--- /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
--- /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;
- }
+ }
* @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);
@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);
}
/**
// 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;
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
{
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";
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)
}
}
+
-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;
+ }
+
+ }
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
{
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();
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()
{
}
}
}).start();
-- ;
++
}
@Override
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
-- };
++ }
});
menuItem.addActionListener(new ActionListener()
});
rthr.start();
}
-- };
++ }
});
VamsasStMenu.add(sessit);
}
} catch (InterruptedException x)
{
}
-- ;
}
if (instance == null)
{
System.err.println(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
-- ;
}
} catch (Throwable ex)
{
|| (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
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);
// 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);
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
{
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);
*/
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);
+ }
}
git://source.jalview.org / jalview.git / commitdiff