--- /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"/>
- <classpathentry kind="src" path="utils"/>
- <classpathentry kind="lib" path="lib/activation.jar"/>
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- <classpathentry kind="lib" path="lib/commons-discovery.jar"/>
- <classpathentry kind="lib" path="lib/jaxrpc.jar"/>
- <classpathentry kind="lib" path="lib/jhall.jar"/>
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- <classpathentry kind="lib" path="lib/regex.jar"/>
- <classpathentry kind="lib" path="lib/saaj.jar"/>
- <classpathentry kind="lib" path="lib/wsdl4j.jar"/>
- <classpathentry kind="lib" path="lib/xercesImpl.jar"/>
- <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
- <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
- <classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
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- <classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
- <attributes>
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- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="lib/httpcore-4.0.1.jar">
- <attributes>
- <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="lib" path="lib/httpmime-4.0.3.jar">
- <attributes>
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- </attributes>
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- <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
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- <classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
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- <classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
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- <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
- <classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
++ <classpathentry kind="src" output="bin/main" path="src">
++ <attributes>
++ <attribute name="gradle_scope" value="main"/>
++ <attribute name="gradle_used_by_scope" value=""/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="src" output="bin/test" path="test">
++ <attributes>
++ <attribute name="test" value="true"/>
++ <attribute name="gradle_scope" value="test"/>
++ <attribute name="gradle_used_by_scope" value=""/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
++ <attributes>
++ <attribute name="module" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
++ <classpathentry kind="lib" path="help"/>
++ <classpathentry kind="lib" path="resources"/>
++ <classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
++ <classpathentry kind="lib" path="j11lib/axis.jar"/>
++ <classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
++ <classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.jar"/>
++ <classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
++ <classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
++ <classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
++ <classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
++ <classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
++ <classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
++ <classpathentry kind="lib" path="j11lib/groovy-2.5.6.jar"/>
++ <classpathentry kind="lib" path="j11lib/groovy-console-2.5.6.jar"/>
++ <classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
++ <classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
++ <classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
++ <classpathentry kind="lib" path="j11lib/i4jruntime.jar"/>
++ <classpathentry kind="lib" path="j11lib/intervalstore-v1.0.jar"/>
++ <classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
++ <classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
++ <classpathentry kind="lib" path="j11lib/java-json.jar"/>
++ <classpathentry kind="lib" path="j11lib/javax.activation-MODULE.jar"/>
++ <classpathentry kind="lib" path="j11lib/javax.annotation-api-MODULE.jar"/>
++ <classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/javax.servlet-api-MODULE.jar"/>
++ <classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
++ <classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
++ <classpathentry kind="lib" path="j11lib/jaxb-api-java9.jar"/>
++ <classpathentry kind="lib" path="j11lib/jaxb-runtime.jar"/>
++ <classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
++ <classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
++ <classpathentry kind="lib" path="j11lib/jersey-client-1.19.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/jersey-core-1.19.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/jersey-json-1.19.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
++ <classpathentry kind="lib" path="j11lib/jetty-io-9.2.10.v20150310.jar"/>
++ <classpathentry kind="lib" path="j11lib/jetty-server-9.2.10.v20150310.jar"/>
++ <classpathentry kind="lib" path="j11lib/jetty-util-9.2.10.v20150310.jar"/>
++ <classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
++ <classpathentry kind="lib" path="j11lib/jhall.jar"/>
++ <classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
++ <classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
++ <classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
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++ <classpathentry kind="lib" path="j11lib/log4j-to-slf4j-2.0-rc2.jar"/>
++ <classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
++ <classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
++ <classpathentry kind="lib" path="j11lib/mimepull.jar"/>
++ <classpathentry kind="lib" path="j11lib/policy.jar"/>
++ <classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
++ <classpathentry kind="lib" path="j11lib/regex.jar"/>
++ <classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
++ <classpathentry kind="lib" path="j11lib/slf4j-api-1.7.7.jar"/>
++ <classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.7.jar"/>
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++ <classpathentry kind="lib" path="j11lib/streambuffer.jar"/>
++ <classpathentry kind="lib" path="j11lib/txw2.jar"/>
++ <classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
++ <classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
++ <classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
++ <classpathentry kind="lib" path="j11lib/wsdl4j-MODULE.jar"/>
++ <classpathentry kind="lib" path="j11lib/xercesImpl.jar"/>
++ <classpathentry kind="lib" path="utils/ant-contrib-1.0b3.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/axis-ant.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/classgraph-4.1.6.jar">
++ <attributes>
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++ <classpathentry kind="lib" path="utils/hamcrest-core-1.3.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
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++ </classpathentry>
++ <classpathentry kind="lib" path="utils/jhall.jar">
++ <attributes>
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++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/jhindexer.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/junit-4.12.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/roxes-ant-tasks-1.2-2004-01-30.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/bsh-2.0b4.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </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"/>
++ </attributes>
++ </classpathentry>
++ <classpathentry kind="lib" path="utils/wsdl4j.jar">
++ <attributes>
++ <attribute name="test" value="true"/>
++ </attributes>
++ </classpathentry>
+ <classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
- <classpathentry kind="lib" path="lib/intervalstore-v1.0.jar"/>
- <classpathentry kind="output" path="classes"/>
++ <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>
- <arguments>
- </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
- org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
- org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
- org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
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- org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
- org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
- org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
- org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
- org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
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- org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
- org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
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- org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
- org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
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- org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
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- org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
- org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
- org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore
- org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
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- org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
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- org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
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- 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
+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.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.blank_lines_between_type_declarations=1
+org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=next_line
+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.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.comment.clear_blank_lines_in_block_comment=false
+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.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.indentation.size=8
+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.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_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.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.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_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_semicolon_in_try_resources=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_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_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_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_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.insert_space_before_opening_bracket_in_array_allocation_expression=do not 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.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.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.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
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.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
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
action.save_project = Guardar proyecto
action.save_project_as = Guardar proyecto como...
action.quit = Salir
+ label.quit_jalview = Salir Javliew?
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.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
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
--- /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
+ package MCview;
+
-import jalview.analysis.AlignSeq;
-import jalview.appletgui.AlignmentPanel;
-import jalview.appletgui.FeatureRenderer;
-import jalview.appletgui.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.InputEvent;import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Image;
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.Panel;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.io.PrintStream;
-import java.util.List;
-import java.util.Vector;
-
-public class AppletPDBCanvas extends Panel
- implements MouseListener, MouseMotionListener, StructureListener
++public class AppletPDBCanvas
+ {
+
- MCMatrix idmat = new MCMatrix(3, 3);
-
- MCMatrix objmat = new MCMatrix(3, 3);
-
- boolean redrawneeded = true;
-
- int omx = 0;
-
- int mx = 0;
-
- int omy = 0;
-
- int my = 0;
-
- public StructureFile pdb;
-
- PDBEntry pdbentry;
-
- int bsize;
-
- Image img;
-
- Graphics ig;
-
- Dimension prefsize;
-
- float[] centre = new float[3];
-
- float[] width = new float[3];
-
- float maxwidth;
-
- float scale;
-
- String inStr;
-
- String inType;
-
- boolean bysequence = true;
-
- boolean depthcue = true;
-
- boolean wire = false;
-
- boolean bymolecule = false;
-
- boolean zbuffer = true;
-
- boolean dragging;
-
- int xstart;
-
- int xend;
-
- int ystart;
-
- int yend;
-
- int xmid;
-
- int ymid;
-
- Font font = new Font("Helvetica", Font.PLAIN, 10);
-
- public SequenceI[] sequence;
-
- final StringBuffer mappingDetails = new StringBuffer();
-
- String appletToolTip = null;
-
- int toolx, tooly;
-
- PDBChain mainchain;
-
- Vector<String> highlightRes;
-
- boolean pdbAction = false;
-
- Bond highlightBond1, highlightBond2;
-
- boolean errorLoading = false;
-
- boolean seqColoursReady = false;
-
- FeatureRenderer fr;
-
- AlignmentPanel ap;
-
- StructureSelectionManager ssm;
-
- public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, DataSourceType protocol)
-
- {
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
-
- ssm = StructureSelectionManager
- .getStructureSelectionManager(ap.av.applet);
-
- try
- {
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
-
- if (protocol == DataSourceType.PASTE)
- {
- pdbentry.setFile("INLINE" + pdb.getId());
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return;
- }
-
- pdbentry.setId(pdb.getId());
-
- ssm.addStructureViewerListener(this);
-
- colourBySequence();
-
- float max = -10;
- int maxchain = -1;
- int pdbstart = 0;
- int pdbend = 0;
- int seqstart = 0;
- int seqend = 0;
-
- // JUST DEAL WITH ONE SEQUENCE FOR NOW
- SequenceI sequence = seq[0];
-
- for (int i = 0; i < pdb.getChains().size(); i++)
- {
-
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence
- .getSequenceAsString());
- mappingDetails.append("\nNo of residues = "
- + pdb.getChains().elementAt(i).residues.size() + "\n\n");
-
- // Now lets compare the sequences to get
- // the start and end points.
- // Align the sequence to the pdb
- // TODO: DNa/Pep switch
- AlignSeq as = new AlignSeq(sequence,
- pdb.getChains().elementAt(i).sequence,
- pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA
- : AlignSeq.PEP);
- as.calcScoreMatrix();
- as.traceAlignment();
- PrintStream ps = new PrintStream(System.out)
- {
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- @Override
- public void println()
- {
- mappingDetails.append("\n");
- }
- };
-
- as.printAlignment(ps);
-
- if (as.maxscore > max)
- {
- max = as.maxscore;
- maxchain = i;
-
- pdbstart = as.seq2start;
- pdbend = as.seq2end;
- seqstart = as.seq1start + sequence.getStart() - 1;
- seqend = as.seq1end + sequence.getEnd() - 1;
- }
-
- mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
- mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
- }
-
- mainchain = pdb.getChains().elementAt(maxchain);
-
- mainchain.pdbstart = pdbstart;
- mainchain.pdbend = pdbend;
- mainchain.seqstart = seqstart;
- mainchain.seqend = seqend;
- mainchain.isVisible = true;
- // mainchain.makeExactMapping(maxAlignseq, sequence);
- // mainchain.transferRESNUMFeatures(sequence, null);
- this.pdb = pdb;
- this.prefsize = new Dimension(getSize().width, getSize().height);
-
- // Initialize the matrices to identity
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 1);
- objmat.addElement(i, j, 1);
- }
- }
- }
-
- addMouseMotionListener(this);
- addMouseListener(this);
-
- addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent evt)
- {
- doKeyPressed(evt);
- }
- });
-
- findCentre();
- findWidth();
-
- setupBonds();
-
- scale = findScale();
- }
-
- Vector<Bond> visiblebonds;
-
- void setupBonds()
- {
- seqColoursReady = false;
- // Sort the bonds by z coord
- visiblebonds = new Vector<Bond>();
-
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- if (pdb.getChains().elementAt(ii).isVisible)
- {
- Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
-
- for (int i = 0; i < tmp.size(); i++)
- {
- visiblebonds.addElement(tmp.elementAt(i));
- }
- }
- }
- seqColoursReady = true;
- colourBySequence();
- redrawneeded = true;
- repaint();
- }
-
- public void findWidth()
- {
- float[] max = new float[3];
- float[] min = new float[3];
-
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
-
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
-
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- if (pdb.getChains().elementAt(ii).isVisible)
- {
- Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
-
- for (Bond tmp : bonds)
- {
- if (tmp.start[0] >= max[0])
- {
- max[0] = tmp.start[0];
- }
-
- if (tmp.start[1] >= max[1])
- {
- max[1] = tmp.start[1];
- }
-
- if (tmp.start[2] >= max[2])
- {
- max[2] = tmp.start[2];
- }
-
- if (tmp.start[0] <= min[0])
- {
- min[0] = tmp.start[0];
- }
-
- if (tmp.start[1] <= min[1])
- {
- min[1] = tmp.start[1];
- }
-
- if (tmp.start[2] <= min[2])
- {
- min[2] = tmp.start[2];
- }
-
- if (tmp.end[0] >= max[0])
- {
- max[0] = tmp.end[0];
- }
-
- if (tmp.end[1] >= max[1])
- {
- max[1] = tmp.end[1];
- }
-
- if (tmp.end[2] >= max[2])
- {
- max[2] = tmp.end[2];
- }
-
- if (tmp.end[0] <= min[0])
- {
- min[0] = tmp.end[0];
- }
-
- if (tmp.end[1] <= min[1])
- {
- min[1] = tmp.end[1];
- }
-
- if (tmp.end[2] <= min[2])
- {
- min[2] = tmp.end[2];
- }
- }
- }
- }
-
- width[0] = Math.abs(max[0] - min[0]);
- width[1] = Math.abs(max[1] - min[1]);
- width[2] = Math.abs(max[2] - min[2]);
-
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
-
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
- }
-
- public float findScale()
- {
- int dim;
- int width;
- int height;
-
- if (getSize().width != 0)
- {
- width = getSize().width;
- height = getSize().height;
- }
- else
- {
- width = prefsize.width;
- height = prefsize.height;
- }
-
- if (width < height)
- {
- dim = width;
- }
- else
- {
- dim = height;
- }
-
- return (float) (dim / (1.5d * maxwidth));
- }
-
- public void findCentre()
- {
- float xtot = 0;
- float ytot = 0;
- float ztot = 0;
-
- int bsize = 0;
-
- // Find centre coordinate
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- if (pdb.getChains().elementAt(ii).isVisible)
- {
- Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
-
- bsize += bonds.size();
-
- for (Bond b : bonds)
- {
- xtot = xtot + b.start[0] + b.end[0];
- ytot = ytot + b.start[1] + b.end[1];
- ztot = ztot + b.start[2] + b.end[2];
- }
- }
- }
-
- centre[0] = xtot / (2 * (float) bsize);
- centre[1] = ytot / (2 * (float) bsize);
- centre[2] = ztot / (2 * (float) bsize);
- }
-
- @Override
- public void paint(Graphics g)
- {
-
- if (errorLoading)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
- g.setColor(Color.black);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.error_loading_pdb_data"),
- 50, getSize().height / 2);
- return;
- }
-
- if (!seqColoursReady)
- {
- g.setColor(Color.black);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
- getSize().height / 2);
- return;
- }
-
- // Only create the image at the beginning -
- // this saves much memory usage
- if ((img == null) || (prefsize.width != getSize().width)
- || (prefsize.height != getSize().height))
- {
-
- try
- {
- prefsize.width = getSize().width;
- prefsize.height = getSize().height;
-
- scale = findScale();
- img = createImage(prefsize.width, prefsize.height);
- ig = img.getGraphics();
-
- redrawneeded = true;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- if (redrawneeded)
- {
- drawAll(ig, prefsize.width, prefsize.height);
- redrawneeded = false;
- }
- if (appletToolTip != null)
- {
- ig.setColor(Color.red);
- ig.drawString(appletToolTip, toolx, tooly);
- }
-
- g.drawImage(img, 0, 0, this);
-
- pdbAction = false;
- }
-
- public void drawAll(Graphics g, int width, int height)
- {
- ig.setColor(Color.black);
- ig.fillRect(0, 0, width, height);
- drawScene(ig);
- drawLabels(ig);
- }
-
- public void setColours(jalview.schemes.ColourSchemeI cs)
- {
- bysequence = false;
- pdb.setColours(cs);
- redrawneeded = true;
- repaint();
- }
-
- // This method has been taken out of PDBChain to allow
- // Applet and Application specific sequence renderers to be used
- void colourBySequence()
- {
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- boolean showFeatures = false;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = new jalview.appletgui.FeatureRenderer(ap.av);
- }
-
- fr.transferSettings(ap.getFeatureRenderer());
-
- showFeatures = true;
- }
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- PDBChain chain;
- if (bysequence && pdb != null)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- chain = pdb.getChains().elementAt(ii);
-
- for (int i = 0; i < chain.bonds.size(); i++)
- {
- Bond tmp = chain.bonds.elementAt(i);
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- if (chain != mainchain)
- {
- continue;
- }
-
- for (int s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s])
- {
- int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
- if (pos > 0)
- {
- pos = sequence[s].findIndex(pos);
- tmp.startCol = sr.getResidueColour(sequence[s], pos,
- finder);
- }
- pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
- if (pos > 0)
- {
- pos = sequence[s].findIndex(pos);
- tmp.endCol = sr.getResidueColour(sequence[s], pos,
- finder);
- }
- }
- }
- }
- }
- }
- }
- }
-
- Zsort zsort;
-
- public void drawScene(Graphics g)
- {
- if (zbuffer)
- {
- if (zsort == null)
- {
- zsort = new Zsort();
- }
-
- zsort.sort(visiblebonds);
- }
-
- Bond tmpBond = null;
- for (int i = 0; i < visiblebonds.size(); i++)
- {
- tmpBond = visiblebonds.elementAt(i);
-
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getSize().width / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
- + (getSize().height / 2));
-
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
- + (getSize().width / 2));
- yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
- + (getSize().height / 2));
-
- xmid = (xend + xstart) / 2;
- ymid = (yend + ystart) / 2;
-
- if (depthcue && !bymolecule)
- {
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
- {
- g.setColor(tmpBond.startCol.darker().darker());
- drawLine(g, xstart, ystart, xmid, ymid);
-
- g.setColor(tmpBond.endCol.darker().darker());
- drawLine(g, xmid, ymid, xend, yend);
- }
- else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
- {
- g.setColor(tmpBond.startCol.darker());
- drawLine(g, xstart, ystart, xmid, ymid);
-
- g.setColor(tmpBond.endCol.darker());
- drawLine(g, xmid, ymid, xend, yend);
- }
- else
- {
- g.setColor(tmpBond.startCol);
- drawLine(g, xstart, ystart, xmid, ymid);
-
- g.setColor(tmpBond.endCol);
- drawLine(g, xmid, ymid, xend, yend);
- }
-
- }
- else if (depthcue && bymolecule)
- {
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
- {
- g.setColor(Color.green.darker().darker());
- drawLine(g, xstart, ystart, xend, yend);
- }
- else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
- {
- g.setColor(Color.green.darker());
- drawLine(g, xstart, ystart, xend, yend);
- }
- else
- {
- g.setColor(Color.green);
- drawLine(g, xstart, ystart, xend, yend);
- }
- }
- else if (!depthcue && !bymolecule)
- {
- g.setColor(tmpBond.startCol);
- drawLine(g, xstart, ystart, xmid, ymid);
- g.setColor(tmpBond.endCol);
- drawLine(g, xmid, ymid, xend, yend);
- }
- else
- {
- drawLine(g, xstart, ystart, xend, yend);
- }
-
- if (highlightBond1 != null && highlightBond1 == tmpBond)
- {
- g.setColor(Color.white);
- drawLine(g, xmid, ymid, xend, yend);
- }
-
- if (highlightBond2 != null && highlightBond2 == tmpBond)
- {
- g.setColor(Color.white);
- drawLine(g, xstart, ystart, xmid, ymid);
- }
-
- }
- }
-
- public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
- {
- if (!wire)
- {
- if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
- {
- g.drawLine(x1, y1, x2, y2);
- g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
- g.drawLine(x1, y1 - 1, x2, y2 - 1);
- }
- else
- {
- g.setColor(g.getColor().brighter());
- g.drawLine(x1, y1, x2, y2);
- g.drawLine(x1 + 1, y1, x2 + 1, y2);
- g.drawLine(x1 - 1, y1, x2 - 1, y2);
- }
- }
- else
- {
- g.drawLine(x1, y1, x2, y2);
- }
- }
-
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
- public void doKeyPressed(KeyEvent evt)
- {
- if (evt.getKeyCode() == KeyEvent.VK_UP)
- {
- scale = (float) (scale * 1.1);
- redrawneeded = true;
- repaint();
- }
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
- {
- scale = (float) (scale * 0.9);
- redrawneeded = true;
- repaint();
- }
- }
-
- @Override
- public void mousePressed(MouseEvent e)
- {
- pdbAction = true;
- Atom fatom = findAtom(e.getX(), e.getY());
- if (fatom != null)
- {
- fatom.isSelected = !fatom.isSelected;
-
- redrawneeded = true;
- repaint();
- if (foundchain != -1)
- {
- PDBChain chain = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- if (fatom.alignmentMapping != -1)
- {
- if (highlightRes == null)
- {
- highlightRes = new Vector<String>();
- }
-
- final String atomString = Integer
- .toString(fatom.alignmentMapping);
- if (highlightRes.contains(atomString))
- {
- highlightRes.removeElement(atomString);
- }
- else
- {
- highlightRes.addElement(atomString);
- }
- }
- }
- }
-
- }
- mx = e.getX();
- my = e.getY();
- omx = mx;
- omy = my;
- dragging = false;
- }
-
- @Override
- public void mouseMoved(MouseEvent e)
- {
- pdbAction = true;
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- highlightBond2.at1.isSelected = false;
- highlightBond1 = null;
- highlightBond2 = null;
- }
-
- Atom fatom = findAtom(e.getX(), e.getY());
-
- PDBChain chain = null;
- if (foundchain != -1)
- {
- chain = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- mouseOverStructure(fatom.resNumber, chain.id);
- }
- }
-
- if (fatom != null)
- {
- toolx = e.getX();
- tooly = e.getY();
-
- appletToolTip = chain.id + ":" + fatom.resNumber + " "
- + fatom.resName;
- redrawneeded = true;
- repaint();
- }
- else
- {
- mouseOverStructure(-1, chain != null ? chain.id : null);
- appletToolTip = null;
- redrawneeded = true;
- repaint();
- }
- }
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- int x = evt.getX();
- int y = evt.getY();
- mx = x;
- my = y;
-
- MCMatrix objmat = new MCMatrix(3, 3);
- objmat.setIdentity();
-
- if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
- {
- objmat.rotatez(((mx - omx)));
- }
- else
- {
- objmat.rotatex(((omy - my)));
- objmat.rotatey(((omx - mx)));
- }
-
- // Alter the bonds
- for (PDBChain chain : pdb.getChains())
- {
- for (Bond tmpBond : chain.bonds)
- {
- // Translate the bond so the centre is 0,0,0
- tmpBond.translate(-centre[0], -centre[1], -centre[2]);
-
- // Now apply the rotation matrix
- tmpBond.start = objmat.vectorMultiply(tmpBond.start);
- tmpBond.end = objmat.vectorMultiply(tmpBond.end);
-
- // Now translate back again
- tmpBond.translate(centre[0], centre[1], centre[2]);
- }
- }
-
- objmat = null;
-
- omx = mx;
- omy = my;
-
- dragging = true;
-
- redrawneeded = true;
-
- repaint();
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- dragging = false;
- return;
- }
-
- void drawLabels(Graphics g)
- {
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond tmpBond : chain.bonds)
- {
- if (tmpBond.at1.isSelected)
- {
- labelAtom(g, tmpBond, 1);
- }
-
- if (tmpBond.at2.isSelected)
- {
- labelAtom(g, tmpBond, 2);
- }
- }
- }
- }
- }
-
- public void labelAtom(Graphics g, Bond b, int n)
- {
- g.setFont(font);
-
- if (n == 1)
- {
- int xstart = (int) (((b.start[0] - centre[0]) * scale)
- + (getSize().width / 2));
- int ystart = (int) (((centre[1] - b.start[1]) * scale)
- + (getSize().height / 2));
-
- g.setColor(Color.red);
- g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
- }
-
- if (n == 2)
- {
- int xstart = (int) (((b.end[0] - centre[0]) * scale)
- + (getSize().width / 2));
- int ystart = (int) (((centre[1] - b.end[1]) * scale)
- + (getSize().height / 2));
-
- g.setColor(Color.red);
- g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
- }
- }
-
- int foundchain = -1;
-
- public Atom findAtom(int x, int y)
- {
- Atom fatom = null;
-
- foundchain = -1;
-
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- int truex;
- Bond tmpBond = null;
-
- if (chain.isVisible)
- {
- Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
-
- for (int i = 0; i < bonds.size(); i++)
- {
- tmpBond = bonds.elementAt(i);
-
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getSize().width / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
- + (getSize().height / 2));
-
- if (Math.abs(truey - y) <= 2)
- {
- fatom = tmpBond.at1;
- foundchain = ii;
- break;
- }
- }
- }
-
- // Still here? Maybe its the last bond
-
- truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
- + (getSize().width / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
- + (getSize().height / 2));
-
- if (Math.abs(truey - y) <= 2)
- {
- fatom = tmpBond.at2;
- foundchain = ii;
- break;
- }
- }
-
- }
-
- if (fatom != null) // )&& chain.ds != null)
- {
- chain = pdb.getChains().elementAt(foundchain);
- }
- }
-
- return fatom;
- }
-
- @Override
- public void update(Graphics g)
- {
- paint(g);
- }
-
- public void highlightRes(int ii)
- {
- if (!seqColoursReady)
- {
- return;
- }
-
- if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
- {
- return;
- }
-
- int index = -1;
- Bond tmpBond;
- for (index = 0; index < mainchain.bonds.size(); index++)
- {
- tmpBond = mainchain.bonds.elementAt(index);
- if (tmpBond.at1.alignmentMapping == ii - 1)
- {
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- }
-
- if (highlightBond2 != null)
- {
- highlightBond2.at1.isSelected = false;
- }
-
- highlightBond1 = null;
- highlightBond2 = null;
-
- if (index > 0)
- {
- highlightBond1 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
-
- redrawneeded = true;
- repaint();
- }
-
- public void setAllchainsVisible(boolean b)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- chain.isVisible = b;
- }
- mainchain.isVisible = true;
- findCentre();
- setupBonds();
- }
-
- // ////////////////////////////////
- // /StructureListener
- @Override
- public String[] getStructureFiles()
- {
- return new String[] { pdbentry.getFile() };
- }
-
- String lastMessage;
-
- public void mouseOverStructure(int pdbResNum, String chain)
- {
- if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
- {
- ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
- }
-
- lastMessage = pdbResNum + chain;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- /**
- * Highlight the specified atoms in the structure.
- *
- * @param atoms
- */
- @Override
- public void highlightAtoms(List<AtomSpec> atoms)
- {
- if (!seqColoursReady)
- {
- return;
- }
- for (AtomSpec atom : atoms)
- {
- int atomIndex = atom.getAtomIndex();
-
- if (highlightRes != null
- && highlightRes.contains((atomIndex - 1) + ""))
- {
- continue;
- }
-
- highlightAtom(atomIndex);
- }
-
- redrawneeded = true;
- repaint();
- }
-
- /**
- * @param atomIndex
- */
- protected void highlightAtom(int atomIndex)
- {
- int index = -1;
- Bond tmpBond;
- for (index = 0; index < mainchain.bonds.size(); index++)
- {
- tmpBond = mainchain.bonds.elementAt(index);
- if (tmpBond.at1.atomIndex == atomIndex)
- {
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- }
-
- if (highlightBond2 != null)
- {
- highlightBond2.at1.isSelected = false;
- }
-
- highlightBond1 = null;
- highlightBond2 = null;
-
- if (index > 0)
- {
- highlightBond1 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- return Color.white;
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return null;
-
- // return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- @Override
- public void updateColours(Object source)
- {
- colourBySequence();
- redrawneeded = true;
- repaint();
- }
-
- @Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean isListeningFor(SequenceI seq)
- {
- if (sequence != null)
- {
- for (SequenceI s : sequence)
- {
- if (s == seq)
- {
- return true;
- }
- }
- }
- return false;
- }
+ }
--- /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
+ package MCview;
+
-import jalview.schemes.ResidueProperties;
-
-import java.awt.Color;
-
+ public class Atom
+ {
- public float x;
-
- public float y;
-
- public float z;
-
- public int number;
-
- public String name;
-
- public String resName;
-
- public int resNumber;
-
- public char insCode = ' ';
-
- public String resNumIns = null;
-
- public int type;
-
- Color color = Color.lightGray;
-
- public String chain;
-
- /**
- * this is a temporary value - designed to store the position in sequence that
- * this atom corresponds to after aligning the chain to a SequenceI object. Do
- * not rely on its value being correct when visualizing sequence colourings on
- * the structure - use the StructureSelectionManager's mapping instead.
- */
- public int alignmentMapping = -1;
-
- public int atomIndex;
-
- public float occupancy = 0;
-
- public float tfactor = 0;
-
- // need these if we ever want to export Atom data
- // public boolean tfacset=true,occset=true;
- public boolean isSelected = false;
-
- public Atom(String str)
- {
- atomIndex = Integer.parseInt(str.substring(6, 11).trim());
-
- name = str.substring(12, 15).trim();
-
- resName = str.substring(17, 20);
- // JAL-1828 treat MSE Selenomethionine as MET (etc)
- resName = ResidueProperties.getCanonicalAminoAcid(resName);
-
- chain = str.substring(21, 22);
-
- resNumber = Integer.parseInt(str.substring(22, 26).trim());
- resNumIns = str.substring(22, 27).trim();
- insCode = str.substring(26, 27).charAt(0);
- this.x = (Float.valueOf(str.substring(30, 38).trim()).floatValue());
- this.y = (Float.valueOf(str.substring(38, 46).trim()).floatValue());
- this.z = (Float.valueOf(str.substring(47, 55).trim()).floatValue());
- // optional entries - see JAL-730
- String tm = str.substring(54, 60).trim();
- if (tm.length() > 0)
- {
- occupancy = (Float.valueOf(tm)).floatValue();
- }
- else
- {
- occupancy = 1f; // default occupancy
- // see note above: occset=false;
- }
- tm = str.substring(60, 66).trim();
- if (tm.length() > 0)
- {
- tfactor = (Float.valueOf(tm).floatValue());
- }
- else
- {
- tfactor = 1f;
- // see note above: tfacset=false;
- }
- }
-
- @Override
- public boolean equals(Object that)
- {
- if (this == that || that == null)
- {
- return true;
- }
- if (that instanceof Atom)
- {
- Atom other = (Atom) that;
- return other.resName.equals(this.resName)
- && other.resNumber == this.resNumber
- && other.resNumIns.equals(this.resNumIns)
- && other.chain.equals(this.chain);
- }
- return false;
- }
+
- public Atom(float x, float y, float z)
- {
- this.x = x;
- this.y = y;
- this.z = z;
- }
+ }
--- /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
+ package MCview;
+
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.InputEvent;import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.Image;
-import java.awt.RenderingHints;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.io.PrintStream;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JPanel;
-import javax.swing.ToolTipManager;
-
-public class PDBCanvas extends JPanel
- implements MouseListener, MouseMotionListener, StructureListener
++public class PDBCanvas
+ {
- boolean redrawneeded = true;
-
- int omx = 0;
-
- int mx = 0;
-
- int omy = 0;
-
- int my = 0;
-
- public StructureFile pdb;
-
- PDBEntry pdbentry;
-
- int bsize;
-
- Image img;
-
- Graphics ig;
-
- Dimension prefsize;
-
- float[] centre = new float[3];
-
- float[] width = new float[3];
-
- float maxwidth;
-
- float scale;
-
- String inStr;
-
- String inType;
-
- boolean bysequence = true;
-
- boolean depthcue = true;
-
- boolean wire = false;
-
- boolean bymolecule = false;
-
- boolean zbuffer = true;
-
- boolean dragging;
-
- int xstart;
-
- int xend;
-
- int ystart;
-
- int yend;
-
- int xmid;
-
- int ymid;
-
- Font font = new Font("Helvetica", Font.PLAIN, 10);
-
- jalview.gui.SeqCanvas seqcanvas;
-
- public SequenceI[] sequence;
-
- final StringBuffer mappingDetails = new StringBuffer();
-
- PDBChain mainchain;
-
- Vector<String> highlightRes;
-
- boolean pdbAction = false;
-
- boolean seqColoursReady = false;
-
- jalview.renderer.seqfeatures.FeatureRenderer fr;
-
- Color backgroundColour = Color.black;
-
- AlignmentPanel ap;
-
- StructureSelectionManager ssm;
-
- String errorMessage;
-
- void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, DataSourceType protocol)
- {
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
-
- ssm = ap.av.getStructureSelectionManager();
-
- try
- {
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
- ap.alignFrame);
-
- if (protocol.equals(jalview.io.DataSourceType.PASTE))
- {
- pdbentry.setFile("INLINE" + pdb.getId());
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return;
- }
-
- if (pdb == null)
- {
- errorMessage = "Error loading file: " + pdbentry.getId();
- return;
- }
- pdbentry.setId(pdb.getId());
-
- ssm.addStructureViewerListener(this);
-
- colourBySequence();
-
- float max = -10;
- int maxchain = -1;
- int pdbstart = 0;
- int pdbend = 0;
- int seqstart = 0;
- int seqend = 0;
-
- // JUST DEAL WITH ONE SEQUENCE FOR NOW
- SequenceI sequence = seq[0];
-
- for (int i = 0; i < pdb.getChains().size(); i++)
- {
-
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence
- .getSequenceAsString());
- mappingDetails.append("\nNo of residues = "
- + pdb.getChains().elementAt(i).residues.size() + "\n\n");
-
- // Now lets compare the sequences to get
- // the start and end points.
- // Align the sequence to the pdb
- AlignSeq as = new AlignSeq(sequence,
- pdb.getChains().elementAt(i).sequence, "pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- PrintStream ps = new PrintStream(System.out)
- {
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- @Override
- public void println()
- {
- mappingDetails.append("\n");
- }
- };
-
- as.printAlignment(ps);
-
- if (as.maxscore > max)
- {
- max = as.maxscore;
- maxchain = i;
-
- pdbstart = as.seq2start;
- pdbend = as.seq2end;
- seqstart = as.seq1start + sequence.getStart() - 1;
- seqend = as.seq1end + sequence.getEnd() - 1;
- }
-
- mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
- mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
- }
-
- mainchain = pdb.getChains().elementAt(maxchain);
-
- mainchain.pdbstart = pdbstart;
- mainchain.pdbend = pdbend;
- mainchain.seqstart = seqstart;
- mainchain.seqend = seqend;
- mainchain.isVisible = true;
-
- this.pdb = pdb;
- this.prefsize = new Dimension(getSize().width, getSize().height);
-
- addMouseMotionListener(this);
- addMouseListener(this);
-
- addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent evt)
- {
- keyPressed(evt);
- }
- });
-
- findCentre();
- findWidth();
-
- setupBonds();
-
- scale = findScale();
-
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- }
-
- Vector<Bond> visiblebonds;
-
- void setupBonds()
- {
- seqColoursReady = false;
- // Sort the bonds by z coord
- visiblebonds = new Vector<Bond>();
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond bond : chain.bonds)
- {
- visiblebonds.addElement(bond);
- }
- }
- }
-
- updateSeqColours();
- seqColoursReady = true;
- redrawneeded = true;
- repaint();
- }
-
- public void findWidth()
- {
- float[] max = new float[3];
- float[] min = new float[3];
-
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
-
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond tmp : chain.bonds)
- {
- if (tmp.start[0] >= max[0])
- {
- max[0] = tmp.start[0];
- }
-
- if (tmp.start[1] >= max[1])
- {
- max[1] = tmp.start[1];
- }
-
- if (tmp.start[2] >= max[2])
- {
- max[2] = tmp.start[2];
- }
-
- if (tmp.start[0] <= min[0])
- {
- min[0] = tmp.start[0];
- }
-
- if (tmp.start[1] <= min[1])
- {
- min[1] = tmp.start[1];
- }
-
- if (tmp.start[2] <= min[2])
- {
- min[2] = tmp.start[2];
- }
-
- if (tmp.end[0] >= max[0])
- {
- max[0] = tmp.end[0];
- }
-
- if (tmp.end[1] >= max[1])
- {
- max[1] = tmp.end[1];
- }
-
- if (tmp.end[2] >= max[2])
- {
- max[2] = tmp.end[2];
- }
-
- if (tmp.end[0] <= min[0])
- {
- min[0] = tmp.end[0];
- }
-
- if (tmp.end[1] <= min[1])
- {
- min[1] = tmp.end[1];
- }
-
- if (tmp.end[2] <= min[2])
- {
- min[2] = tmp.end[2];
- }
- }
- }
- }
- /*
- * System.out.println("xmax " + max[0] + " min " + min[0]);
- * System.out.println("ymax " + max[1] + " min " + min[1]);
- * System.out.println("zmax " + max[2] + " min " + min[2]);
- */
-
- width[0] = Math.abs(max[0] - min[0]);
- width[1] = Math.abs(max[1] - min[1]);
- width[2] = Math.abs(max[2] - min[2]);
-
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
-
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
- }
-
- public float findScale()
- {
- int dim;
- int width;
- int height;
-
- if (getWidth() != 0)
- {
- width = getWidth();
- height = getHeight();
- }
- else
- {
- width = prefsize.width;
- height = prefsize.height;
- }
-
- if (width < height)
- {
- dim = width;
- }
- else
- {
- dim = height;
- }
-
- return (float) (dim / (1.5d * maxwidth));
- }
-
- public void findCentre()
- {
- float xtot = 0;
- float ytot = 0;
- float ztot = 0;
-
- int bsize = 0;
-
- // Find centre coordinate
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- bsize += chain.bonds.size();
-
- for (Bond bond : chain.bonds)
- {
- xtot = xtot + bond.start[0] + bond.end[0];
- ytot = ytot + bond.start[1] + bond.end[1];
- ztot = ztot + bond.start[2] + bond.end[2];
- }
- }
- }
-
- centre[0] = xtot / (2 * (float) bsize);
- centre[1] = ytot / (2 * (float) bsize);
- centre[2] = ztot / (2 * (float) bsize);
- }
-
- @Override
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
-
- if (!seqColoursReady || errorMessage != null)
- {
- g.setColor(Color.black);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(errorMessage == null ? "Retrieving PDB data...."
- : errorMessage, 20, getHeight() / 2);
- return;
- }
-
- // Only create the image at the beginning -
- // this saves much memory usage
- if ((img == null) || (prefsize.width != getWidth())
- || (prefsize.height != getHeight()))
-
- {
- prefsize.width = getWidth();
- prefsize.height = getHeight();
-
- scale = findScale();
- img = createImage(prefsize.width, prefsize.height);
- ig = img.getGraphics();
- Graphics2D ig2 = (Graphics2D) ig;
-
- ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
-
- redrawneeded = true;
- }
-
- if (redrawneeded)
- {
- drawAll(ig, prefsize.width, prefsize.height);
- redrawneeded = false;
- }
-
- g.drawImage(img, 0, 0, this);
-
- pdbAction = false;
- }
-
- public void drawAll(Graphics g, int width, int height)
- {
- g.setColor(backgroundColour);
- g.fillRect(0, 0, width, height);
- drawScene(g);
- drawLabels(g);
- }
-
- public void updateSeqColours()
- {
- if (pdbAction)
- {
- return;
- }
-
- colourBySequence();
-
- redrawneeded = true;
- repaint();
- }
-
- // This method has been taken out of PDBChain to allow
- // Applet and Application specific sequence renderers to be used
- void colourBySequence()
- {
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- boolean showFeatures = false;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = new FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.alignFrame.getFeatureRenderer());
-
- showFeatures = true;
- }
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- PDBChain chain;
- if (bysequence && pdb != null)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- chain = pdb.getChains().elementAt(ii);
-
- for (int i = 0; i < chain.bonds.size(); i++)
- {
- Bond tmp = chain.bonds.elementAt(i);
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- if (chain != mainchain)
- {
- continue;
- }
-
- for (int s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s])
- {
- int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
- if (pos > 0)
- {
- pos = sequence[s].findIndex(pos);
- tmp.startCol = sr.getResidueColour(sequence[s], pos,
- finder);
- }
- pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
- if (pos > 0)
- {
- pos = sequence[s].findIndex(pos);
- tmp.endCol = sr.getResidueColour(sequence[s], pos,
- finder);
- }
-
- }
- }
- }
- }
- }
- }
- }
-
- Zsort zsort;
-
- public void drawScene(Graphics g)
- {
- if (zbuffer)
- {
- if (zsort == null)
- {
- zsort = new Zsort();
- }
-
- zsort.sort(visiblebonds);
- }
-
- Bond tmpBond = null;
- for (int i = 0; i < visiblebonds.size(); i++)
- {
- tmpBond = visiblebonds.elementAt(i);
-
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getWidth() / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
- + (getHeight() / 2));
-
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
- + (getWidth() / 2));
- yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
- + (getHeight() / 2));
-
- xmid = (xend + xstart) / 2;
- ymid = (yend + ystart) / 2;
- if (depthcue && !bymolecule)
- {
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
- {
-
- g.setColor(tmpBond.startCol.darker().darker());
- drawLine(g, xstart, ystart, xmid, ymid);
- g.setColor(tmpBond.endCol.darker().darker());
- drawLine(g, xmid, ymid, xend, yend);
-
- }
- else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
- {
- g.setColor(tmpBond.startCol.darker());
- drawLine(g, xstart, ystart, xmid, ymid);
-
- g.setColor(tmpBond.endCol.darker());
- drawLine(g, xmid, ymid, xend, yend);
- }
- else
- {
- g.setColor(tmpBond.startCol);
- drawLine(g, xstart, ystart, xmid, ymid);
-
- g.setColor(tmpBond.endCol);
- drawLine(g, xmid, ymid, xend, yend);
- }
- }
- else if (depthcue && bymolecule)
- {
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
- {
- g.setColor(Color.green.darker().darker());
- drawLine(g, xstart, ystart, xend, yend);
- }
- else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
- {
- g.setColor(Color.green.darker());
- drawLine(g, xstart, ystart, xend, yend);
- }
- else
- {
- g.setColor(Color.green);
- drawLine(g, xstart, ystart, xend, yend);
- }
- }
- else if (!depthcue && !bymolecule)
- {
- g.setColor(tmpBond.startCol);
- drawLine(g, xstart, ystart, xmid, ymid);
- g.setColor(tmpBond.endCol);
- drawLine(g, xmid, ymid, xend, yend);
- }
- else
- {
- drawLine(g, xstart, ystart, xend, yend);
- }
-
- if (highlightBond1 != null && highlightBond1 == tmpBond)
- {
- g.setColor(
- tmpBond.endCol.brighter().brighter().brighter().brighter());
- drawLine(g, xmid, ymid, xend, yend);
- }
-
- if (highlightBond2 != null && highlightBond2 == tmpBond)
- {
- g.setColor(tmpBond.startCol.brighter().brighter().brighter()
- .brighter());
- drawLine(g, xstart, ystart, xmid, ymid);
- }
-
- }
-
- }
-
- public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
- {
- if (!wire)
- {
- if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
- {
- g.drawLine(x1, y1, x2, y2);
- g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
- g.drawLine(x1, y1 - 1, x2, y2 - 1);
- }
- else
- {
- g.setColor(g.getColor().brighter());
- g.drawLine(x1, y1, x2, y2);
- g.drawLine(x1 + 1, y1, x2 + 1, y2);
- g.drawLine(x1 - 1, y1, x2 - 1, y2);
- }
- }
- else
- {
- g.drawLine(x1, y1, x2, y2);
- }
- }
-
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
- public void keyPressed(KeyEvent evt)
- {
- if (evt.getKeyCode() == KeyEvent.VK_UP)
- {
- scale = (float) (scale * 1.1);
- redrawneeded = true;
- repaint();
- }
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
- {
- scale = (float) (scale * 0.9);
- redrawneeded = true;
- repaint();
- }
- }
-
- @Override
- public void mousePressed(MouseEvent e)
- {
- pdbAction = true;
- Atom fatom = findAtom(e.getX(), e.getY());
- if (fatom != null)
- {
- fatom.isSelected = !fatom.isSelected;
-
- redrawneeded = true;
- repaint();
- if (foundchain != -1)
- {
- PDBChain chain = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- if (fatom.alignmentMapping != -1)
- {
- if (highlightRes == null)
- {
- highlightRes = new Vector<String>();
- }
-
- final String atomString = Integer
- .toString(fatom.alignmentMapping);
- if (highlightRes.contains(atomString))
- {
- highlightRes.remove(atomString);
- }
- else
- {
- highlightRes.add(atomString);
- }
- }
- }
- }
-
- }
- mx = e.getX();
- my = e.getY();
- omx = mx;
- omy = my;
- dragging = false;
- }
-
- @Override
- public void mouseMoved(MouseEvent e)
- {
- pdbAction = true;
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- highlightBond2.at1.isSelected = false;
- highlightBond1 = null;
- highlightBond2 = null;
- }
-
- Atom fatom = findAtom(e.getX(), e.getY());
-
- PDBChain chain = null;
- if (foundchain != -1)
- {
- chain = pdb.getChains().elementAt(foundchain);
- if (chain == mainchain)
- {
- mouseOverStructure(fatom.resNumber, chain.id);
- }
- }
-
- if (fatom != null)
- {
- this.setToolTipText(
- chain.id + ":" + fatom.resNumber + " " + fatom.resName);
- }
- else
- {
- mouseOverStructure(-1, chain != null ? chain.id : null);
- this.setToolTipText(null);
- }
- }
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- int x = evt.getX();
- int y = evt.getY();
- mx = x;
- my = y;
-
- MCMatrix objmat = new MCMatrix(3, 3);
- objmat.setIdentity();
-
- if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
- {
- objmat.rotatez(((mx - omx)));
- }
- else
- {
- objmat.rotatex(((my - omy)));
- objmat.rotatey(((omx - mx)));
- }
-
- // Alter the bonds
- for (PDBChain chain : pdb.getChains())
- {
- for (Bond tmpBond : chain.bonds)
- {
- // Translate the bond so the centre is 0,0,0
- tmpBond.translate(-centre[0], -centre[1], -centre[2]);
-
- // Now apply the rotation matrix
- tmpBond.start = objmat.vectorMultiply(tmpBond.start);
- tmpBond.end = objmat.vectorMultiply(tmpBond.end);
-
- // Now translate back again
- tmpBond.translate(centre[0], centre[1], centre[2]);
- }
- }
-
- objmat = null;
-
- omx = mx;
- omy = my;
-
- dragging = true;
-
- redrawneeded = true;
-
- repaint();
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- dragging = false;
- return;
- }
-
- void drawLabels(Graphics g)
- {
-
- for (PDBChain chain : pdb.getChains())
- {
- if (chain.isVisible)
- {
- for (Bond tmpBond : chain.bonds)
- {
- if (tmpBond.at1.isSelected)
- {
- labelAtom(g, tmpBond, 1);
- }
-
- if (tmpBond.at2.isSelected)
- {
- labelAtom(g, tmpBond, 2);
- }
- }
- }
- }
- }
-
- public void labelAtom(Graphics g, Bond b, int n)
- {
- g.setFont(font);
- g.setColor(Color.red);
- if (n == 1)
- {
- int xstart = (int) (((b.start[0] - centre[0]) * scale)
- + (getWidth() / 2));
- int ystart = (int) (((centre[1] - b.start[1]) * scale)
- + (getHeight() / 2));
-
- g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
- }
-
- if (n == 2)
- {
- int xstart = (int) (((b.end[0] - centre[0]) * scale)
- + (getWidth() / 2));
- int ystart = (int) (((centre[1] - b.end[1]) * scale)
- + (getHeight() / 2));
-
- g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
- }
- }
-
- int foundchain = -1;
-
- public Atom findAtom(int x, int y)
- {
- Atom fatom = null;
-
- foundchain = -1;
-
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- int truex;
- Bond tmpBond = null;
-
- if (chain.isVisible)
- {
- for (Bond bond : chain.bonds)
- {
- tmpBond = bond;
-
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
- + (getWidth() / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
- + (getHeight() / 2));
-
- if (Math.abs(truey - y) <= 2)
- {
- fatom = tmpBond.at1;
- foundchain = ii;
- break;
- }
- }
- }
-
- // Still here? Maybe its the last bond
-
- truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
- + (getWidth() / 2));
-
- if (Math.abs(truex - x) <= 2)
- {
- int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
- + (getHeight() / 2));
-
- if (Math.abs(truey - y) <= 2)
- {
- fatom = tmpBond.at2;
- foundchain = ii;
- break;
- }
- }
-
- }
-
- if (fatom != null) // )&& chain.ds != null)
- { // dead code? value of chain is either overwritten or discarded
- chain = pdb.getChains().elementAt(foundchain);
- }
- }
-
- return fatom;
- }
-
- Bond highlightBond1, highlightBond2;
-
- public void highlightRes(int ii)
- {
- if (!seqColoursReady)
- {
- return;
- }
-
- if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
- {
- return;
- }
-
- int index = -1;
- Bond tmpBond;
- for (index = 0; index < mainchain.bonds.size(); index++)
- {
- tmpBond = mainchain.bonds.elementAt(index);
- if (tmpBond.at1.alignmentMapping == ii - 1)
- {
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- }
-
- if (highlightBond2 != null)
- {
- highlightBond2.at1.isSelected = false;
- }
-
- highlightBond1 = null;
- highlightBond2 = null;
-
- if (index > 0)
- {
- highlightBond1 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
-
- redrawneeded = true;
- repaint();
- }
-
- public void setAllchainsVisible(boolean b)
- {
- for (int ii = 0; ii < pdb.getChains().size(); ii++)
- {
- PDBChain chain = pdb.getChains().elementAt(ii);
- chain.isVisible = b;
- }
- mainchain.isVisible = true;
- findCentre();
- setupBonds();
- }
-
- // ////////////////////////////////
- // /StructureListener
- @Override
- public String[] getStructureFiles()
- {
- return new String[] { pdbentry.getFile() };
- }
-
- String lastMessage;
-
- public void mouseOverStructure(int pdbResNum, String chain)
- {
- if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
- {
- ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
- }
-
- lastMessage = pdbResNum + chain;
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- /**
- * Highlight the specified atoms in the structure.
- *
- * @param atoms
- */
- @Override
- public void highlightAtoms(List<AtomSpec> atoms)
- {
- if (!seqColoursReady)
- {
- return;
- }
-
- for (AtomSpec atom : atoms)
- {
- int atomIndex = atom.getAtomIndex();
- if (highlightRes != null
- && highlightRes.contains((atomIndex - 1) + ""))
- {
- continue;
- }
-
- highlightAtom(atomIndex);
- }
-
- redrawneeded = true;
- repaint();
- }
-
- /**
- * Highlight the atom at the specified index.
- *
- * @param atomIndex
- */
- protected void highlightAtom(int atomIndex)
- {
- int index = -1;
- Bond tmpBond;
- for (index = 0; index < mainchain.bonds.size(); index++)
- {
- tmpBond = mainchain.bonds.elementAt(index);
- if (tmpBond.at1.atomIndex == atomIndex)
- {
- if (highlightBond1 != null)
- {
- highlightBond1.at2.isSelected = false;
- }
-
- if (highlightBond2 != null)
- {
- highlightBond2.at1.isSelected = false;
- }
-
- highlightBond1 = null;
- highlightBond2 = null;
-
- if (index > 0)
- {
- highlightBond1 = mainchain.bonds.elementAt(index - 1);
- highlightBond1.at2.isSelected = true;
- }
-
- if (index != mainchain.bonds.size())
- {
- highlightBond2 = mainchain.bonds.elementAt(index);
- highlightBond2.at1.isSelected = true;
- }
-
- break;
- }
- }
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- return Color.white;
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return null;
-
- // return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- @Override
- public void updateColours(Object source)
- {
- colourBySequence();
- redrawneeded = true;
- repaint();
- }
-
- @Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
+
- @Override
- public boolean isListeningFor(SequenceI seq)
- {
- if (sequence != null)
- {
- for (SequenceI s : sequence)
- {
- if (s == seq)
- {
- return true;
- }
- }
- }
- return false;
- }
+ }
}
// 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();
}
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 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;
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 (Platform.isWinRightButton(evt))
- if ((evt.getModifiersEx()
- & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
++ if (Platform.isWinRightButton(evt))
{
- showPopupMenu(evt);
- return;
- if (!Platform.isAMac())
++ if ((evt.getModifiersEx()
++ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ {
- 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 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()
+ {
+ }
+ });
+ }
}
/**
*/
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"));
+ 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();
+
+ }
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
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)
+ {
+ e.printStackTrace();
+ } catch (Throwable t)
+ {
+ 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();
+ }
}
String file = null, data = 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
{
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 && vamsasImport == null
+ if (!Platform.isJS() && !headless && file == null
+ && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
file = jalview.bin.Cache.getDefault("STARTUP_FILE",
jalview.bin.Cache.getDefault("www.jalview.org",
}
try
{
- Map<String, Object> vbinding = new HashMap<>();
+ Map<String, java.lang.Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
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;
// 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();
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.GeneLociI;
+import jalview.util.JSONUtils;
import jalview.util.MapList;
import java.io.BufferedReader;
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;
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;
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();
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
{
- // BH 2019 never called?
- org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
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>()
- {
- @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();
- }
- };
++ List<Object> responses = (List<Object>) JSONUtils.parse(respons);
++ return new RvalsIterator(responses);
} 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
++class RvalsIterator implements Iterator<Reader>, AutoCloseable
+ {
- private Iterator rvals;
++ private Iterator<Object> rvals;
+
- protected RvalsIterator(JSONArray responses)
++ protected RvalsIterator(List<Object> responses)
+ {
+ this.rvals = responses.iterator();
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return rvals.hasNext();
+ }
+
+ @Override
+ public Reader next()
+ {
- JSONObject val = (JSONObject) rvals.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 instanceof JSONObject) ? ((JSONObject) sval).toString()
- : sval.toString());
-
++ return new StringReader(sval.toString());
+ }
+
+ @Override
+ public void remove()
+ {
- throw new Error(
- MessageManager.getString("error.not_implemented_remove"));
-
++ throw new UnsupportedOperationException();
+ }
+
+ @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);
++ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public void close()
+ {
+ while (rvals.hasNext())
+ {
+ rvals.next();
+ }
+ }
+ }
--- /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.isMac())
+ {
+ 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(jalviewDesktop.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.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)
{
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
-
- // TESTING code here
- boolean TESTING = true;
- if (TESTING)
+ lastSaveSuccessful = false;
+ }
+ else
+ {
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+ try
{
- out.print("; TESTSTART\n");
- int count = 20;
- for (int i = 0; i < count; i++)
- {
- // Thread.sleep(1000);
- out.println("; TEST: " + (count - 1 - i));
- }
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
+ PrintWriter out = new PrintWriter(
+ new FileWriter(tempFilePath));
-
+ 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() }));
+ lastSaveSuccessful = true;
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ ex.printStackTrace();
}
- out.print(output);
- if (TESTING)
+
+ if (doBackup)
{
- out.print("; TESTEND\n");
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
}
- out.close();
- 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();
-
}
- }
-
- 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())
- {
- 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())
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- 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(
});
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;
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.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
*/
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.UrlConstants;
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;
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;
- doVamsasClientCheck();
+ if (!Platform.isJS())
+ {
+ doVamsasClientCheck();
+ }
doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ /*
+ if (!Platform.isAMac())
+ {
+ // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
+ }
+ else
+ {
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ }
+ */
+
+ try
+ {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Exception e)
+ {
+ System.out.println("Exception when trying to set APQHandlers");
+ e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println("Throwable when trying to set APQHandlers");
+ t.printStackTrace();
+ }
+
+
+ addWindowListener(new WindowAdapter()
+ {
+
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
+
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
+
boolean showjconsole = jalview.bin.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);
- }
- jconsole = new Console(this, showjconsole);
- // add essential build information
- jconsole.setHeader(
- "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
- + "\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.getProperty("VERSION").equals("DEVELOPMENT")
- ? "\nJava path:"
- + System.getProperty(
- "java.home")
- + File.separator + "bin"
- + File.separator + "java"
- : "")
- );
-
- showConsole(showjconsole);
-
- showNews.setVisible(false);
-
- experimentalFeatures.setSelected(showExperimental());
-
- getIdentifiersOrgData();
-
- checkURLLinks();
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
+ }
+
+ 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"
+ + "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"));
++ + System.getProperty("os.version")
++ + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
++ ? "\nJava path:"
++ + System.getProperty(
++ "java.home")
++ + File.separator + "bin"
++ + File.separator + "java"
++ : ""));
+
+ showConsole(showjconsole);
+
+ showNews.setVisible(false);
+
+ experimentalFeatures.setSelected(showExperimental());
+
+ 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.
++ // 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);
- }
-
- });
}
/**
public void run()
{
Cache.log.debug("Starting news thread.");
-
jvnews = new BlogReader(me);
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
}
}
}).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();
}
}
private void doVamsasClientCheck()
{
- if (jalview.bin.Cache.vamsasJarsPresent())
+ if (Cache.vamsasJarsPresent())
{
setupVamsasDisconnectedGui();
VamsasMenu.setVisible(true);
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());
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)
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"));
}
/**
@Override
public void quit()
{
+ //System.out.println("********** Desktop.quit()");
+ //System.out.println(savingFiles.toString());
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
screen.width + "");
}
/**
- * 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());
}
}
*/
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()
// 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
// 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
*/
@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.
});
rthr.start();
}
-- };
++ }
});
VamsasStMenu.add(sessit);
}
@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
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;
}
/**
- * 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
} 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
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.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 JSlider slider = new JSlider();
+ JSlider slider = new JSlider();
- private JTextField thresholdValue = new JTextField(20);
+ JTextField thresholdValue = new JTextField(20);
private JCheckBox thresholdIsMin = new JCheckBox();
/*
* 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)
{
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
*/
- final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
- true, true);
+ JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
+ true);
String filterBy = setSelectedAttribute(attCombo, filter);
JComboBox<Condition> condCombo = new JComboBox<>();
|| (pattern != null && pattern.trim().length() > 0))
{
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 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,
fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
ap.paintAlignment(true, true);
- updateFiltersTab();
+ updateFiltersPanel();
}
}
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(
* 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
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)
/**
* 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);
/**
* 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");
* @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=GRCh38,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38";
+
+ private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
+
+ /*
* 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);
+ String ref = headerLine == null ? null : 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
{
VCFHeaderLine ref = header
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String vcfAssembly = ref.getValue();
+ String reference = 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)
+ {
+ reference = reference.toLowerCase();
+ vcfSpecies = DEFAULT_SPECIES;
+
+ /*
+ * 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;
+ }
+ }
+ }
+
+ 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 seqRef = seqCoords.getAssemblyId();
MapList map = seqCoords.getMap();
- 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();
*/
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');
+ 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");
.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);
}
});
+ Float specversion = Float.parseFloat(System.getProperty("java.specification.version"));
+
desktopMenubar.add(FileMenu);
desktopMenubar.add(toolsMenu);
VamsasMenu.setVisible(false);
VamsasMenu.add(vamsasImport);
VamsasMenu.add(vamsasSave);
VamsasMenu.add(vamsasStop);
- toolsMenu.add(preferences);
- if (!Platform.isJS())
- if (!Platform.isAMac() || specversion < 11)
++ if (!Platform.isMac() || 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.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
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('\\', '/');
++ 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()));
}
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();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- if (dbrefs[d].hasMap())
+ DBRefEntry ref = dbrefs.get(d);
+ dbref.setSource(ref.getSource());
+ dbref.setVersion(ref.getVersion());
+ dbref.setAccessionId(ref.getAccessionId());
+ if (ref.hasMap())
{
- Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
jds, recurse);
dbref.setMapping(mp);
}
* @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;
}
- @SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
- 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));
++ @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());
++ // 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;
- }
- }
++ 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;
++ }
+ }
- }
-
- @Override
- public String getFilename()
- {
- return file;
- }
- };
- }
/**
* 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);
- //
- // }
- //
++//
++// @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() ?
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.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);
+ }
- return isAMac.booleanValue();
+ /**
+ * 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 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)
- {
- return e.isControlDown();
- }
- // 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?
- }
- if (aMac)
++ if (aMac)
++ {
++ /*
++ * answer false for right mouse button
++ */
++ if (e.isPopupTrigger())
++ {
++ return false;
++ }
++ return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
++ & e.getModifiersEx()) != 0; // getModifiers()) != 0;
++ }
++ return e.isControlDown();
++ }
+
+ // 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)
{
- /*
- * answer false for right mouse button
- */
- if (e.isPopupTrigger())
+ 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()
- & e.getModifiersEx()) != 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;
}
- return e.isControlDown();
+ }
+
+ 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;
+ }
+ @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;
}
-
}
*
*/
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)
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)
{
git://source.jalview.org / jalview.git / commitdiff