}
}
@Override
- public void paintComponent(Graphics g1)
+ public void paintComponent(Graphics g1)
{
drawPanel();
}
@Override
- public void hyperlinkUpdate(HyperlinkEvent e)
+ public void hyperlinkUpdate(HyperlinkEvent e)
{
Desktop.hyperlinkUpdate(e);
}
if (row.graphGroup > -1)
{
graphGroupSeen.set(row.graphGroup);
- Integer key = new Integer(row.graphGroup);
+ Integer key = Integer.valueOf(row.graphGroup);
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
String refSeqId = null;
- public boolean annotateAlignmentView(AlignViewportI viewport, String file,
+ public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
}
public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
- String file, DataSourceType sourceType)
+ Object file, DataSourceType sourceType)
{
BufferedReader in = null;
try
{
if (sourceType == DataSourceType.FILE)
{
- in = new BufferedReader(new FileReader(file));
+ in = FileLoader.getBufferedReader(file);
}
else if (sourceType == DataSourceType.URL)
{
- URL url = new URL(file);
+ URL url = new URL(file.toString());
in = new BufferedReader(new InputStreamReader(url.openStream()));
}
else if (sourceType == DataSourceType.PASTE)
{
- in = new BufferedReader(new StringReader(file));
+ in = new BufferedReader(new StringReader(file.toString()));
}
else if (sourceType == DataSourceType.CLASSLOADER)
{
autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
(aa[aai].groupRef == null ? null
: aa[aai].groupRef.getName())),
- new Integer(1));
+ Integer.valueOf(1));
}
}
}
{
displayChar = token;
// foo
- value = new Float(token).floatValue();
+ value = Float.valueOf(token).floatValue();
parsedValue = true;
continue;
} catch (NumberFormatException ex)
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.io.File;
import java.io.IOException;
* BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
* User configurable options are:
* BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
- * BACKUPFILES_SUFFIX - a template to insert after the file extension. Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
- * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
- * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
- * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
- * BACKUPFILES_REVERSE_ORDER - if true then "logfile" style numbering and file rolling will occur. If false then ever-increasing version numbering will occur, but old files will still be deleted if there are more than ROLL_MAX backup files.
- * BACKUPFILES_CONFIRM_DELETE_OLD - if true then prompt/confirm with the user when deleting older backup/version files.
+ * The rest of the options are now saved as BACKUPFILES_PRESET, BACKUPFILES_SAVED and BACKUPFILES_CUSTOM
+ * (see BackupFilesPresetEntry)
*/
public class BackupFiles
public static final String ENABLED = NS + "_ENABLED";
- public static final String SUFFIX = NS + "_SUFFIX";
-
- public static final String NO_MAX = NS + "_NO_MAX";
-
- public static final String ROLL_MAX = NS + "_ROLL_MAX";
-
- public static final String SUFFIX_DIGITS = NS + "_SUFFIX_DIGITS";
-
public static final String NUM_PLACEHOLDER = "%n";
- public static final String REVERSE_ORDER = NS + "_REVERSE_ORDER";
-
- public static final String CONFIRM_DELETE_OLD = NS
- + "_CONFIRM_DELETE_OLD";
-
private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
private static final String TEMP_FILE_EXT = ".tmp";
// REVERSE_ORDER
public BackupFiles(File file)
{
- this(file, ".bak" + NUM_PLACEHOLDER, false, 3, 3, false);
- }
-
- public BackupFiles(File file, String defaultSuffix, boolean defaultNoMax,
- int defaultMax, int defaultDigits, boolean defaultReverseOrder)
- {
classInit();
this.file = file;
- this.suffix = Cache.getDefault(SUFFIX, defaultSuffix);
- this.noMax = Cache.getDefault(NO_MAX, defaultNoMax);
- this.max = Cache.getDefault(ROLL_MAX, defaultMax);
- this.digits = Cache.getDefault(SUFFIX_DIGITS, defaultDigits);
- this.reverseOrder = Cache.getDefault(REVERSE_ORDER,
- defaultReverseOrder);
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+ this.suffix = bfpe.suffix;
+ this.noMax = bfpe.keepAll;
+ this.max = bfpe.rollMax;
+ this.digits = bfpe.digits;
+ this.reverseOrder = bfpe.reverse;
// create a temp file to save new data in
File temp = null;
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)
/**
* Constructor which does not parse the file immediately
*
- * @param file
+ * @param file File or String filename
* @param paste
* @throws IOException
*/
- public FeaturesFile(String file, DataSourceType paste)
+ public FeaturesFile(Object file, DataSourceType paste)
throws IOException
{
super(false, file, paste);
* @param type
* @throws IOException
*/
- public FeaturesFile(boolean parseImmediately, String file,
+ public FeaturesFile(boolean parseImmediately, Object file,
DataSourceType type) throws IOException
{
super(parseImmediately, file, type);
float score = Float.NaN;
try
{
- score = new Float(gffColumns[6]).floatValue();
+ score = Float.valueOf(gffColumns[6]).floatValue();
} catch (NumberFormatException ex)
{
sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.utils.UrlDownloadClient;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
import java.io.IOException;
+import java.io.InputStreamReader;
import java.util.StringTokenizer;
import java.util.Vector;
boolean raiseGUI = true;
+ private File selectedFile;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
this.raiseGUI = raiseGUI;
}
- public void LoadFile(AlignViewport viewport, String file,
+ public void LoadFile(AlignViewport viewport, Object file,
DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
- LoadFile(file, protocol, format);
+ if (file instanceof File) {
+ this.selectedFile = (File) file;
+ file = selectedFile.getPath();
+ }
+ LoadFile(file.toString(), protocol, format);
}
public void LoadFile(String file, DataSourceType protocol,
}
/**
+ * Load alignment from (file, protocol) of type format and wait till loaded
+ *
+ * @param file
+ * @param sourceType
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(File file,
+ DataSourceType sourceType, FileFormatI format)
+ {
+ this.selectedFile = file;
+ this.file = file.getPath();
+ this.protocol = sourceType;
+ this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
+
+ /**
* Load alignment from FileParse source of type format and wait till loaded
*
* @param source
}
/**
- * start thread and wait until finished, then return the alignFrame that's
- * (hopefully) been read.
+ * runs the 'run' method (in this thread), then return the alignFrame that's
+ * (hopefully) been read
*
* @return
*/
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;
}
public void updateRecentlyOpened()
{
- Vector recent = new Vector();
+ Vector<String> recent = new Vector<>();
if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
- String historyItems = jalview.bin.Cache.getProperty(type);
+ String historyItems = Cache.getProperty(type);
StringTokenizer st;
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ recent.addElement(st.nextToken().trim());
}
}
format = new IdentifyFile().identify(source, false);
// identify stream and rewind rather than close
}
+ else if (selectedFile != null) {
+ format = new IdentifyFile().identify(selectedFile, protocol);
+ }
else
{
format = new IdentifyFile().identify(file, protocol);
"IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
- alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
+ // BH 2018 switch to File object here instead of filename
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
}
else
{
file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
- UrlDownloadClient.download(file, tempStructureFileStr);
- al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+
+ // BH - switching to File object here so as to hold
+ // ._bytes array directly
+ File tempFile = new File(tempStructureFileStr);
+ UrlDownloadClient.download(file, tempFile);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE,
format);
source = fa.getAlignFile();
}
else
{
- al = fa.readFile(file, protocol, format);
+ if (selectedFile == null) {
+ al = fa.readFile(file, protocol, format);
+
+ } else {
+ al = fa.readFile(selectedFile, protocol, format);
+ }
source = fa.getAlignFile(); // keep reference for later if
+
// necessary.
}
}
if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
}
if (proxyColourScheme != null)
{
return tempStructFile.toString();
}
+ /**
+ *
+ * @param file a File, or a String which is a name of a file
+ * @return
+ * @throws FileNotFoundException
+ */
+ public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
+ if (file instanceof String)
+ {
+ return new BufferedReader(new FileReader((String) file));
+ }
+ byte[] bytes = Platform.getFileBytes((File) file);
+ if (bytes != null)
+ {
+ return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
+ }
+ return new BufferedReader(new FileReader((File) file));
+ }
+
}
/**
* Creates a new JPredFile object.
*
+ * BH allows File or String
+ *
* @param inFile
* DOCUMENT ME!
* @param sourceType
* @throws IOException
* DOCUMENT ME!
*/
- public JPredFile(String inFile, DataSourceType sourceType)
+ public JPredFile(Object inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
{
ascore = symbols.nextToken();
- Float score = new Float(ascore);
+ Float score = Float.valueOf(ascore);
scores.addElement(score);
}
seq_entries.addElement(newseq.toString());
ids.addElement(id);
- Symscores.put(id, new Integer(ids.size() - 1));
+ Symscores.put(id, Integer.valueOf(ids.size() - 1));
}
}
}
}
/**
- * DOCUMENT ME!
*
* @param args
- * DOCUMENT ME!
+ * @j2sIgnore
*/
public static void main(String[] args)
{
*/
package jalview.io;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
+import java.util.List;
+
+import com.stevesoft.pat.Regex;
+
public class ModellerDescription
{
/**
resCode(int v)
{
- val = new Integer(v);
+ val = Integer.valueOf(v);
field = val.toString();
}
};
private resCode validResidueCode(String field)
{
Integer val = null;
- com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
+ Regex r = new Regex(
"\\s*((([-0-9]+).?)|FIRST|LAST|@)");
if (!r.search(field))
if (seq.getDatasetSequence() != null
&& seq.getDatasetSequence().getDBRefs() != null)
{
- jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
- .getDBRefs();
- int i, j;
- for (i = 0, j = dbr.length; i < j; i++)
+ List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
+ for (int i = 0, ni = dbr.size(); i < ni; i++)
{
- if (dbr[i] != null)
+ DBRefEntry dbri = dbr.get(i);
+ if (dbri != null)
{
// JBPNote PDB dbRefEntry needs properties to propagate onto
// ModellerField
// JBPNote Need to get info from the user about whether the sequence
// is the one being modelled, or if it is a template.
- if (dbr[i].getSource()
+ if (dbri.getSource()
.equals(jalview.datamodel.DBRefSource.PDB))
{
- fields.put(Fields[LOCALID], dbr[i].getAccessionId());
+ fields.put(Fields[LOCALID], dbri.getAccessionId());
t = 2;
break;
}
import java.io.IOException;
import java.util.StringTokenizer;
+import com.stevesoft.pat.Regex;
+
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* tree distances and topology are unreliable when they are parsed. TODO: on
boolean printRootInfo = true;
- private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {
- new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
+ private Regex[] NodeSafeName = new Regex[] {
+ new Regex().perlCode("m/[\\[,:'()]/"), // test for
// requiring
// quotes
- new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
+ new Regex().perlCode("s/'/''/"), // escaping quote
// characters
- new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
+ new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
// transformation
};
boolean ascending = false; // flag indicating that we are leaving the
// current node
- com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+ Regex majorsyms = new Regex(
"[(\\['),;]");
int nextcp = 0;
continue;
}
-
- ;
d++;
if (c.right() == null)
// Deal with quoted fields
case '\'':
- com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
+ Regex qnodename = new Regex(
"'([^']|'')+'");
if (qnodename.searchFrom(nf, fcp))
nodename = new String(
qnodename.stringMatched().substring(1, nl - 1));
// unpack any escaped colons
- com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+ Regex xpandquotes = Regex
.perlCode("s/''/'/");
String widernodename = xpandquotes.replaceAll(nodename);
nodename = widernodename;
* '"+nf.substring(cp,fcp)+"'"); }
*/
// verify termination.
- com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
+ Regex comment = new Regex(
"]");
if (comment.searchFrom(nf, fcp))
{
Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
nf);
}
-
- ;
}
// Parse simpler field strings
String fstring = nf.substring(ncp, fcp);
+ fstring.substring(cend + 1);
}
- com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
+ Regex uqnodename = new Regex(
"\\b([^' :;\\](),]+)");
- com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
+ Regex nbootstrap = new Regex(
"\\s*([0-9+]+)\\s*:");
- com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
+ Regex ndist = new Regex(
":([-0-9Ee.+]+)");
if (!parsednodename && uqnodename.search(fstring)
{
try
{
- bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+ bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
.intValue();
HasBootstrap = true;
} catch (Exception e)
{
try
{
- distance = (new Float(ndist.stringMatched(1))).floatValue();
+ distance = (Float.valueOf(ndist.stringMatched(1))).floatValue();
HasDistances = true;
nodehasdistance = true;
} catch (Exception e)
if (code.toLowerCase().equals("b"))
{
int v = -1;
- Float iv = new Float(value);
+ Float iv = Float.valueOf(value);
v = iv.intValue(); // jalview only does integer bootstraps
// currently
c.setBootstrap(v);
}
}
- // Test
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
try
trf.parse();
System.out.println("Original file :\n");
- com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+ Regex nonl = new Regex("\n+", "");
System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
System.out.println("Parsed file.\n");
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+ import jalview.datamodel.GeneLociI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
private static final int MAX_SOURCES = 40;
- private static final String[][] PRIMARY_SOURCES = new String[][] {
- DBRefSource.CODINGDBS, DBRefSource.DNACODINGDBS,
- DBRefSource.PROTEINDBS };
+ // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
final String linkImageURL;
@Override
public int compare(DBRefEntry ref1, DBRefEntry ref2)
{
- if (ref1.isChromosome())
+ if (ref1 instanceof GeneLociI)
{
return -1;
}
- if (ref2.isChromosome())
+ if (ref2 instanceof GeneLociI)
{
return 1;
}
String s1 = ref1.getSource();
String s2 = ref2.getSource();
- boolean s1Primary = isPrimarySource(s1);
- boolean s2Primary = isPrimarySource(s2);
+ boolean s1Primary = DBRefSource.isPrimarySource(s1);
+ boolean s2Primary = DBRefSource.isPrimarySource(s2);
if (s1Primary && !s2Primary)
{
return -1;
return comp;
}
- private boolean isPrimarySource(String source)
- {
- for (String[] primary : PRIMARY_SOURCES)
- {
- for (String s : primary)
- {
- if (source.equals(s))
- {
- return true;
- }
- }
- }
- return false;
- }
+// private boolean isPrimarySource(String source)
+// {
+// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+// {
+// for (String s : primary)
+// {
+// if (source.equals(s))
+// {
+// return true;
+// }
+// }
+// }
+// return false;
+// }
};
public SequenceAnnotationReport(String linkURL)
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- DBRefEntry[] dbrefs = ds.getDBRefs();
+ List<DBRefEntry> dbrefs = ds.getDBRefs();
if (dbrefs == null)
{
return 0;
}
// note this sorts the refs held on the sequence!
- Arrays.sort(dbrefs, comparator);
+ dbrefs.sort(comparator);
boolean ellipsis = false;
String source = null;
String lastSource = null;
* @return vector of alignment sequences in order of SeqCigar array (but
* missing unfound seqcigars)
*/
- private Vector findAlignmentSequences(AlignmentI jal,
+ private Vector<SequenceI> findAlignmentSequences(AlignmentI jal,
SeqCigar[] sequences)
{
SeqCigar[] tseqs = new SeqCigar[sequences.length];
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
- Vector alsq = new Vector();
- List<SequenceI> jalsqs;
- synchronized (jalsqs = jal.getSequences())
+ Vector<SequenceI> alsq = new Vector<>();
+ List<SequenceI> jalsqs = jal.getSequences();
+ synchronized (jalsqs)
{
for (SequenceI asq : jalsqs)
{
Integer nindx = (Integer) nodespecs.get(nname);
if (nindx == null)
{
- nindx = new Integer(1);
+ nindx = Integer.valueOf(1);
}
nname = nindx.toString() + " " + nname;
return nname;
String oval = nodespec.substring(0, nodespec.indexOf(' '));
try
{
- occurence = new Integer(oval).intValue();
+ occurence = Integer.valueOf(oval).intValue();
} catch (Exception e)
{
System.err.println("Invalid nodespec '" + nodespec + "'");
*/
public class VCFLoader
{
+ private static final String DEFAULT_SPECIES = "homo_sapiens";
+
/**
* A class to model the mapping from sequence to VCF coordinates. Cases include
* <ul>
/*
* Lookup keys, and default values, for Preference entries that describe
- * patterns for VCF and VEP fields to capture
+ * patterns for VCF and VEP fields to capture
*/
private static final String VEP_FIELDS_PREF = "VEP_FIELDS";
private static final String DEFAULT_VEP_FIELDS = ".*";// "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG";
/*
+ * Lookup keys, and default values, for Preference entries that give
+ * mappings from tokens in the 'reference' header to species or assembly
+ */
+ private static final String VCF_ASSEMBLY = "VCF_ASSEMBLY";
+
+ private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh37,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
+
+ private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
+
+ private static final String DEFAULT_REFERENCE = "grch37"; // fallback default is human GRCh37
+
+ /*
* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
private static final String PIPE_REGEX = "\\|";
/*
- * key for Allele Frequency output by VEP
- * see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
- */
- private static final String ALLELE_FREQUENCY_KEY = "AF";
-
- /*
* delimiter that separates multiple consequence data blocks
*/
private static final String COMMA = ",";
private VCFHeader header;
/*
+ * species (as a valid Ensembl term) the VCF is for
+ */
+ private String vcfSpecies;
+
+ /*
+ * genome assembly version (as a valid Ensembl identifier) the VCF is for
+ */
+ private String vcfAssembly;
+
+ /*
* a Dictionary of contigs (if present) referenced in the VCF file
*/
private SAMSequenceDictionary dictionary;
*/
public SequenceI loadVCFContig(String contig)
{
- String ref = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY)
- .getValue();
+ VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
+ if (headerLine == null)
+ {
+ Cache.log.error("VCF reference header not found");
+ return null;
+ }
+ String ref = headerLine.getValue();
if (ref.startsWith("file://"))
{
ref = ref.substring(7);
}
+ setSpeciesAndAssembly(ref);
SequenceI seq = null;
File dbFile = new File(ref);
{
HtsContigDb db = new HtsContigDb("", dbFile);
seq = db.getSequenceProxy(contig);
- loadSequenceVCF(seq, ref);
+ loadSequenceVCF(seq);
db.close();
}
else
{
- System.err.println("VCF reference not found: " + ref);
+ Cache.log.error("VCF reference not found: " + ref);
}
return seq;
{
VCFHeaderLine ref = header
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String vcfAssembly = ref.getValue();
+ String reference = ref == null ? null : ref.getValue();
+
+ setSpeciesAndAssembly(reference);
int varCount = 0;
int seqCount = 0;
*/
for (SequenceI seq : seqs)
{
- int added = loadSequenceVCF(seq, vcfAssembly);
+ int added = loadSequenceVCF(seq);
if (added > 0)
{
seqCount++;
}
/**
+ * Attempts to determine and save the species and genome assembly version to
+ * which the VCF data applies. This may be done by parsing the {@code reference}
+ * header line, configured in a property file, or (potentially) confirmed
+ * interactively by the user.
+ * <p>
+ * The saved values should be identifiers valid for Ensembl's REST service
+ * {@code map} endpoint, so they can be used (if necessary) to retrieve the
+ * mapping between VCF coordinates and sequence coordinates.
+ *
+ * @param reference
+ * @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
+ */
+ protected void setSpeciesAndAssembly(String reference)
+ {
+ if (reference == null)
+ {
+ Cache.log.error("No VCF ##reference found, defaulting to "
+ + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
+ reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
+ }
+ reference = reference.toLowerCase();
+
+ /*
+ * for a non-human species, or other assembly identifier,
+ * specify as a Jalview property file entry e.g.
+ * VCF_ASSEMBLY = hs37=GRCh37,assembly19=GRCh37
+ * VCF_SPECIES = c_elegans=celegans
+ * to map a token in the reference header to a value
+ */
+ String prop = Cache.getDefault(VCF_ASSEMBLY, DEFAULT_VCF_ASSEMBLY);
+ for (String token : prop.split(","))
+ {
+ String[] tokens = token.split("=");
+ if (tokens.length == 2)
+ {
+ if (reference.contains(tokens[0].trim().toLowerCase()))
+ {
+ vcfAssembly = tokens[1].trim();
+ break;
+ }
+ }
+ }
+
+ vcfSpecies = DEFAULT_SPECIES;
+ prop = Cache.getProperty(VCF_SPECIES);
+ if (prop != null)
+ {
+ for (String token : prop.split(","))
+ {
+ String[] tokens = token.split("=");
+ if (tokens.length == 2)
+ {
+ if (reference.contains(tokens[0].trim().toLowerCase()))
+ {
+ vcfSpecies = tokens[1].trim();
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Opens the VCF file and parses header data
*
* @param filePath
*/
protected void transferAddedFeatures(SequenceI seq)
{
- DBRefEntry[] dbrefs = seq.getDBRefs();
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
if (dbrefs == null)
{
return;
* and returns the number of variant features added
*
* @param seq
- * @param vcfAssembly
* @return
*/
- protected int loadSequenceVCF(SequenceI seq, String vcfAssembly)
+ protected int loadSequenceVCF(SequenceI seq)
{
- VCFMap vcfMap = getVcfMap(seq, vcfAssembly);
+ VCFMap vcfMap = getVcfMap(seq);
if (vcfMap == null)
{
return 0;
* Answers a map from sequence coordinates to VCF chromosome ranges
*
* @param seq
- * @param vcfAssembly
* @return
*/
- private VCFMap getVcfMap(SequenceI seq, String vcfAssembly)
+ private VCFMap getVcfMap(SequenceI seq)
{
/*
* simplest case: sequence has id and length matching a VCF contig
String species = seqCoords.getSpeciesId();
String chromosome = seqCoords.getChromosomeId();
String seqRef = seqCoords.getAssemblyId();
- MapList map = seqCoords.getMap();
+ MapList map = seqCoords.getMapping();
- if (!vcfSpeciesMatchesSequence(vcfAssembly, species))
+ // note this requires the configured species to match that
+ // returned with the Ensembl sequence; todo: support aliases?
+ if (!vcfSpecies.equalsIgnoreCase(species))
{
+ Cache.log.warn("No VCF loaded to " + seq.getName()
+ + " as species not matched");
return null;
}
- if (vcfAssemblyMatchesSequence(vcfAssembly, seqRef))
+ if (seqRef.equalsIgnoreCase(vcfAssembly))
{
return new VCFMap(chromosome, map);
}
- if (!"GRCh38".equalsIgnoreCase(seqRef) // Ensembl
- || !vcfAssembly.contains("Homo_sapiens_assembly19")) // gnomAD
- {
- return null;
- }
-
/*
- * map chromosomal coordinates from sequence to VCF if the VCF
- * data has a different reference assembly to the sequence
+ * VCF data has a different reference assembly to the sequence:
+ * query Ensembl to map chromosomal coordinates from sequence to VCF
*/
- // TODO generalise for cases other than GRCh38 -> GRCh37 !
- // - or get the user to choose in a dialog
-
List<int[]> toVcfRanges = new ArrayList<>();
List<int[]> fromSequenceRanges = new ArrayList<>();
- String toRef = "GRCh37";
for (int[] range : map.getToRanges())
{
}
int[] newRange = mapReferenceRange(range, chromosome, "human", seqRef,
- toRef);
+ vcfAssembly);
if (newRange == null)
{
Cache.log.error(
String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
- chromosome, seqRef, range[0], range[1], toRef));
+ chromosome, seqRef, range[0], range[1],
+ vcfAssembly));
continue;
}
else
}
/**
- * Answers true if we determine that the VCF data uses the same reference
- * assembly as the sequence, else false
- *
- * @param vcfAssembly
- * @param seqRef
- * @return
- */
- private boolean vcfAssemblyMatchesSequence(String vcfAssembly,
- String seqRef)
- {
- // TODO improve on this stub, which handles gnomAD and
- // hopes for the best for other cases
-
- if ("GRCh38".equalsIgnoreCase(seqRef) // Ensembl
- && vcfAssembly.contains("Homo_sapiens_assembly19")) // gnomAD
- {
- return false;
- }
- return true;
- }
-
- /**
- * Answers true if the species inferred from the VCF reference identifier
- * matches that for the sequence
- *
- * @param vcfAssembly
- * @param speciesId
- * @return
- */
- boolean vcfSpeciesMatchesSequence(String vcfAssembly, String speciesId)
- {
- // PROBLEM 1
- // there are many aliases for species - how to equate one with another?
- // PROBLEM 2
- // VCF ##reference header is an unstructured URI - how to extract species?
- // perhaps check if ref includes any (Ensembl) alias of speciesId??
- // TODO ask the user to confirm this??
-
- if (vcfAssembly.contains("Homo_sapiens") // gnomAD exome data example
- && "HOMO_SAPIENS".equals(speciesId)) // Ensembl species id
- {
- return true;
- }
-
- if (vcfAssembly.contains("c_elegans") // VEP VCF response example
- && "CAENORHABDITIS_ELEGANS".equals(speciesId)) // Ensembl
- {
- return true;
- }
-
- // this is not a sustainable solution...
-
- return false;
- }
-
- /**
* Queries the VCF reader for any variants that overlap the mapped chromosome
* ranges of the sequence, and adds as variant features. Returns the number of
* overlapping variants found.
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
- import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu webService = new JMenu();
+ public JMenu webService = new JMenu();// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
- protected JMenuItem webServiceNoServices;
+ public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
- protected JLabel statusBar = new JLabel();
+ public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+ // sufficient for
+ // AlignFrame.printWriter
protected JMenu outputTextboxMenu = new JMenu();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+ protected JMenuItem openFeatureSettings;
+
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName("jalview-alignment");
+
jbInit();
setJMenuBar(alignFrameMenuBar);
@Override
public void actionPerformed(ActionEvent e)
{
- outputText_actionPerformed(e);
+ outputText_actionPerformed(e.getActionCommand());
}
});
System.err.println(e.toString());
}
- if (!Platform.isAMac())
+ if (Platform.allowMnemonics()) // was "not mac and not JS"
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
@Override
public void actionPerformed(ActionEvent e)
{
- saveAs_actionPerformed(e);
+ saveAs_actionPerformed();
}
};
// FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- copy_actionPerformed(e);
+ copy_actionPerformed();
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- cut_actionPerformed(e);
+ cut_actionPerformed();
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
@Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ delete_actionPerformed();
}
});
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
/*
* Translate as cDNA with sub-menu of translation tables
*/
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
boolean first = true;
for (final GeneticCodeI table : GeneticCodes.getInstance()
.getCodeTables())
}
});
- JMenuItem openFeatureSettings = new JMenuItem(
+ openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
{
featureSettings_actionPerformed(e);
}
});
+
+ /*
+ * add sub-menu of database we can fetch from
+ */
JMenuItem fetchSequence = new JMenuItem(
MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- fetchSequence_actionPerformed(e);
+ fetchSequence_actionPerformed();
}
});
associatedData_actionPerformed(e);
}
});
- loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+ loadVcf = new JMenuItem(
+ MessageManager.getString("label.load_vcf_file"));
loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
loadVcf.addActionListener(new ActionListener()
{
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
false);
al = new ActionListener()
{
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
al = new ActionListener()
{
@Override
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(webService);
+ if (!Platform.isJS())
+ {
+ alignFrameMenuBar.add(webService);
+ }
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(exportAnnotations);
fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
- fileMenu.add(loadVcf);
+ if (!Platform.isJS())
+ {
+ fileMenu.add(loadVcf);
+ }
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(expandAlignment);
calculateMenu.add(extractScores);
- calculateMenu.addSeparator();
- calculateMenu.add(runGroovy);
+ if (!Platform.isJS())
+ {
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+ }
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- exportImageMenu.add(htmlMenuItem);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(htmlMenuItem);
+ }
exportImageMenu.add(epsFile);
exportImageMenu.add(createPNG);
- exportImageMenu.add(createBioJS);
- exportImageMenu.add(createSVG);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
+ }
addSequenceMenu.add(addFromFile);
addSequenceMenu.add(addFromText);
addSequenceMenu.add(addFromURL);
{
}
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String formatName)
{
}
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
}
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ protected void delete_actionPerformed()
{
}
{
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed()
{
}
}
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
}
import jalview.util.Platform;
import java.awt.FlowLayout;
- import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class GDesktop extends JFrame
{
+
protected static JMenu windowMenu = new JMenu();
JMenuBar desktopMenubar = new JMenuBar();
JMenu HelpMenu = new JMenu();
- protected JMenu VamsasMenu = new JMenu();
-
- protected JMenu VamsasStMenu = new JMenu();
-
JMenuItem inputLocalFileMenuItem = new JMenuItem();
JMenuItem inputURLMenuItem = new JMenuItem();
JMenu inputMenu = new JMenu();
- protected JMenuItem vamsasStart = new JMenuItem();
-
- protected JMenuItem vamsasImport = new JMenuItem();
-
- protected JMenuItem vamsasSave = new JMenuItem();
-
JMenuItem inputSequence = new JMenuItem();
- protected JMenuItem vamsasStop = new JMenuItem();
-
JMenuItem closeAll = new JMenuItem();
JMenuItem raiseRelated = new JMenuItem();
*/
public GDesktop()
{
+ super();
try
{
jbInit();
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(
javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(),
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(),
false));
inputLocalFileMenuItem
.addActionListener(new java.awt.event.ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- documentationMenuItem_actionPerformed(e);
+ documentationMenuItem_actionPerformed();
}
});
this.getContentPane().setLayout(flowLayout1);
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- vamsasStart.setVisible(false);
- vamsasStart.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasStart_actionPerformed(e);
- }
- });
- vamsasImport.setText(
- MessageManager.getString("action.load_vamsas_session"));
- vamsasImport.setVisible(false);
- vamsasImport.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasImport_actionPerformed(e);
- }
- });
- vamsasSave.setText(
- MessageManager.getString("action.save_vamsas_session"));
- vamsasSave.setVisible(false);
- vamsasSave.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasSave_actionPerformed(e);
- }
- });
inputSequence
.setText(MessageManager.getString("action.fetch_sequences"));
inputSequence.addActionListener(new ActionListener()
inputSequence_actionPerformed(e);
}
});
- vamsasStop
- .setText(MessageManager.getString("label.stop_vamsas_session"));
- vamsasStop.setVisible(false);
- vamsasStop.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- vamsasStop_actionPerformed(e);
- }
- });
closeAll.setText(MessageManager.getString("action.close_all"));
closeAll.addActionListener(new ActionListener()
{
}
});
+ Float specversion = Float.parseFloat(System.getProperty("java.specification.version"));
+
desktopMenubar.add(FileMenu);
desktopMenubar.add(toolsMenu);
- VamsasMenu.setVisible(false);
- desktopMenubar.add(VamsasMenu);
desktopMenubar.add(HelpMenu);
desktopMenubar.add(windowMenu);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
FileMenu.addSeparator();
- FileMenu.add(saveState);
+ //FileMenu.add(saveState);
FileMenu.add(saveAsState);
FileMenu.add(loadState);
FileMenu.addSeparator();
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);
*/
protected void quit()
{
+ //System.out.println("********** GDesktop.quit()");
}
/**
{
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void documentationMenuItem_actionPerformed(ActionEvent e)
+ protected void documentationMenuItem_actionPerformed()
{
}
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;
import java.awt.event.KeyListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
- import java.util.HashMap;
- import java.util.Map;
+ import java.util.Arrays;
+ import java.util.List;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
- import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
*/
protected JComboBox<Object> epsRendering = new JComboBox<>();
+ protected JComboBox<Object> htmlRendering = new JComboBox<>();
+
+ protected JComboBox<Object> svgRendering = new JComboBox<>();
+
protected JLabel userIdWidthlabel = new JLabel();
protected JCheckBox autoIdWidth = new JCheckBox();
protected JPanel presetsPanel = new JPanel();
+ protected JLabel presetsComboLabel = new JLabel();
+
+ protected JCheckBox customiseCheckbox = new JCheckBox();
+
protected JButton revertButton = new JButton();
- protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+ protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
+
+ private int backupfilesPresetsComboLastSelected = 0;
protected JPanel suffixPanel = new JPanel();
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- tabbedPane.add(initBackupsTab(),
- MessageManager.getString("label.backups"));
+ if (!Platform.isJS())
+ {
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
/*
* See WsPreferences for the real work of configuring this tab.
*/
- wsTab.setLayout(new BorderLayout());
- tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ if (!Platform.isJS())
+ {
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+ }
/*
* Handler to validate a tab before leaving it - currently only for
}
/**
- * Initialises the Output tabbed panel.
+ * Initialises the Output tab
*
* @return
*/
{
JPanel outputTab = new JPanel();
outputTab.setLayout(null);
- JLabel epsLabel = new JLabel();
+
+ JLabel epsLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "EPS"));
epsLabel.setFont(LABEL_FONT);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
epsRendering.setFont(LABEL_FONT);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
+ JLabel htmlLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "HTML"));
+ htmlLabel.setFont(LABEL_FONT);
+ htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
+ htmlRendering.setFont(LABEL_FONT);
+ htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
+ JLabel svgLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "SVG"));
+ svgLabel.setFont(LABEL_FONT);
+ svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
+ svgRendering.setFont(LABEL_FONT);
+ svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
+
JLabel jLabel1 = new JLabel();
jLabel1.setFont(LABEL_FONT);
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
jLabel1.setText(MessageManager.getString("label.append_start_end"));
jLabel1.setFont(LABEL_FONT);
+
fastajv.setFont(LABEL_FONT);
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
clustaljv.setText(MessageManager.getString("label.clustal") + " ");
TitledBorder titledBorder2 = new TitledBorder(
MessageManager.getString("label.file_output"));
jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
GridLayout gridLayout3 = new GridLayout();
jPanel11.setLayout(gridLayout3);
gridLayout3.setRows(8);
MessageManager.getString("label.automatically_set_id_width"));
autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.adjusts_width_generated_eps_png")));
- autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+ autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
autoIdWidth.addActionListener(new ActionListener()
{
userIdWidthlabel.setToolTipText(
JvSwingUtils.wrapTooltip(true, MessageManager.getString(
"label.manually_specify_width_left_column")));
- userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+ userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
userIdWidth.addActionListener(new ActionListener()
{
modellerOutput.setFont(LABEL_FONT);
modellerOutput
.setText(MessageManager.getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
embbedBioJSON.setFont(LABEL_FONT);
embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
- embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
+ embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
outputTab.add(userIdWidth);
outputTab.add(userIdWidthlabel);
outputTab.add(modellerOutput);
- outputTab.add(embbedBioJSON);
- outputTab.add(epsLabel);
- outputTab.add(epsRendering);
+ if (!Platform.isJS())
+ {
+ /*
+ * JalviewJS doesn't support Lineart option or SVG output
+ */
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(htmlLabel);
+ outputTab.add(htmlRendering);
+ outputTab.add(svgLabel);
+ outputTab.add(svgRendering);
+ }
outputTab.add(jPanel11);
return outputTab;
}
GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
new Insets(0, 2, 5, 5), 70, 1));
+ versioncheck.setVisible(false);
+
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
connectTab.add(spacePanel,
docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
structureTab.add(docFieldPref);
+ /*
+ * hide Chimera options in JalviewJS
+ */
+ if (Platform.isJS())
+ {
+ pathLabel.setVisible(false);
+ chimeraPath.setVisible(false);
+ viewerLabel.setVisible(false);
+ structViewer.setVisible(false);
+ }
+
return structureTab;
}
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
+
+ if (Platform.isJS())
+ {
+ startupCheckbox.setVisible(false);
+ startupFileTextfield.setVisible(false);
+ }
+
return visualTab;
}
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();
private boolean warnAboutSuffixReverseChange()
{
- boolean savedSuffixReverse = Cache.getDefault(BackupFiles.REVERSE_ORDER,
- false);
- int savedSuffixDigits = Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3);
- String savedSuffixTemplate = Cache.getDefault(BackupFiles.SUFFIX,
- ".bak" + BackupFiles.NUM_PLACEHOLDER);
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ boolean savedSuffixReverse = bfpe.reverse;
+ int savedSuffixDigits = bfpe.digits;
+ String savedSuffixTemplate = bfpe.suffix;
boolean nowSuffixReverse = suffixReverse.isSelected();
int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
gbc.gridy++; // row 1
backupsTab.add(presetsPanel, gbc);
- // gbc.anchor = GridBagConstraints.NORTHWEST;
// now using whole row
gbc.gridwidth = 2;
gbc.gridheight = 1;
return backupsTab;
}
- protected static final int BACKUPFILESSCHEMECUSTOMISE = 0;
-
- private static final IntKeyStringValueEntry[] backupfilesPresetEntries = {
- new IntKeyStringValueEntry(1,
- MessageManager.getString("label.default")),
- new IntKeyStringValueEntry(2,
- MessageManager.getString("label.single_file")),
- new IntKeyStringValueEntry(3,
- MessageManager.getString("label.keep_all_versions")),
- new IntKeyStringValueEntry(4,
- MessageManager.getString("label.rolled_backups")),
- // ...
- // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last)
- new IntKeyStringValueEntry(BACKUPFILESSCHEMECUSTOMISE,
- MessageManager.getString("label.customise")) };
-
- private static final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
- {
- /**
- *
- */
- private static final long serialVersionUID = 125L;
-
- {
- put(1, new BackupFilesPresetEntry(
- ".bak" + BackupFiles.NUM_PLACEHOLDER, 3, false, false, 3,
- false));
- put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false));
- put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
- 3, false, true, 10, true));
- put(4, new BackupFilesPresetEntry(
- "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9,
- false));
- }
- };
-
private JPanel initBackupsTabPresetsPanel()
{
String title = MessageManager.getString("label.schemes");
- // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title);
- // TitledBorder tb = new TitledBorder(title);
- // tb.setTitleFont(LABEL_FONT);
- // presetsPanel.setBorder(tb);
presetsPanel.setLayout(new GridBagLayout());
// "Scheme: "
gbc.gridx = 0;
gbc.gridy = 0;
- presetsPanel.add(new JLabel(title + ":"), gbc);
- for (int i = 0; i < backupfilesPresetEntries.length; i++)
+ presetsComboLabel = new JLabel(title + ":");
+ presetsPanel.add(presetsComboLabel, gbc);
+
+ List<Object> entries = Arrays
+ .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+ List<String> tooltips = Arrays.asList(
+ BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
+ backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
+ tooltips);
+ /*
+ for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
{
- backupfilesPresetsCombo.addItem(backupfilesPresetEntries[i]);
+ backupfilesPresetsCombo
+ .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
}
+ */
- // put "Previously saved scheme" item in italics (it's not really
- // selectable, as such -- it deselects itself when selected) and
- // "Customise" in bold
- backupfilesPresetsCombo
- .setRenderer(new BackupFilesPresetsComboBoxRenderer());
backupfilesPresetsCombo.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- backupsTabUpdatePresets();
+ int key = getComboIntStringKey(backupfilesPresetsCombo);
+ if (!customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = key;
+ }
+ if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+ {
+ if (customiseCheckbox.isSelected())
+ {
+ // got here by clicking on customiseCheckbox so don't change the values
+ backupfilesCustomOptionsSetEnabled();
+ }
+ else
+ {
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
+ }
+ else
+ {
+ customiseCheckbox.setSelected(false);
+ backupsTabUpdatePresets();
+ backupfilesCustomOptionsSetEnabled();
+ }
}
});
presetsPanel.add(backupfilesPresetsCombo, gbc);
revertButton.setText(MessageManager.getString("label.cancel_changes"));
+ revertButton.setToolTipText(
+ MessageManager.getString("label.cancel_changes_description"));
revertButton.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- loadLastSavedBackupsOptions();
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
+ backupfilesCustomOptionsSetEnabled();
}
});
revertButton.setFont(LABEL_FONT);
+ customiseCheckbox.setFont(LABEL_FONT);
+ customiseCheckbox.setText(MessageManager.getString("label.customise"));
+ customiseCheckbox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ int currently = getComboIntStringKey(backupfilesPresetsCombo);
+ if (customiseCheckbox.isSelected())
+ {
+ backupfilesPresetsComboLastSelected = currently;
+ setComboIntStringKey(backupfilesPresetsCombo,
+ BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ }
+ else
+ {
+ setComboIntStringKey(backupfilesPresetsCombo,
+ backupfilesPresetsComboLastSelected);
+
+ }
+ backupfilesCustomOptionsSetEnabled();
+ }
+ });
+ customiseCheckbox.setToolTipText(
+ MessageManager.getString("label.customise_description"));
+
+ // customise checkbox
+ gbc.gridx = 0;
+ gbc.gridy++;
+ presetsPanel.add(customiseCheckbox, gbc);
+
// "Cancel changes" button (aligned with combo box above)
gbc.gridx = 1;
- gbc.gridy++;
presetsPanel.add(revertButton, gbc);
return presetsPanel;
private JPanel initBackupsTabFilenameExamplesPanel()
{
String title = MessageManager
- .getString("label.summary_of_backups_scheme");
+ .getString("label.scheme_examples");
TitledBorder tb = new TitledBorder(title);
exampleFilesPanel.setBorder(tb);
exampleFilesPanel.setLayout(new GridBagLayout());
{
IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
.getSelectedItem();
- int key = entry.getKey();
- String value = entry.getValue();
+ int key = entry.k;
+ String value = entry.v;
- // BACKUPFILESSCHEMECUSTOMISE (==0) reserved for "Custom"
- if (key != BACKUPFILESSCHEMECUSTOMISE)
+ if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .containsKey(key))
{
- if (backupfilesPresetEntriesValues.containsKey(key))
- {
- backupsSetOptions(backupfilesPresetEntriesValues.get(key));
- }
- else
- {
- System.out.println("Preset '" + value + "' not implemented");
- }
+ backupsSetOptions(
+ BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(key));
+ }
+ else
+ {
+ Cache.log.error(
+ "Preset '" + value + "' [key:" + key + "] not implemented");
}
- backupfilesCustomOptionsSetEnabled();
+ // Custom options will now be enabled when the customiseCheckbox is checked
+ // (performed above)
+ // backupfilesCustomOptionsSetEnabled();
updateBackupFilesExampleLabel();
}
- protected int getComboIntStringKey(JComboBox<IntKeyStringValueEntry> c)
+ protected int getComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2)
{
- IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem();
- return e != null ? e.getKey() : 0;
+ IntKeyStringValueEntry e;
+ try
+ {
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
+ .getSelectedItem();
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry.");
+ e = null;
+ }
+ return e != null ? e.k : 0;
}
- protected void setComboIntStringKey(JComboBox<IntKeyStringValueEntry> c,
+ protected void setComboIntStringKey(
+ JComboBox<Object> backupfilesPresetsCombo2,
int key)
{
- for (int i = 0; i < c.getItemCount(); i++)
+ for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
{
- IntKeyStringValueEntry e = c.getItemAt(i);
- if (e.getKey() == key)
+ IntKeyStringValueEntry e;
+ try
+ {
+ e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+ continue;
+ }
+ if (e.k == key)
{
- c.setSelectedIndex(i);
+ backupfilesPresetsCombo2.setSelectedIndex(i);
break;
}
}
- backupsTabUpdatePresets();
+ // backupsTabUpdatePresets();
}
private JPanel initBackupsTabSuffixPanel()
{
updateBackupFilesExampleLabel();
backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
});
- KeyListener kl = new KeyListener()
+ suffixTemplate.addKeyListener(new KeyListener()
{
@Override
public void keyReleased(KeyEvent e)
{
updateBackupFilesExampleLabel();
backupfilesCustomOptionsSetEnabled();
+ backupfilesRevertButtonSetEnabled(true);
}
@Override
}
}
- };
- suffixTemplate.addKeyListener(kl);
+ });
// digits spinner
suffixDigitsLabel
.setText(MessageManager.getString("label.index_digits"));
suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
suffixDigitsLabel.setFont(LABEL_FONT);
- int defaultmin = 1;
- int defaultmax = 6;
ChangeListener c = new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
};
- setIntegerSpinner(suffixDigitsSpinner, defaultmin, defaultmax, 3, c);
+ setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
+ BackupFilesPresetEntry.DIGITSMAX, 3, c);
suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
MessageManager.getString("label.increment_index"));
}
if (okay)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
else
{
- boolean savedSuffixReverse = Cache
- .getDefault(BackupFiles.REVERSE_ORDER, false);
+ boolean savedSuffixReverse = BackupFilesPresetEntry
+ .getSavedBackupEntry().reverse;
suffixReverse.setSelected(savedSuffixReverse);
}
}
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
keepRollMaxOptionsEnabled();
updateBackupFilesExampleLabel();
}
@Override
public void stateChanged(ChangeEvent e)
{
+ backupfilesRevertButtonSetEnabled(true);
updateBackupFilesExampleLabel();
}
};
- setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c);
+ setIntegerSpinner(backupfilesRollMaxSpinner,
+ BackupFilesPresetEntry.ROLLMAXMIN,
+ BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
backupfilesConfirmDelete.setLabels(
MessageManager.getString("label.always_ask"),
MessageManager.getString("label.auto_delete"));
+ backupfilesConfirmDelete.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ backupfilesRevertButtonSetEnabled(true);
+ }
+ });
// update the enabled section
keepRollMaxOptionsEnabled();
kgbc.gridwidth = GridBagConstraints.REMAINDER;
kgbc.fill = GridBagConstraints.HORIZONTAL;
kgbc.weightx = 1.0;
- /*
- keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc);
-
- // fourth row (indented)
- kgbc.gridy = 3;
- keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc);
- */
JPanel jp = new JPanel();
jp.setLayout(new FlowLayout());
int uppersurround = 0;
StringBuilder exampleSB = new StringBuilder();
boolean firstLine = true;
+ int lineNumber = 0;
if (reverse)
{
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
if (index == min + lowersurround && index < max - uppersurround - 1)
{
exampleSB.append("\n...");
+ lineNumber++;
}
else if (index > min + lowersurround && index < max - uppersurround)
{
else
{
exampleSB.append("\n");
+ lineNumber++;
}
exampleSB.append(BackupFilenameParts.getBackupFilename(index,
base, suffix, digits));
}
+ // add some extra empty lines to pad out the example files box. ugh, please tell
+ // me how to do this better
+ int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
+ if (remainingLines > 0)
+ {
+ for (int i = 0; i < remainingLines; i++)
+ {
+ exampleSB.append("\n ");
+ lineNumber++;
+ }
+ }
+
backupfilesExampleLabel.setText(exampleSB.toString());
}
i = Integer.parseInt((String) s.getValue());
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Exception casting the initial value of s.getValue()");
}
}
i = (Integer) s.getValue();
} catch (Exception e)
{
- System.out.println("Failed casting (Integer) JSpinner s.getValue()");
+ Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
}
return i;
}
private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
{
boolean enabled = tryEnabled && enableBackupFiles.isSelected()
- && getComboIntStringKey(backupfilesPresetsCombo) == 0
+ && customiseCheckbox.isSelected()
&& suffixTemplate.getText()
.indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
keepfilesPanel.setEnabled(enabled);
private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
{
boolean enabled = tryEnabled && enableBackupFiles.isSelected()
- && getComboIntStringKey(backupfilesPresetsCombo) == 0;
+ && customiseCheckbox.isSelected();
suffixPanel.setEnabled(enabled);
suffixTemplateLabel.setEnabled(enabled);
suffixTemplate.setEnabled(enabled);
backupfilesSuffixTemplateDigitsSetEnabled();
}
+ private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
+ {
+ boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+ && customiseCheckbox.isSelected() && backupfilesCustomChanged();
+ revertButton.setEnabled(enabled);
+ }
+
+ private boolean backupfilesCustomChanged()
+ {
+ BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+ .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+ BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
+ return !custom.equals(current);
+ }
+
+ protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
+ {
+ String suffix = suffixTemplate.getText();
+ int digits = getSpinnerInt(suffixDigitsSpinner, 3);
+ boolean reverse = suffixReverse.isSelected();
+ boolean keepAll = backupfilesKeepAll.isSelected();
+ int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
+ boolean confirmDelete = backupfilesConfirmDelete.isSelected();
+
+ BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+ reverse, keepAll, rollMax, confirmDelete);
+
+ return bfpe;
+ }
+
protected void backupfilesCustomOptionsSetEnabled()
{
- int scheme = getComboIntStringKey(backupfilesPresetsCombo);
- boolean enabled = scheme == 0 && enableBackupFiles.isSelected();
+ boolean enabled = customiseCheckbox.isSelected();
+ backupfilesRevertButtonSetEnabled(enabled);
backupfilesSuffixTemplateSetEnabled(enabled);
backupfilesKeepAllSetEnabled(enabled);
}
{
boolean enabled = enableBackupFiles.isSelected();
presetsPanel.setEnabled(enabled);
+ presetsComboLabel.setEnabled(enabled);
backupfilesPresetsCombo.setEnabled(enabled);
+ customiseCheckbox.setEnabled(enabled);
+ revertButton.setEnabled(enabled);
}
protected void backupsOptionsSetEnabled()
}
}
- class IntKeyStringValueEntry
- {
- int k;
-
- String v;
-
- public IntKeyStringValueEntry(int k, String v)
- {
- this.k = k;
- this.v = v;
- }
-
- @Override
- public String toString()
- {
- return this.getValue();
- }
-
- public int getKey()
- {
- return k;
- }
-
- public String getValue()
- {
- return v;
- }
- }
-
- class BackupFilesPresetEntry
- {
- String suffix;
-
- int digits;
-
- boolean reverse;
-
- boolean keepAll;
-
- int rollMax;
-
- boolean confirmDelete;
-
- public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
- boolean keepAll, int rollMax, boolean confirmDelete)
- {
- this.suffix = suffix;
- this.digits = digits;
- this.reverse = reverse;
- this.keepAll = keepAll;
- this.rollMax = rollMax;
- this.confirmDelete = confirmDelete;
- }
- }
-
- class BackupFilesPresetsComboBoxRenderer extends DefaultListCellRenderer
- {
- /**
- *
- */
- private static final long serialVersionUID = 88L;
-
- @Override
- public Component getListCellRendererComponent(JList list, Object value,
- int index, boolean isSelected, boolean cellHasFocus)
- {
- super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
-
- try {
- IntKeyStringValueEntry e = (IntKeyStringValueEntry) value;
- if (e.getKey() == GPreferences.BACKUPFILESSCHEMECUSTOMISE)
- {
- // "Customise" item
- this.setFont(this.getFont().deriveFont(Font.BOLD));
- }
- } catch (Exception e) {
- return this;
- }
-
- return this;
- }
- }
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+ import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
*/
public class Jalview2XML
{
+
+ // BH 2018 we add the .jvp binary extension to J2S so that
+ // it will declare that binary when we do the file save from the browser
+
+ static
+ {
+ Platform.addJ2SBinaryType(".jvp?");
+ }
+
private static final String VIEWER_PREFIX = "viewer_";
private static final String RNA_PREFIX = "rna_";
public boolean isResolvable()
{
return super.isResolvable() && mp.getTo() != null;
- };
+ }
@Override
boolean resolve()
} catch (Exception foo)
{
}
- ;
jout.close();
} catch (Exception ex)
{
try
{
// create backupfiles object and get new temp filename destination
- BackupFiles backupfiles = new BackupFiles(jarFile);
- FileOutputStream fos = new FileOutputStream(
- backupfiles.getTempFilePath());
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
+ FileOutputStream fos = new FileOutputStream(doBackup ?
+ backupfiles.getTempFilePath() : jarFile);
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
} catch (Exception foo)
{
}
jout.close();
boolean success = true;
- backupfiles.setWriteSuccess(success);
- success = backupfiles.rollBackupsAndRenameTempFile();
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(success);
+ success = backupfiles.rollBackupsAndRenameTempFile();
+ }
return success;
} catch (Exception ex)
// using save and then load
try
{
+ fileName = fileName.replace('\\', '/');
System.out.println("Writing jar entry " + fileName);
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
{
if (jout != null)
{
+ jarEntryName = jarEntryName.replace('\\','/');
System.out.println("Writing jar entry " + jarEntryName);
jout.putNextEntry(new JarEntry(jarEntryName));
DataOutputStream dout = new DataOutputStream(jout);
vamsasSeq.setName(jds.getName());
vamsasSeq.setSequence(jds.getSequenceAsString());
vamsasSeq.setDescription(jds.getDescription());
- jalview.datamodel.DBRefEntry[] dbrefs = null;
+ List<DBRefEntry> dbrefs = null;
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
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);
}
- // vamsasSeq.addDBRef(dbref);
vamsasSeq.getDBRef().add(dbref);
}
}
* @param file
* - HTTP URL or filename
*/
- public AlignFrame loadJalviewAlign(final String file)
+ public AlignFrame loadJalviewAlign(final Object file)
{
jalview.gui.AlignFrame af = null;
public void run()
{
setLoadingFinishedForNewStructureViewers();
- };
+ }
});
} catch (Exception x)
{
return af;
}
- private jarInputStreamProvider createjarInputStreamProvider(
- final String file) throws MalformedURLException
- {
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider()
- {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException
- {
- if (_url != null)
- {
- return new JarInputStream(_url.openStream());
- }
- else
- {
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename()
- {
- return file;
- }
- };
- }
+ @SuppressWarnings("unused")
+ private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+
+ // BH 2018 allow for bytes already attached to File object
+ try {
+ String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+ byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
+ : null;
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (file.startsWith("http://")) {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider() {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException {
+ if (bytes != null) {
+// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
+ return new JarInputStream(new ByteArrayInputStream(bytes));
+ }
+ if (_url != null) {
+// System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
+ return new JarInputStream(_url.openStream());
+ } else {
+// System.out.println("Jalview2XML: opening file jarInputStream for " + file);
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ @Override
+ public String getFilename() {
+ return file;
+ }
+ };
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
/**
* Recover jalview session from a jalview project archive. Caller may
if (jarentry != null && jarentry.getName().endsWith(".xml"))
{
- InputStreamReader in = new InputStreamReader(jin, UTF_8);
- // JalviewModel object = new JalviewModel();
-
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.unmarshal(streamReader, JalviewModel.class);
JalviewModel object = jbe.getValue();
- /*
- Unmarshaller unmar = new Unmarshaller(object);
- unmar.setValidation(false);
- object = (JalviewModel) unmar.unmarshal(in);
- */
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
- safeInt(view.getHeight()), uniqueSeqSetId, viewId);
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+// {
+//
+// @Override
+// protected void processKeyEvent(java.awt.event.KeyEvent e) {
+// System.out.println("Jalview2XML AF " + e);
+// super.processKeyEvent(e);
+//
+// }
+//
+// }
+ ;
af.setFileName(file, FileFormat.Jalview);
}
else
{
- featureOrder.put(featureType, new Float(
+ featureOrder.put(featureType, Float.valueOf(
fs / jm.getFeatureSettings().getSetting().size()));
}
if (safeBoolean(setting.isDisplay()))
for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
{
Group grp = jm.getFeatureSettings().getGroup().get(gs);
- fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+ fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
}
// FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
// fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
return datasetId;
}
+ /**
+ * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
+ * constructed as a special subclass GeneLocus.
+ *
+ * @param datasetSequence
+ * @param sequence
+ */
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
for (int d = 0; d < sequence.getDBRef().size(); d++)
{
DBRef dr = sequence.getDBRef().get(d);
- jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
- dr.getSource(), dr.getVersion(), dr.getAccessionId());
+ DBRefEntry entry;
+ if (dr.isLocus())
+ {
+ entry = new GeneLocus(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
+ else
+ {
+ entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
if (dr.getMapping() != null)
{
entry.setMap(addMapping(dr.getMapping()));
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+ import jalview.util.Platform;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
import java.util.Map;
import java.util.Vector;
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
public class StructureSelectionManager
{
StringBuilder sb = new StringBuilder(64);
for (StructureMapping sm : mappings)
{
- if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+ if (Platform.pathEquals(sm.pdbfile, pdbfile)
+ && seqs.contains(sm.sequence))
{
sb.append(sm.mappingDetails);
sb.append(NEWLINE);
instances.remove(jalviewLite);
try
{
- mnger.finalize();
+ /* bsoares 2019-03-20 finalize deprecated, no apparent external
+ * resources to close
+ */
+ // mnger.finalize();
} catch (Throwable x)
{
}
*/
package jalview.util;
-import jalview.bin.Jalview;
-import jalview.gui.EPSOptions;
-import jalview.gui.IProgressIndicator;
-import jalview.gui.SVGOptions;
import jalview.io.JalviewFileChooser;
-import java.awt.Component;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileOutputStream;
+import java.io.IOException;
import javax.imageio.ImageIO;
public static final String PNG_DESCRIPTION = "Portable network graphics";
- public static final String HTML_EXTENSION = "html";
-
- public static final String HTML_DESCRIPTION = "Hypertext Markup Language";
-
EpsGraphics2D pg;
- SVGGraphics2D g2;
-
Graphics graphics;
FileOutputStream out;
TYPE type;
- private IProgressIndicator pIndicator;
-
- private long pSessionId;
-
- private boolean headless;
-
public enum TYPE
{
EPS("EPS", MessageManager.getString("label.eps_file"), EPS_EXTENSION,
EPS_DESCRIPTION),
- PNG("PNG", MessageManager.getString("label.png_image"),
- PNG_EXTENSION, PNG_DESCRIPTION),
+ PNG("PNG", MessageManager.getString("label.png_image"), PNG_EXTENSION,
+ PNG_DESCRIPTION),
SVG("SVG", "SVG", SVG_EXTENSION, SVG_DESCRIPTION);
- private String name;
+ public final String name;
- private String label;
+ public final String label;
- private String extension;
+ public final String extension;
- private String description;
+ public final String description;
TYPE(String name, String label, String ext, String desc)
{
}
- 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:
}
}
return graphics;
}
+ /**
+ * For SVG or PNG, writes the generated graphics data to the file output
+ * stream. For EPS, flushes the output graphics (which is written to file as
+ * it is generated).
+ */
public void writeImage()
{
try
}
}
- void setupEPS(int width, int height, String title)
- {
- boolean accurateText = true;
-
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for EPS rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- EPSOptions eps = new EPSOptions();
- renderStyle = eps.getValue();
-
- if (renderStyle == null || eps.cancelled)
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "EPS"));
- return;
- }
- }
-
- if (renderStyle.equalsIgnoreCase("text"))
- {
- accurateText = false;
- }
-
- try
- {
- pg = new EpsGraphics2D(title, out, 0, 0, width, height);
- Graphics2D ig2 = pg;
- ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
-
- pg.setAccurateTextMode(accurateText);
-
- graphics = pg;
- setProgressMessage(MessageManager
- .formatMessage("status.export_complete", type.getName()));
- } catch (Exception ex)
- {
- }
- }
-
- void setupPNG(int width, int height)
+ /**
+ * Sets up a graphics object for the PNG image to be written on
+ *
+ * @param width
+ * @param height
+ */
+ protected void setupPNG(int width, int height)
{
bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
graphics = bi.getGraphics();
Graphics2D ig2 = (Graphics2D) graphics;
ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
- setProgressMessage(MessageManager
- .formatMessage("status.export_complete", type.getName()));
-
}
- void setupSVG(int width, int height, String title)
+ /**
+ * A helper method to configure the SVG output graphics, with choice of Text
+ * or Lineart character rendering
+ *
+ * @param width
+ * @param height
+ * @param useLineart
+ * true for Lineart character rendering, false for Text
+ */
+ protected void setupSVG(int width, int height, boolean useLineart)
{
-
- g2 = new SVGGraphics2D(width, height);
- Graphics2D ig2 = g2;
-
- String renderStyle = jalview.bin.Cache.getDefault("SVG_RENDERING",
- "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for EPS rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
+ SVGGraphics2D g2 = new SVGGraphics2D(width, height);
+ if (useLineart)
{
- SVGOptions svgOption = new SVGOptions();
- renderStyle = svgOption.getValue();
-
- if (renderStyle == null || svgOption.cancelled)
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "SVG"));
- return;
- }
- }
-
- if (renderStyle.equalsIgnoreCase("Lineart"))
- {
- ig2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
graphics = g2;
}
- static JalviewFileChooser getPNGChooser()
- {
- if (Jalview.isHeadlessMode())
- {
- return null;
- }
- return new JalviewFileChooser(PNG_EXTENSION, PNG_DESCRIPTION);
- }
-
- static JalviewFileChooser getEPSChooser()
+ /**
+ * A helper method that sets up the EPS graphics output with user choice of
+ * Text or Lineart character rendering
+ *
+ * @param width
+ * @param height
+ * @param title
+ * @param useLineart
+ * true for Lineart character rendering, false for Text
+ * @throws IOException
+ */
+ protected void setupEPS(int width, int height, String title,
+ boolean useLineart) throws IOException
{
- if (Jalview.isHeadlessMode())
- {
- return null;
- }
- return new JalviewFileChooser(EPS_EXTENSION, EPS_DESCRIPTION);
- }
-
- private void setProgressMessage(String message)
- {
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(message, pSessionId);
- }
- }
-
- static JalviewFileChooser getSVGChooser()
- {
- if (Jalview.isHeadlessMode())
- {
- return null;
- }
- return new JalviewFileChooser(SVG_EXTENSION, SVG_DESCRIPTION);
+ pg = new EpsGraphics2D(title, out, 0, 0, width, height);
+ Graphics2D ig2 = pg;
+ ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ pg.setAccurateTextMode(useLineart);
+ graphics = pg;
}
}
*/
package jalview.util;
+import jalview.javascript.json.JSON;
+
+import java.awt.Toolkit;
import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.URL;
+import java.util.Properties;
+
+import javax.swing.SwingUtilities;
+
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
/**
* System platform information used by Applet and Application
*/
public class Platform
{
- private static Boolean isAMac = null, isWindows = null;
+
+ private static boolean isJS = /** @j2sNative true || */
+ false;
+
+ private static Boolean isNoJSMac = null, isNoJSWin = null, isMac = null,
+ isWin = null;
private static Boolean isHeadless = null;
/**
- * sorry folks - Macs really are different
+ * added to group mouse events into Windows and nonWindows (mac, unix, linux)
*
- * @return true if we do things in a special way.
+ * @return
*/
- public static boolean isAMac()
+ public static boolean isMac()
{
- if (isAMac == null)
- {
- isAMac = System.getProperty("os.name").indexOf("Mac") > -1;
- }
+ return (isMac == null
+ ? (isMac = (System.getProperty("os.name").indexOf("Mac") >= 0))
+ : isMac);
+ }
+
+ /**
+ * added to group mouse events into Windows and nonWindows (mac, unix, linux)
+ *
+ * @return
+ */
+ public static boolean isWin()
+ {
+ return (isWin == null
+ ? (isWin = (System.getProperty("os.name").indexOf("Win") >= 0))
+ : isWin);
+ }
- return isAMac.booleanValue();
+ /**
+ *
+ * @return true if HTML5 JavaScript
+ */
+ public static boolean isJS()
+ {
+ return isJS;
+ }
+ /**
+ * sorry folks - Macs really are different
+ *
+ * BH: disabled for SwingJS -- will need to check key-press issues
+ *
+ * @return true if we do things in a special way.
+ */
+ public static boolean isAMacAndNotJS()
+ {
+ return (isNoJSMac == null ? (isNoJSMac = !isJS && isMac()) : isNoJSMac);
}
/**
*
* @return true if we have to cope with another platform variation
*/
- public static boolean isWindows()
+ public static boolean isWindowsAndNotJS()
{
- if (isWindows == null)
- {
- isWindows = System.getProperty("os.name").indexOf("Win") > -1;
- }
- return isWindows.booleanValue();
+ return (isNoJSWin == null ? (isNoJSWin = !isJS && isWin()) : isNoJSWin);
}
/**
}
/**
- * escape a string according to the local platform's escape character
+ * Answers the input with every backslash replaced with a double backslash (an
+ * 'escaped' single backslash)
*
- * @param file
- * @return escaped file
+ * @param s
+ * @return
*/
- public static String escapeString(String file)
+ public static String escapeBackslashes(String s)
{
- StringBuffer f = new StringBuffer();
- int p = 0, lastp = 0;
- while ((p = file.indexOf('\\', lastp)) > -1)
- {
- f.append(file.subSequence(lastp, p));
- f.append("\\\\");
- lastp = p + 1;
- }
- f.append(file.substring(lastp));
- return f.toString();
+ return s == null ? null : s.replace("\\", "\\\\");
}
/**
* Answers true if the mouse event has Meta-down (Command key on Mac) or
* Ctrl-down (on other o/s). Note this answers _false_ if the Ctrl key is
- * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-click on Mac,
- * you can use e.isPopupTrigger().
+ * pressed instead of the Meta/Cmd key on Mac. To test for Ctrl-pressed on
+ * Mac, you can use e.isPopupTrigger().
*
* @param e
* @return
*/
public static boolean isControlDown(MouseEvent e)
{
- boolean aMac = isAMac();
- return isControlDown(e, aMac);
+ return isControlDown(e, isMac());
}
/**
*/
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);
+ }
}
import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
* @param type
* @return
*/
- protected boolean showFeatureOfType(String type)
+ public boolean showFeatureOfType(String type)
{
return type == null ? false : (av.getFeaturesDisplayed() == null ? true
: av.getFeaturesDisplayed().isVisible(type));
{
featureOrder = new Hashtable<>();
}
- featureOrder.put(type, new Float(position));
+ featureOrder.put(type, Float.valueOf(position));
return position;
}
}
if (newGroupsVisible)
{
- featureGroups.put(group, new Boolean(true));
+ featureGroups.put(group, Boolean.valueOf(true));
return true;
}
return false;
@Override
public void setGroupVisibility(String group, boolean visible)
{
- featureGroups.put(group, new Boolean(visible));
+ featureGroups.put(group, Boolean.valueOf(visible));
}
@Override
for (String gst : toset)
{
Boolean st = featureGroups.get(gst);
- featureGroups.put(gst, new Boolean(visible));
+ featureGroups.put(gst, Boolean.valueOf(visible));
if (st != null)
{
rdrw = rdrw || (visible != st.booleanValue());
return filter == null ? true : filter.matches(sf);
}
+ /**
+ * Answers true unless the specified group is set to hidden. Defaults to true
+ * if group visibility is not set.
+ *
+ * @param group
+ * @return
+ */
+ public boolean isGroupVisible(String group)
+ {
+ if (!featureGroups.containsKey(group))
+ {
+ return true;
+ }
+ return featureGroups.get(group);
+ }
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator<String> order)
+ {
+ Arrays.sort(renderOrder, order);
+ }
+
@Override
public boolean isVisible(SequenceFeature feature)
{
}
return true;
}
-
}
package jalview.ws;
import jalview.analysis.AlignSeq;
+ import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Enumeration;
+ import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+ import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
- sfetcher = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(progressIndicatorFrame);
+ sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
// set default behaviour for transferring excess sequence data to the
// dataset
trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
Arrays.asList(dataset));
List<String> warningMessages = new ArrayList<>();
+ // clear any old feature display settings recorded from past sessions
+ featureDisplaySettings = null;
+
int db = 0;
while (sdataset.size() > 0 && db < dbSources.length)
{
}
if (retrieved != null)
{
- transferReferences(sdataset, dbsource.getDbSource(), retrieved,
+ transferReferences(sdataset, dbsource, retrieved,
trimDsSeqs, warningMessages);
}
}
&& (i < 50); seqIndex++, i++)
{
SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = DBRefUtils
+ List<DBRefEntry> uprefs = DBRefUtils
.selectRefs(sequence.getDBRefs(), new String[]
{ dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
- if (uprefs != null && uprefs.length > 0)
+ if (uprefs != null && uprefs.size() > 0)
{
- for (int j = 0; j < uprefs.length; j++)
+ for (int j = 0, n = uprefs.size(); j < n; j++)
{
- addSeqId(sequence, uprefs[j].getAccessionId());
+ DBRefEntry upref = uprefs.get(j);
+ addSeqId(sequence, upref.getAccessionId());
queries.addElement(
- uprefs[j].getAccessionId().toUpperCase());
+ upref.getAccessionId().toUpperCase());
}
}
else
* @param warningMessages
* a list of messages to add to
*/
- boolean transferReferences(Vector<SequenceI> sdataset, String dbSource,
+ boolean transferReferences(Vector<SequenceI> sdataset,
+ DbSourceProxy dbSourceProxy,
AlignmentI retrievedAl, boolean trimDatasetSeqs,
List<String> warningMessages)
{
return false;
}
+ String dbSource = dbSourceProxy.getDbName();
boolean modified = false;
SequenceI[] retrieved = recoverDbSequences(
retrievedAl.getSequencesArray());
// taking into account all accessionIds and names in the file
Vector<SequenceI> sequenceMatches = new Vector<>();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = DBRefUtils
+ List<DBRefEntry> entryRefs = DBRefUtils
.selectRefs(retrievedSeq.getDBRefs(), new String[]
{ dbSource });
if (entryRefs == null)
+ dbSource + " on " + retrievedSeq.getName());
continue;
}
- for (int j = 0; j < entryRefs.length; j++)
+ for (int j = 0, n = entryRefs.size(); j < n; j++)
{
- String accessionId = entryRefs[j].getAccessionId();
+ DBRefEntry ref = entryRefs.get(j);
+ String accessionId = ref.getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase()))
{
// could be useful to extend this so we try to find any 'significant'
// information in common between two sequence objects.
/*
- * DBRefEntry[] entryRefs =
+ * List<DBRefEntry> entryRefs =
* jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {
* dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String
* name = entry.getName().elementAt(j).toString(); if
* seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
* sequenceMatches.addElement(sequence); } } } }
*/
+ if (sequenceMatches.size() > 0)
+ {
+ addFeatureSettings(dbSourceProxy);
+ }
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
// TODO: test for legacy where uniprot or EMBL refs exist but no
// mappings are made (but content matches retrieved set)
boolean updateRefFrame = sequence.getDBRefs() == null
- || sequence.getDBRefs().length == 0;
+ || sequence.getDBRefs().size() == 0;
// TODO:
// verify sequence against the entry sequence
return modified;
}
+ Map<String, FeatureSettingsModelI> featureDisplaySettings = null;
+
+ private void addFeatureSettings(DbSourceProxy dbSourceProxy)
+ {
+ FeatureSettingsModelI fsettings = dbSourceProxy
+ .getFeatureColourScheme();
+ if (fsettings != null)
+ {
+ if (featureDisplaySettings == null)
+ {
+ featureDisplaySettings = new HashMap<>();
+ }
+ featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings);
+ }
+ }
+
+ /**
+ *
+ * @return any feature settings associated with sources that have provided sequences
+ */
+ public List<FeatureSettingsModelI>getFeatureSettingsModels()
+ {
+ return featureDisplaySettings == null
+ ? Arrays.asList(new FeatureSettingsModelI[0])
+ : Arrays.asList(featureDisplaySettings.values()
+ .toArray(new FeatureSettingsModelI[1]));
+ }
/**
* Adds the message to the list unless it already contains it
*
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- Vector<SequenceI> nseq = new Vector<>();
- for (int i = 0; sequencesArray != null
- && i < sequencesArray.length; i++)
+ int n;
+ if (sequencesArray == null || (n = sequencesArray.length) == 0)
+ return sequencesArray;
+ ArrayList<SequenceI> nseq = new ArrayList<>();
+ for (int i = 0;i < n; i++)
{
- nseq.addElement(sequencesArray[i]);
- DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
+ nseq.add(sequencesArray[i]);
+ List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
Mapping map = null;
- for (int r = 0; (dbr != null) && r < dbr.length; r++)
+ if (dbr != null)
{
- if ((map = dbr[r].getMap()) != null)
+ for (int r = 0, rn = dbr.size(); r < rn; r++)
{
- if (map.getTo() != null && !nseq.contains(map.getTo()))
+ if ((map = dbr.get(r).getMap()) != null)
{
- nseq.addElement(map.getTo());
- }
+ if (map.getTo() != null && !nseq.contains(map.getTo()))
+ {
+ nseq.add(map.getTo());
+ }
+ }
}
}
}
+ // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
if (nseq.size() > 0)
{
- sequencesArray = new SequenceI[nseq.size()];
- nseq.toArray(sequencesArray);
+ return nseq.toArray(new SequenceI[nseq.size()]);
}
return sequencesArray;
}
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
/**
* This implements the run-time discovery of sequence database clients.
/**
* return an ordered list of database sources excluding alignment only databases
*/
- public String[] getOrderedSupportedSources()
+ public String[] getNonAlignmentSources()
{
String[] srcs = this.getSupportedDb();
- ArrayList<String> src = new ArrayList<>();
+ List<String> src = new ArrayList<>();
for (int i = 0; i < srcs.length; i++)
{
- boolean skip = false;
+ boolean accept = true;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
// Skip the alignment databases for the moment - they're not useful for
// verifying a single sequence against its reference source
if (dbs.isAlignmentSource())
{
- skip = true;
+ accept = false;
+ break;
}
}
- if (skip)
- {
- continue;
- }
+ if (accept)
{
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()]);
}
}
*
*/
public class EpsGraphics2D extends java.awt.Graphics2D
+ implements AutoCloseable
{
public static final String VERSION = "0.8.8";
* OutputStream is automatically flushed before being closed. If you forget to
* do this, the file may be incomplete.
*/
+ @Override
public void close() throws IOException
{
flush();
* Draws a 3D rectangle outline. If it is raised, light appears to come from
* the top left.
*/
+ @Override
public void draw3DRect(int x, int y, int width, int height, boolean raised)
{
Color originalColor = getColor();
* Fills a 3D rectangle. If raised, it has bright fill and light appears to
* come from the top left.
*/
+ @Override
public void fill3DRect(int x, int y, int width, int height, boolean raised)
{
Color originalColor = getColor();
/**
* Draws a Shape on the EPS document.
*/
+ @Override
public void draw(Shape s)
{
draw(s, "stroke");
/**
* Draws an Image on the EPS document.
*/
+ @Override
public boolean drawImage(Image img, AffineTransform xform,
ImageObserver obs)
{
/**
* Draws a BufferedImage on the EPS document.
*/
+ @Override
public void drawImage(BufferedImage img, BufferedImageOp op, int x, int y)
{
BufferedImage img1 = op.filter(img, null);
/**
* Draws a RenderedImage on the EPS document.
*/
+ @Override
public void drawRenderedImage(RenderedImage img, AffineTransform xform)
{
Hashtable properties = new Hashtable();
/**
* Draws a RenderableImage by invoking its createDefaultRendering method.
*/
+ @Override
public void drawRenderableImage(RenderableImage img, AffineTransform xform)
{
drawRenderedImage(img.createDefaultRendering(), xform);
/**
* Draws a string at (x,y)
*/
+ @Override
public void drawString(String str, int x, int y)
{
drawString(str, (float) x, (float) y);
/**
* Draws a string at (x,y)
*/
+ @Override
public void drawString(String s, float x, float y)
{
if (s != null && s.length() > 0)
* Draws the characters of an AttributedCharacterIterator, starting from
* (x,y).
*/
+ @Override
public void drawString(AttributedCharacterIterator iterator, int x, int y)
{
drawString(iterator, (float) x, (float) y);
* Draws the characters of an AttributedCharacterIterator, starting from
* (x,y).
*/
+ @Override
public void drawString(AttributedCharacterIterator iterator, float x,
float y)
{
/**
* Draws a GlyphVector at (x,y)
*/
+ @Override
public void drawGlyphVector(GlyphVector g, float x, float y)
{
Shape shape = g.getOutline(x, y);
/**
* Fills a Shape on the EPS document.
*/
+ @Override
public void fill(Shape s)
{
draw(s, "fill");
* Checks whether or not the specified Shape intersects the specified
* Rectangle, which is in device space.
*/
+ @Override
public boolean hit(Rectangle rect, Shape s, boolean onStroke)
{
return s.intersects(rect);
/**
* Returns the device configuration associated with this EpsGraphics2D object.
*/
+ @Override
public GraphicsConfiguration getDeviceConfiguration()
{
GraphicsConfiguration gc = null;
* Sets the Composite to be used by this EpsGraphics2D. EpsGraphics2D does not
* make use of these.
*/
+ @Override
public void setComposite(Composite comp)
{
_composite = comp;
* Sets the Paint attribute for the EpsGraphics2D object. Only Paint objects
* of type Color are respected by EpsGraphics2D.
*/
+ @Override
public void setPaint(Paint paint)
{
_paint = paint;
* Sets the stroke. Only accepts BasicStroke objects (or subclasses of
* BasicStroke).
*/
+ @Override
public void setStroke(Stroke s)
{
if (s instanceof BasicStroke)
/**
* Sets a rendering hint. These are not used by EpsGraphics2D.
*/
+ @Override
public void setRenderingHint(RenderingHints.Key hintKey, Object hintValue)
{
// Do nothing.
* Returns the value of a single preference for the rendering algorithms.
* Rendering hints are not used by EpsGraphics2D.
*/
+ @Override
public Object getRenderingHint(RenderingHints.Key hintKey)
{
return null;
/**
* Sets the rendering hints. These are ignored by EpsGraphics2D.
*/
+ @Override
public void setRenderingHints(Map hints)
{
// Do nothing.
/**
* Adds rendering hints. These are ignored by EpsGraphics2D.
*/
+ @Override
public void addRenderingHints(Map hints)
{
// Do nothing.
/**
* Returns the preferences for the rendering algorithms.
*/
+ @Override
public RenderingHints getRenderingHints()
{
return new RenderingHints(null);
* Translates the origin of the EpsGraphics2D context to the point (x,y) in
* the current coordinate system.
*/
+ @Override
public void translate(int x, int y)
{
translate((double) x, (double) y);
* Concatenates the current EpsGraphics2D Transformation with a translation
* transform.
*/
+ @Override
public void translate(double tx, double ty)
{
transform(AffineTransform.getTranslateInstance(tx, ty));
/**
* Concatenates the current EpsGraphics2D Transform with a rotation transform.
*/
+ @Override
public void rotate(double theta)
{
rotate(theta, 0, 0);
* Concatenates the current EpsGraphics2D Transform with a translated rotation
* transform.
*/
+ @Override
public void rotate(double theta, double x, double y)
{
transform(AffineTransform.getRotateInstance(theta, x, y));
* Concatenates the current EpsGraphics2D Transform with a scaling
* transformation.
*/
+ @Override
public void scale(double sx, double sy)
{
transform(AffineTransform.getScaleInstance(sx, sy));
/**
* Concatenates the current EpsGraphics2D Transform with a shearing transform.
*/
+ @Override
public void shear(double shx, double shy)
{
transform(AffineTransform.getShearInstance(shx, shy));
* Composes an AffineTransform object with the Transform in this EpsGraphics2D
* according to the rule last-specified-first-applied.
*/
+ @Override
public void transform(AffineTransform Tx)
{
_transform.concatenate(Tx);
/**
* Sets the AffineTransform to be used by this EpsGraphics2D.
*/
+ @Override
public void setTransform(AffineTransform Tx)
{
if (Tx == null)
/**
* Gets the AffineTransform used by this EpsGraphics2D.
*/
+ @Override
public AffineTransform getTransform()
{
return new AffineTransform(_transform);
/**
* Returns the current Paint of the EpsGraphics2D object.
*/
+ @Override
public Paint getPaint()
{
return _paint;
/**
* returns the current Composite of the EpsGraphics2D object.
*/
+ @Override
public Composite getComposite()
{
return _composite;
/**
* Sets the background color to be used by the clearRect method.
*/
+ @Override
public void setBackground(Color color)
{
if (color == null)
/**
* Gets the background color that is used by the clearRect method.
*/
+ @Override
public Color getBackground()
{
return _backgroundColor;
* Returns the Stroke currently used. Guaranteed to be an instance of
* BasicStroke.
*/
+ @Override
public Stroke getStroke()
{
return _stroke;
* Intersects the current clip with the interior of the specified Shape and
* sets the clip to the resulting intersection.
*/
+ @Override
public void clip(Shape s)
{
if (_clip == null)
/**
* Returns the FontRenderContext.
*/
+ @Override
public FontRenderContext getFontRenderContext()
{
return _fontRenderContext;
/**
* Returns a new Graphics object that is identical to this EpsGraphics2D.
*/
+ @Override
public Graphics create()
{
return new EpsGraphics2D(this);
* Returns an EpsGraphics2D object based on this Graphics object, but with a
* new translation and clip area.
*/
+ @Override
public Graphics create(int x, int y, int width, int height)
{
Graphics g = create();
* Returns the current Color. This will be a default value (black) until it is
* changed using the setColor method.
*/
+ @Override
public Color getColor()
{
return _color;
/**
* Sets the Color to be used when drawing all future shapes, text, etc.
*/
+ @Override
public void setColor(Color c)
{
if (c == null)
* Sets the paint mode of this EpsGraphics2D object to overwrite the
* destination EpsDocument with the current color.
*/
+ @Override
public void setPaintMode()
{
// Do nothing - paint mode is the only method supported anyway.
* <b><i><font color="red">Not implemented</font></i></b> - performs no
* action.
*/
+ @Override
public void setXORMode(Color c1)
{
methodNotSupported();
/**
* Returns the Font currently being used.
*/
+ @Override
public Font getFont()
{
return _font;
/**
* Sets the Font to be used in future text.
*/
+ @Override
public void setFont(Font font)
{
if (font == null)
font = Font.decode(null);
}
_font = font;
- append("/" + _font.getPSName() + " findfont " + ((int) _font.getSize())
+ append("/" + _font.getPSName() + " findfont " + (_font.getSize())
+ " scalefont setfont");
}
/**
* Gets the font metrics of the current font.
*/
+ @Override
public FontMetrics getFontMetrics()
{
return getFontMetrics(getFont());
/**
* Gets the font metrics for the specified font.
*/
+ @Override
public FontMetrics getFontMetrics(Font f)
{
BufferedImage image = new BufferedImage(1, 1,
/**
* Returns the bounding rectangle of the current clipping area.
*/
+ @Override
public Rectangle getClipBounds()
{
if (_clip == null)
/**
* Intersects the current clip with the specified rectangle.
*/
+ @Override
public void clipRect(int x, int y, int width, int height)
{
clip(new Rectangle(x, y, width, height));
/**
* Sets the current clip to the rectangle specified by the given coordinates.
*/
+ @Override
public void setClip(int x, int y, int width, int height)
{
setClip(new Rectangle(x, y, width, height));
/**
* Gets the current clipping area.
*/
+ @Override
public Shape getClip()
{
if (_clip == null)
/**
* Sets the current clipping area to an arbitrary clip shape.
*/
+ @Override
public void setClip(Shape clip)
{
if (clip != null)
* <b><i><font color="red">Not implemented</font></i></b> - performs no
* action.
*/
+ @Override
public void copyArea(int x, int y, int width, int height, int dx, int dy)
{
methodNotSupported();
/**
* Draws a straight line from (x1,y1) to (x2,y2).
*/
+ @Override
public void drawLine(int x1, int y1, int x2, int y2)
{
Shape shape = new Line2D.Float(x1, y1, x2, y2);
/**
* Fills a rectangle with top-left corner placed at (x,y).
*/
+ @Override
public void fillRect(int x, int y, int width, int height)
{
Shape shape = new Rectangle(x, y, width, height);
/**
* Draws a rectangle with top-left corner placed at (x,y).
*/
+ @Override
public void drawRect(int x, int y, int width, int height)
{
Shape shape = new Rectangle(x, y, width, height);
* Clears a rectangle with top-left corner placed at (x,y) using the current
* background color.
*/
+ @Override
public void clearRect(int x, int y, int width, int height)
{
Color originalColor = getColor();
/**
* Draws a rounded rectangle.
*/
+ @Override
public void drawRoundRect(int x, int y, int width, int height,
int arcWidth, int arcHeight)
{
/**
* Fills a rounded rectangle.
*/
+ @Override
public void fillRoundRect(int x, int y, int width, int height,
int arcWidth, int arcHeight)
{
/**
* Draws an oval.
*/
+ @Override
public void drawOval(int x, int y, int width, int height)
{
Shape shape = new Ellipse2D.Float(x, y, width, height);
/**
* Fills an oval.
*/
+ @Override
public void fillOval(int x, int y, int width, int height)
{
Shape shape = new Ellipse2D.Float(x, y, width, height);
/**
* Draws an arc.
*/
+ @Override
public void drawArc(int x, int y, int width, int height, int startAngle,
int arcAngle)
{
/**
* Fills an arc.
*/
+ @Override
public void fillArc(int x, int y, int width, int height, int startAngle,
int arcAngle)
{
/**
* Draws a polyline.
*/
+ @Override
public void drawPolyline(int[] xPoints, int[] yPoints, int nPoints)
{
if (nPoints > 0)
/**
* Draws a polygon made with the specified points.
*/
+ @Override
public void drawPolygon(int[] xPoints, int[] yPoints, int nPoints)
{
Shape shape = new Polygon(xPoints, yPoints, nPoints);
/**
* Draws a polygon.
*/
+ @Override
public void drawPolygon(Polygon p)
{
draw(p);
/**
* Fills a polygon made with the specified points.
*/
+ @Override
public void fillPolygon(int[] xPoints, int[] yPoints, int nPoints)
{
Shape shape = new Polygon(xPoints, yPoints, nPoints);
/**
* Fills a polygon.
*/
+ @Override
public void fillPolygon(Polygon p)
{
draw(p, "fill");
/**
* Draws the specified characters, starting from (x,y)
*/
+ @Override
public void drawChars(char[] data, int offset, int length, int x, int y)
{
String string = new String(data, offset, length);
/**
* Draws the specified bytes, starting from (x,y)
*/
+ @Override
public void drawBytes(byte[] data, int offset, int length, int x, int y)
{
String string = new String(data, offset, length);
/**
* Draws an image.
*/
+ @Override
public boolean drawImage(Image img, int x, int y, ImageObserver observer)
{
return drawImage(img, x, y, Color.white, observer);
/**
* Draws an image.
*/
+ @Override
public boolean drawImage(Image img, int x, int y, int width, int height,
ImageObserver observer)
{
/**
* Draws an image.
*/
+ @Override
public boolean drawImage(Image img, int x, int y, Color bgcolor,
ImageObserver observer)
{
/**
* Draws an image.
*/
+ @Override
public boolean drawImage(Image img, int x, int y, int width, int height,
Color bgcolor, ImageObserver observer)
{
/**
* Draws an image.
*/
+ @Override
public boolean drawImage(Image img, int dx1, int dy1, int dx2, int dy2,
int sx1, int sy1, int sx2, int sy2, ImageObserver observer)
{
/**
* Draws an image.
*/
+ @Override
public boolean drawImage(Image img, int dx1, int dy1, int dx2, int dy2,
int sx1, int sy1, int sx2, int sy2, Color bgcolor,
ImageObserver observer)
* only remaining EpsGraphics2D instance pointing at a EpsDocument object,
* then the EpsDocument object shall become eligible for garbage collection.
*/
+ @Override
public void dispose()
{
_document = null;
}
+ /* bsoares 2019-03-20
+ * finalize is now deprecated. Implementing AutoCloseable instead
/**
* Finalizes the object.
- */
+ @Override
public void finalize()
{
super.finalize();
}
+ */
/**
* Returns the entire contents of the EPS document, complete with headers and
* bounding box. The returned String is suitable for being written directly to
* disk as an EPS file.
*/
+ @Override
public String toString()
{
StringWriter writer = new StringWriter();
* Returns true if the specified rectangular area might intersect the current
* clipping area.
*/
+ @Override
public boolean hitClip(int x, int y, int width, int height)
{
if (_clip == null)
/**
* Returns the bounding rectangle of the current clipping area.
*/
+ @Override
public Rectangle getClipBounds(Rectangle r)
{
if (_clip == null)
import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.ws.params.InvalidArgumentException;
import java.io.IOException;
import java.util.ArrayList;
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
- seq1.setDBRefs(null);
+ seq1.setDBRefs(null);
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
new Mapping(mapfordna1));
dna1.addDBRef(dna1xref);
- assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
+ assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
new Mapping(mapfordna2));
dna2.addDBRef(dna2xref);
- assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
+ assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
/*
* execute method under test:
* verify CDS has a dbref with mapping to peptide
*/
assertNotNull(cds1Dss.getDBRefs());
- assertEquals(2, cds1Dss.getDBRefs().length);
- dbref = cds1Dss.getDBRefs()[0];
+ assertEquals(2, cds1Dss.getDBRefs().size());
+ dbref = cds1Dss.getDBRefs().get(0);
assertEquals(dna1xref.getSource(), dbref.getSource());
// version is via ensembl's primary ref
assertEquals(dna1xref.getVersion(), dbref.getVersion());
*/
assertNotNull(pep1.getDBRefs());
// FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
- assertEquals(2, pep1.getDBRefs().length);
- dbref = pep1.getDBRefs()[1];
+ assertEquals(2, pep1.getDBRefs().size());
+ dbref = pep1.getDBRefs().get(1);
assertEquals("ENSEMBL", dbref.getSource());
assertEquals("0", dbref.getVersion());
assertEquals("CDS|dna1", dbref.getAccessionId());
/*
* verify cDNA has added a dbref with mapping to CDS
*/
- assertEquals(3, dna1.getDBRefs().length);
- DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+ assertEquals(3, dna1.getDBRefs().size());
+ DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
assertSame(cds1Dss, dbRefEntry.getMap().getTo());
MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
new int[] { 1, 6 }, 1, 1);
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
- assertEquals(3, dna2.getDBRefs().length);
- dbRefEntry = dna2.getDBRefs()[2];
+ assertEquals(3, dna2.getDBRefs().size());
+ dbRefEntry = dna2.getDBRefs().get(2);
assertSame(cds2Dss, dbRefEntry.getMap().getTo());
dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
new int[] { 1, 9 }, 1, 1);
/*
* verify CDS has added a dbref with mapping to cDNA
*/
- assertEquals(2, cds1Dss.getDBRefs().length);
- dbRefEntry = cds1Dss.getDBRefs()[1];
+ assertEquals(2, cds1Dss.getDBRefs().size());
+ dbRefEntry = cds1Dss.getDBRefs().get(1);
assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
4, 6, 10, 12 }, 1, 1);
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
- assertEquals(2, cds2Dss.getDBRefs().length);
- dbRefEntry = cds2Dss.getDBRefs()[1];
+ assertEquals(2, cds2Dss.getDBRefs().size());
+ dbRefEntry = cds2Dss.getDBRefs().get(1);
assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
9, 13, 15 }, 1, 1);
* transcript 'CDS' is 10-16, 17-21
* which is 'gene' 158-164, 210-214
*/
- MapList toMap = toLoci.getMap();
+ MapList toMap = toLoci.getMapping();
assertEquals(1, toMap.getFromRanges().size());
assertEquals(2, toMap.getFromRanges().get(0).length);
assertEquals(1, toMap.getFromRanges().get(0)[0]);
AlignmentUtils.transferGeneLoci(from, map, to);
assertEquals("GRCh38", toLoci.getAssemblyId());
assertEquals("7", toLoci.getChromosomeId());
- toMap = toLoci.getMap();
+ toMap = toLoci.getMapping();
assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
toMap.toString());
}
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.setProperty("VCF_FIELDS", ".*");
Cache.setProperty("VEP_FIELDS", ".*");
+ Cache.setProperty("VCF_ASSEMBLY", "GRCh38=GRCh38");
Cache.initLogger();
}
* verify SNP variant feature(s) computed and added to protein
* first codon AGC varies to ACC giving S/T
*/
- DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs();
+ List<DBRefEntry> dbRefs = al.getSequenceAt(1).getDBRefs();
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
* verify variant feature(s) computed and added to protein
* last codon GCT varies to GGT giving A/G in the last peptide position
*/
- DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs();
+ List<DBRefEntry> dbRefs = al.getSequenceAt(3).getDBRefs();
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
* and GAG/GGG which is E/G in position 4
* the insertion variant is not transferred to the peptide
*/
- DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs();
+ List<DBRefEntry> dbRefs = al.findName("transcript3").getDBRefs();
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.DBRefEntry;
+ import jalview.datamodel.GeneLocus;
import jalview.datamodel.HiddenSequences;
+ import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceCollectionI;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
+ import jalview.util.MapList;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
af.getViewport()
.getGlobalColourScheme() instanceof RNAHelicesColour,
"Couldn't apply RNA helices colourscheme");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
.getSchemeName()),
"Recognise T-Coffee score from string");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.alignPanel.alignmentChanged();
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
File tfile = File.createTempFile("JalviewTest", ".jvp");
tfile.deleteOnExit();
String filePath = tfile.getAbsolutePath();
- assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+ af.saveAlignment(filePath, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
/*
.getAlignViewport(),
"Didn't restore correct view association for the PCA view");
}
+
+ /**
+ * Test save and reload of DBRefEntry including GeneLocus in project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverGeneLocus() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+
+ AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
+ SequenceI pep = ap.getAlignment().getSequenceAt(0);
+ SequenceI cds = ap.getAlignment().getSequenceAt(1);
+
+ /*
+ * give 'protein' a dbref to self, a dbref with map to CDS,
+ * and a dbref with map to gene 'locus'
+ */
+ DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null);
+ pep.addDBRef(dbref1);
+ Mapping cdsmap = new Mapping(cds,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
+ DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap);
+ pep.addDBRef(dbref2);
+ Mapping locusmap = new Mapping(null,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3));
+ DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap);
+ pep.addDBRef(dbref3);
+
+ File tfile = File.createTempFile("testStoreAndRecoverGeneLocus",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
+ SequenceI rpep = rap.getAlignment().getSequenceAt(0);
+ assertEquals(rpep.getName(), "P30419");
+ DBRefEntry[] dbrefs = rpep.getDBRefs();
+ assertEquals(dbrefs.length, 3);
+ DBRefEntry dbRef = dbrefs[0];
+ assertFalse(dbRef instanceof GeneLocus);
+ assertNull(dbRef.getMap());
+ assertEquals(dbRef, dbref1);
+
+ /*
+ * restored dbrefs with mapping have a different 'map to'
+ * sequence but otherwise match the original dbrefs
+ */
+ dbRef = dbrefs[1];
+ assertFalse(dbRef instanceof GeneLocus);
+ assertTrue(dbRef.equalRef(dbref2));
+ assertNotNull(dbRef.getMap());
+ SequenceI rcds = rap.getAlignment().getSequenceAt(1);
+ assertSame(dbRef.getMap().getTo(), rcds);
+ // compare MapList but not map.to
+ assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap());
+
+ /*
+ * GeneLocus map.to is null so can compare Mapping objects
+ */
+ dbRef = dbrefs[2];
+ assertTrue(dbRef instanceof GeneLocus);
+ assertEquals(dbRef, dbref3);
+ }
}
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.Enumeration;
+ import java.util.HashMap;
import java.util.List;
+ import java.util.Map;
import java.util.Vector;
+ import org.testng.Assert;
import org.testng.annotations.BeforeClass;
+ import org.testng.annotations.Test;
public class SequenceFetcherTest
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @Test(groups = "Functional")
+ public void testNoDuplicatesInFetchDbRefs()
+ {
+ Map<String, List<DbSourceProxy>> seen = new HashMap<>();
+ jalview.ws.SequenceFetcher sfetcher = new jalview.ws.SequenceFetcher();
+ String dupes = "";
+ for (String src : sfetcher.getOrderedSupportedSources())
+ {
+ List<DbSourceProxy> seenitem = seen.get(src);
+ if (seenitem != null)
+ {
+ dupes += (dupes.length() > 0 ? "," : "") + src;
+ }
+ else
+ {
+ seen.put(src, sfetcher.getSourceProxy(src));
+ }
+ }
+ if (dupes.length() > 0)
+ {
+ Assert.fail("Duplicate sources : " + dupes);
+ }
+ }
+
/**
* simple run method to test dbsources.
*
* @param argv
+ * @j2sIgnore
*/
public static void main(String[] argv)
{
git://source.jalview.org / jalview.git / commitdiff