JAL-3210 test commit

diff --git a/.classpath b/.classpath
deleted file mode 100644 (file)
index 7186f56..0000000
--- a/.classpath
+++ /dev/null
@@ -1,90 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <classpathentry kind="output" path="bin/default"/>
-       <classpathentry output="bin/main" kind="src" path="src">
-               <attributes>
-                       <attribute name="gradle_scope" value="main"/>
-                       <attribute name="gradle_used_by_scope" value=""/>
-               </attributes>
-       </classpathentry>
-       <classpathentry output="bin/test" kind="src" path="test">
-               <attributes>
-                       <attribute name="gradle_scope" value="test"/>
-                       <attribute name="gradle_used_by_scope" value=""/>
-                       <attribute name="test" value="true"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11/"/>
-       <classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
-       <classpathentry kind="output" path="bin/main"/>
-       <classpathentry kind="lib" path="help"/>
-       <classpathentry kind="lib" path="resources"/>
-       <classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.servlet-api-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/regex.jar"/>
-       <classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
-       <classpathentry kind="lib" path="j11lib/policy.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxb-api-java9.jar"/>
-       <classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.activation-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.7.jar"/>
-       <classpathentry kind="lib" path="j11lib/i4jruntime.jar"/>
-       <classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
-       <classpathentry kind="lib" path="j11lib/txw2.jar"/>
-       <classpathentry kind="lib" path="j11lib/jersey-json-1.19.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
-       <classpathentry kind="lib" path="j11lib/groovy-2.5.6.jar"/>
-       <classpathentry kind="lib" path="j11lib/Jmol-14.29.17-no_netscape.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxb-runtime.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
-       <classpathentry kind="lib" path="j11lib/slf4j-api-1.7.7.jar"/>
-       <classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
-       <classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
-       <classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
-       <classpathentry kind="lib" path="j11lib/stax-ex.jar"/>
-       <classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/libquaqua64-8.0.jnilib.jar"/>
-       <classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/jersey-client-1.19.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/jetty-io-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="j11lib/intervalstore-v1.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/groovy-console-2.5.6.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
-       <classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
-       <classpathentry kind="lib" path="j11lib/jersey-core-1.19.1.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/xercesImpl.jar"/>
-       <classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
-       <classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/log4j-to-slf4j-2.0-rc2.jar"/>
-       <classpathentry kind="lib" path="j11lib/wsdl4j-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/jhall.jar"/>
-       <classpathentry kind="lib" path="j11lib/stax2-api-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/axis.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.annotation-api-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/java-json.jar"/>
-       <classpathentry kind="lib" path="j11lib/mimepull.jar"/>
-       <classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/streambuffer.jar"/>
-       <classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
-       <classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
-</classpath>

diff --git a/.classpath.js b/.classpath.js
deleted file mode 100644 (file)
index 7186f56..0000000
--- a/.classpath.js
+++ /dev/null
@@ -1,90 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <classpathentry kind="output" path="bin/default"/>
-       <classpathentry output="bin/main" kind="src" path="src">
-               <attributes>
-                       <attribute name="gradle_scope" value="main"/>
-                       <attribute name="gradle_used_by_scope" value=""/>
-               </attributes>
-       </classpathentry>
-       <classpathentry output="bin/test" kind="src" path="test">
-               <attributes>
-                       <attribute name="gradle_scope" value="test"/>
-                       <attribute name="gradle_used_by_scope" value=""/>
-                       <attribute name="test" value="true"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11/"/>
-       <classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
-       <classpathentry kind="output" path="bin/main"/>
-       <classpathentry kind="lib" path="help"/>
-       <classpathentry kind="lib" path="resources"/>
-       <classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.servlet-api-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/regex.jar"/>
-       <classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
-       <classpathentry kind="lib" path="j11lib/policy.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxb-api-java9.jar"/>
-       <classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.activation-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.7.jar"/>
-       <classpathentry kind="lib" path="j11lib/i4jruntime.jar"/>
-       <classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
-       <classpathentry kind="lib" path="j11lib/txw2.jar"/>
-       <classpathentry kind="lib" path="j11lib/jersey-json-1.19.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
-       <classpathentry kind="lib" path="j11lib/groovy-2.5.6.jar"/>
-       <classpathentry kind="lib" path="j11lib/Jmol-14.29.17-no_netscape.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxb-runtime.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
-       <classpathentry kind="lib" path="j11lib/slf4j-api-1.7.7.jar"/>
-       <classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
-       <classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
-       <classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
-       <classpathentry kind="lib" path="j11lib/stax-ex.jar"/>
-       <classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/libquaqua64-8.0.jnilib.jar"/>
-       <classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/jersey-client-1.19.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/jetty-io-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="j11lib/intervalstore-v1.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/groovy-console-2.5.6.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
-       <classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
-       <classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
-       <classpathentry kind="lib" path="j11lib/jersey-core-1.19.1.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/xercesImpl.jar"/>
-       <classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
-       <classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
-       <classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.jar"/>
-       <classpathentry kind="lib" path="j11lib/log4j-to-slf4j-2.0-rc2.jar"/>
-       <classpathentry kind="lib" path="j11lib/wsdl4j-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/jhall.jar"/>
-       <classpathentry kind="lib" path="j11lib/stax2-api-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/axis.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
-       <classpathentry kind="lib" path="j11lib/javax.annotation-api-MODULE.jar"/>
-       <classpathentry kind="lib" path="j11lib/java-json.jar"/>
-       <classpathentry kind="lib" path="j11lib/mimepull.jar"/>
-       <classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
-       <classpathentry kind="lib" path="j11lib/streambuffer.jar"/>
-       <classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
-       <classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
-</classpath>

diff --git a/.gitignore b/.gitignore
index a2a64e7..46cc0e5 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -19,7 +19,7 @@ TESTNG
 /site
 /.gradle
 /build
-/utils/HelpLinksChecker.out
+/utils/HelpLinksChecker.touch
 /getdown/website
 /getdown/full_app
 /getdown/files
@@ -29,3 +29,4 @@ TESTNG
 /utils/install4j/jalview-installers-*.install4j
 *.swp
 /bin
+/doc/building.html

diff --git a/.project b/.project
deleted file mode 100644 (file)
index 0e79b2b..0000000
--- a/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-       <name>jalview-js</name>
-       <comment></comment>
-       <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/>
-               </buildCommand>
-               <buildCommand>
-                       <name>org.eclipse.buildship.core.gradleprojectbuilder</name>
-                       <arguments/>
-               </buildCommand>
-       </buildSpec>
-       <linkedResources/>
-       <filteredResources/>
-</projectDescription>

diff --git a/.settings/org.eclipse.buildship.core.prefs b/.settings/org.eclipse.buildship.core.prefs
deleted file mode 100644 (file)
index e889521..0000000
--- a/.settings/org.eclipse.buildship.core.prefs
+++ /dev/null
@@ -1,2 +0,0 @@
-connection.project.dir=
-eclipse.preferences.version=1

diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
deleted file mode 100644 (file)
index 6df8729..0000000
--- a/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,299 +0,0 @@
-#
-#Mon Aug 12 14:34:05 BST 2019
-org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration=insert
-org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries=true
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters=insert
-org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter=insert
-org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while=do not insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration=do not insert
-org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags=insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws=do not insert
-org.eclipse.jdt.core.formatter.comment.format_javadoc_comments=true
-org.eclipse.jdt.core.formatter.indentation.size=8
-org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments=insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments=insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for=insert
-org.eclipse.jdt.core.formatter.disabling_tag=@formatter\:off
-org.eclipse.jdt.core.formatter.continuation_indentation=4
-org.eclipse.jdt.core.formatter.blank_lines_before_imports=1
-org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16
-org.eclipse.jdt.core.formatter.blank_lines_after_package=1
-org.eclipse.jdt.core.formatter.insert_space_after_binary_operator=insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations=insert
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=16
-org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference=do not insert
-org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
-org.eclipse.jdt.core.formatter.comment.indent_root_tags=true
-org.eclipse.jdt.core.formatter.enabling_tag=@formatter\:on
-org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block=insert
-org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return=insert
-org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
-org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert
-org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments=insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=insert
-org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer=insert
-org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations=1
-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression=do not insert
-org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter=insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits=insert
-org.eclipse.jdt.core.formatter.indent_statements_compare_to_block=true
-org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration=next_line
-org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch=insert
-org.eclipse.jdt.core.formatter.comment.line_length=80
-org.eclipse.jdt.core.formatter.use_on_off_tags=true
-org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant=insert
-org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for=do not insert
-org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments=false
-org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
-org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=next_line
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation=do not insert
-org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
-org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for=insert
-org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
-org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments=insert
-org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
-org.eclipse.jdt.core.formatter.alignment_for_binary_expression=16
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference=insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations=insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation=do not insert
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call=16
-org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header=true
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-org.eclipse.jdt.core.formatter.compact_else_if=true
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters=do not insert
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-org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
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-org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter=insert
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-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
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-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch=do not insert
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-org.eclipse.jdt.core.formatter.join_wrapped_lines=true
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-org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries=true
-org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration=next_line
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for=insert
-org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
-org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
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-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=do not insert
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-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer=insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_try=do not insert
-org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
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-org.eclipse.jdt.core.formatter.blank_lines_before_field=1
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-org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer=2
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-org.eclipse.jdt.core.formatter.comment.format_html=true
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-org.eclipse.jdt.core.formatter.indent_empty_lines=false
-eclipse.preferences.version=1
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_unary_operator=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations=do not insert
-org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=true
-org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
-org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=insert
-org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator=insert
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-org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk=1
-org.eclipse.jdt.core.formatter.insert_new_line_after_label=do not insert
-org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header=true
-org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference=do not insert
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-org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression=16
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-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert
-org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases=true
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if=do not insert
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-org.eclipse.jdt.core.formatter.comment.format_block_comments=false
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-org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
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-org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert
-org.eclipse.jdt.core.compiler.compliance=11
-org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert
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-org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case=do not insert
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-org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference=do not insert
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-org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
-org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast=insert
-org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line
-org.eclipse.jdt.core.formatter.brace_position_for_enum_constant=next_line
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-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for=insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized=insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments=do not insert
-org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation=do not insert
-org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters=do not insert
-org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header=true
-org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow=insert
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-org.eclipse.jdt.core.formatter.join_lines_in_comments=true
-org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters=do not insert
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-org.eclipse.jdt.core.formatter.comment.indent_parameter_description=true
-org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert
-org.eclipse.jdt.core.formatter.tabulation.char=space
-org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations=do not insert
-org.eclipse.jdt.core.formatter.blank_lines_between_import_groups=1
-org.eclipse.jdt.core.formatter.lineSplit=76
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diff --git a/.settings/org.eclipse.jdt.groovy.core.prefs b/.settings/org.eclipse.jdt.groovy.core.prefs
deleted file mode 100644 (file)
index 74af1ba..0000000
--- a/.settings/org.eclipse.jdt.groovy.core.prefs
+++ /dev/null
@@ -1,2 +0,0 @@
-eclipse.preferences.version=1
-groovy.compiler.level=25

diff --git a/.settings/org.eclipse.jdt.ui.prefs b/.settings/org.eclipse.jdt.ui.prefs
deleted file mode 100644 (file)
index ed6a53d..0000000
--- a/.settings/org.eclipse.jdt.ui.prefs
+++ /dev/null
@@ -1,68 +0,0 @@
-eclipse.preferences.version=1
-editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
-formatter_profile=_Jalview
-formatter_settings_version=16
-org.eclipse.jdt.ui.ignorelowercasenames=true
-org.eclipse.jdt.ui.importorder=jalview;java;javax;org;com;
-org.eclipse.jdt.ui.ondemandthreshold=99
-org.eclipse.jdt.ui.staticondemandthreshold=99
-sp_cleanup.add_default_serial_version_id=true
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-sp_cleanup.add_missing_methods=false
-sp_cleanup.add_missing_nls_tags=false
-sp_cleanup.add_missing_override_annotations=true
-sp_cleanup.add_missing_override_annotations_interface_methods=true
-sp_cleanup.add_serial_version_id=false
-sp_cleanup.always_use_blocks=true
-sp_cleanup.always_use_parentheses_in_expressions=false
-sp_cleanup.always_use_this_for_non_static_field_access=false
-sp_cleanup.always_use_this_for_non_static_method_access=false
-sp_cleanup.convert_functional_interfaces=false
-sp_cleanup.convert_to_enhanced_for_loop=false
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-sp_cleanup.format_source_code=true
-sp_cleanup.format_source_code_changes_only=true
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-sp_cleanup.make_local_variable_final=true
-sp_cleanup.make_parameters_final=false
-sp_cleanup.make_private_fields_final=true
-sp_cleanup.make_type_abstract_if_missing_method=false
-sp_cleanup.make_variable_declarations_final=false
-sp_cleanup.never_use_blocks=false
-sp_cleanup.never_use_parentheses_in_expressions=true
-sp_cleanup.on_save_use_additional_actions=true
-sp_cleanup.organize_imports=true
-sp_cleanup.qualify_static_field_accesses_with_declaring_class=false
-sp_cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true
-sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true
-sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
-sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
-sp_cleanup.remove_private_constructors=true
-sp_cleanup.remove_redundant_modifiers=false
-sp_cleanup.remove_redundant_semicolons=true
-sp_cleanup.remove_redundant_type_arguments=true
-sp_cleanup.remove_trailing_whitespaces=false
-sp_cleanup.remove_trailing_whitespaces_all=true
-sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
-sp_cleanup.remove_unnecessary_casts=true
-sp_cleanup.remove_unnecessary_nls_tags=false
-sp_cleanup.remove_unused_imports=true
-sp_cleanup.remove_unused_local_variables=false
-sp_cleanup.remove_unused_private_fields=true
-sp_cleanup.remove_unused_private_members=false
-sp_cleanup.remove_unused_private_methods=true
-sp_cleanup.remove_unused_private_types=true
-sp_cleanup.sort_members=false
-sp_cleanup.sort_members_all=false
-sp_cleanup.use_anonymous_class_creation=false
-sp_cleanup.use_blocks=true
-sp_cleanup.use_blocks_only_for_return_and_throw=false
-sp_cleanup.use_lambda=true
-sp_cleanup.use_parentheses_in_expressions=false
-sp_cleanup.use_this_for_non_static_field_access=false
-sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
-sp_cleanup.use_this_for_non_static_method_access=false
-sp_cleanup.use_this_for_non_static_method_access_only_if_necessary=true
-sp_cleanup.use_type_arguments=false