From a944dbc2b3c42f94c3e0c4c4dcb5bad1fe49f1cb Mon Sep 17 00:00:00 2001 From: hansonr Date: Wed, 17 Oct 2018 12:17:05 -0500 Subject: [PATCH] nonfunctional testing directory - just so I can see how it compiles. --- .project | 2 +- .settings/org.eclipse.jdt.core.prefs | 285 +- .settings/org.eclipse.jdt.ui.prefs | 62 +- .../xml/binding/jalviewBH/JalviewModel.java | 5241 ++++++++++++++++++++ src/jalview/xml/binding/jalviewBH/SequenceSet.java | 324 ++ src/jalview/xml/binding/jalviewBH/VAMSAS.java | 109 + 6 files changed, 5677 insertions(+), 346 deletions(-) create mode 100644 src/jalview/xml/binding/jalviewBH/JalviewModel.java create mode 100644 src/jalview/xml/binding/jalviewBH/SequenceSet.java create mode 100644 src/jalview/xml/binding/jalviewBH/VAMSAS.java diff --git a/.project b/.project index d0dfc7e..6c40472 100644 --- a/.project +++ b/.project @@ -1,6 +1,6 @@ - Jalview Release 2.7 + Jalview Release 2.7-old diff --git a/.settings/org.eclipse.jdt.core.prefs 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-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_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.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_binary_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 diff --git a/.settings/org.eclipse.jdt.ui.prefs b/.settings/org.eclipse.jdt.ui.prefs index 2de9ab9..2b24877 100644 --- a/.settings/org.eclipse.jdt.ui.prefs +++ b/.settings/org.eclipse.jdt.ui.prefs @@ -1,67 +1,7 @@ eclipse.preferences.version=1 -editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true -formatter_profile=_Jalview -formatter_settings_version=12 +formatter_settings_version=14 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 -sp_cleanup.add_generated_serial_version_id=false -sp_cleanup.add_missing_annotations=true -sp_cleanup.add_missing_deprecated_annotations=true -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 -sp_cleanup.correct_indentation=false -sp_cleanup.format_source_code=true -sp_cleanup.format_source_code_changes_only=true -sp_cleanup.insert_inferred_type_arguments=false -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=false -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_type_arguments=false -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=false -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=false -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 diff --git a/src/jalview/xml/binding/jalviewBH/JalviewModel.java b/src/jalview/xml/binding/jalviewBH/JalviewModel.java new file mode 100644 index 0000000..413c3dd --- /dev/null +++ b/src/jalview/xml/binding/jalviewBH/JalviewModel.java @@ -0,0 +1,5241 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 04:36:20 PM BST +// + +package jalview.xml.binding.jalviewBH; + +import jalview.schemabinding.version2.AnnotationColourScheme; +import jalview.schemabinding.version2.WebServiceParameterSet; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlID; +import javax.xml.bind.annotation.XmlSchemaType; +import javax.xml.bind.annotation.XmlType; +import javax.xml.bind.annotation.XmlValue; +import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; +import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +import javax.xml.datatype.XMLGregorianCalendar; + +/** + *

+ * Java class for JalviewModel complex type. + * + *

+ * The following schema fragment specifies the expected content contained within + * this class. + * + * 

+ * <complexType name="JalviewModel">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         <sequence>
+ *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org}pdbentry">
+ *                             <sequence>
+ *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 <complexType>
+ *                                   <simpleContent>
+ *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </extension>
+ *                                   </simpleContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 <complexType>
+ *                                   <complexContent>
+ *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </restriction>
+ *                                   </complexContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                             <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   </sequence>
+ *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   </sequence>
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence minOccurs="0">
+ *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="FeatureSettings" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             </sequence>
+ *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *         </sequence>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType( + name = "JalviewModel", + namespace = "www.jalview.org", + propOrder = + { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport", + "userColours", "tree", "featureSettings" }) +public class JalviewModel +{ + + @XmlElement(required = true) + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar creationDate; + + @XmlElement(required = true) + protected String version; + + @XmlElement(required = true) + protected VAMSAS vamsasModel; + + @XmlElement(name = "JSeq") + protected List jSeq; + + @XmlElement(name = "JGroup") + protected List jGroup; + + @XmlElement(name = "Viewport") + protected List viewport; + + @XmlElement(name = "UserColours") + protected List userColours; + + protected List tree; + + + @XmlElement(nillable=true) + protected String bhTest = "bhtest"; + + @XmlElement(name = "FeatureSettings") + protected JalviewModel.FeatureSettings featureSettings; + + /** + * Gets the value of the creationDate property. + * + * @return possible object is {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getCreationDate() + { + return creationDate; + } + + /** + * Sets the value of the creationDate property. + * + * @param value + * allowed object is {@link XMLGregorianCalendar } + * + */ + public void setCreationDate(XMLGregorianCalendar value) + { + this.creationDate = value; + } + + /** + * Gets the value of the version property. + * + * @return possible object is {@link String } + * + */ + public String getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setVersion(String value) + { + this.version = value; + } + + /** + * Gets the value of the vamsasModel property. + * + * @return possible object is {@link VAMSAS } + * + */ + public VAMSAS getVamsasModel() + { + return vamsasModel; + } + + /** + * Sets the value of the vamsasModel property. + * + * @param value + * allowed object is {@link VAMSAS } + * + */ + public void setVamsasModel(VAMSAS value) + { + this.vamsasModel = value; + } + + /** + * Gets the value of the jSeq property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the jSeq property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+   * getJSeq().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq } + * + * + */ + public List getJSeq() + { + if (jSeq == null) + { + jSeq = new ArrayList(); + } + return this.jSeq; + } + + /** + * Gets the value of the jGroup property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the jGroup property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+   * getJGroup().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JGroup } + * + * + */ + public List getJGroup() + { + if (jGroup == null) + { + jGroup = new ArrayList(); + } + return this.jGroup; + } + + /** + * Gets the value of the viewport property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the viewport property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+   * getViewport().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport } + * + * + */ + public List getViewport() + { + if (viewport == null) + { + viewport = new ArrayList(); + } + return this.viewport; + } + + /** + * Gets the value of the userColours property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the userColours property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+   * getUserColours().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.UserColours } + * + * + */ + public List getUserColours() + { + if (userColours == null) + { + userColours = new ArrayList(); + } + return this.userColours; + } + + /** + * Gets the value of the tree property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the tree property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+   * getTree().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Tree } + * + * + */ + public List getTree() + { + if (tree == null) + { + tree = new ArrayList(); + } + return this.tree; + } + + /** + * Gets the value of the featureSettings property. + * + * @return possible object is {@link JalviewModel.FeatureSettings } + * + */ + public JalviewModel.FeatureSettings getFeatureSettings() + { + return featureSettings; + } + + /** + * Sets the value of the featureSettings property. + * + * @param value + * allowed object is {@link JalviewModel.FeatureSettings } + * + */ + public void setFeatureSettings(JalviewModel.FeatureSettings value) + { + this.featureSettings = value; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+   *                 </sequence>
+   *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "setting", "group" }) + public static class FeatureSettings + { + + @XmlElement(namespace = "www.jalview.org") + protected List setting; + + @XmlElement(namespace = "www.jalview.org") + protected List group; + + /** + * Gets the value of the setting property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the setting property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getSetting().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.FeatureSettings.Setting } + * + * + */ + public List getSetting() + { + if (setting == null) + { + setting = new ArrayList(); + } + return this.setting; + } + + /** + * Gets the value of the group property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the group property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getGroup().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.FeatureSettings.Group } + * + * + */ + public List getGroup() + { + if (group == null) + { + group = new ArrayList(); + } + return this.group; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Group + { + + @XmlAttribute(name = "name", required = true) + protected String name; + + @XmlAttribute(name = "display", required = true) + protected boolean display; + + /** + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setName(String value) + { + this.name = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() + { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) + { + this.display = value; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "attributeName", "matcherSet" }) + public static class Setting + { + + @XmlElement(namespace = "www.jalview.org") + protected List attributeName; + + @XmlElement(namespace = "www.jalview.org") + protected Object/*FeatureMatcherSet*/ matcherSet; + + @XmlAttribute(name = "type", required = true) + protected String type; + + @XmlAttribute(name = "colour", required = true) + protected int colour; + + @XmlAttribute(name = "display", required = true) + protected boolean display; + + @XmlAttribute(name = "order") + protected Float order; + + @XmlAttribute(name = "mincolour") + protected Integer mincolour; + + @XmlAttribute(name = "noValueColour") + protected Object/*NoValueColour*/ noValueColour; + + @XmlAttribute(name = "threshold") + protected Float threshold; + + @XmlAttribute(name = "threshstate") + protected Integer threshstate; + + @XmlAttribute(name = "max") + protected Float max; + + @XmlAttribute(name = "min") + protected Float min; + + @XmlAttribute(name = "colourByLabel") + protected Boolean colourByLabel; + + @XmlAttribute(name = "autoScale") + protected Boolean autoScale; + + /** + * Gets the value of the attributeName property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the attributeName property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+       * getAttributeName().add(newItem);
+       *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link String + * } + * + * + */ + public List getAttributeName() + { + if (attributeName == null) + { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Gets the value of the matcherSet property. + * + * @return possible object is {@link FeatureMatcherSet } + * + */ + public Object/*FeatureMatcherSet*/ getMatcherSet() + { + return matcherSet; + } + + /** + * Sets the value of the matcherSet property. + * + * @param value + * allowed object is {@link FeatureMatcherSet } + * + */ + public void setMatcherSet(Object/*FeatureMatcherSet*/ value) + { + this.matcherSet = value; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } + + /** + * Gets the value of the colour property. + * + */ + public int getColour() + { + return colour; + } + + /** + * Sets the value of the colour property. + * + */ + public void setColour(int value) + { + this.colour = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() + { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) + { + this.display = value; + } + + /** + * Gets the value of the order property. + * + * @return possible object is {@link Float } + * + */ + public Float getOrder() + { + return order; + } + + /** + * Sets the value of the order property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setOrder(Float value) + { + this.order = value; + } + + /** + * Gets the value of the mincolour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getMincolour() + { + return mincolour; + } + + /** + * Sets the value of the mincolour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setMincolour(Integer value) + { + this.mincolour = value; + } + + /** + * Gets the value of the noValueColour property. + * + * @return possible object is {@link NoValueColour } + * + */ + public Object/*NoValueColour*/ getNoValueColour() + { + if (noValueColour == null) + { + return null/* NoValueColour */;// NoValueColour.MIN; + } + else + { + return noValueColour; + } + } + + /** + * Sets the value of the noValueColour property. + * + * @param value + * allowed object is {@link NoValueColour } + * + */ + public void setNoValueColour(Object/*NoValueColour*/ value) + { + this.noValueColour = value; + } + + /** + * Gets the value of the threshold property. + * + * @return possible object is {@link Float } + * + */ + public Float getThreshold() + { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setThreshold(Float value) + { + this.threshold = value; + } + + /** + * Gets the value of the threshstate property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getThreshstate() + { + return threshstate; + } + + /** + * Sets the value of the threshstate property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setThreshstate(Integer value) + { + this.threshstate = value; + } + + /** + * Gets the value of the max property. + * + * @return possible object is {@link Float } + * + */ + public Float getMax() + { + return max; + } + + /** + * Sets the value of the max property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMax(Float value) + { + this.max = value; + } + + /** + * Gets the value of the min property. + * + * @return possible object is {@link Float } + * + */ + public Float getMin() + { + return min; + } + + /** + * Sets the value of the min property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMin(Float value) + { + this.min = value; + } + + /** + * Gets the value of the colourByLabel property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isColourByLabel() + { + return colourByLabel; + } + + /** + * Sets the value of the colourByLabel property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourByLabel(Boolean value) + { + this.colourByLabel = value; + } + + /** + * Gets the value of the autoScale property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isAutoScale() + { + return autoScale; + } + + /** + * Sets the value of the autoScale property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setAutoScale(Boolean value) + { + this.autoScale = value; + } + + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "seq", "annotationColours" }) + public static class JGroup + { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List seq; + + @XmlElement(namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + + @XmlAttribute(name = "start") + protected Integer start; + + @XmlAttribute(name = "end") + protected Integer end; + + @XmlAttribute(name = "name") + protected String name; + + @XmlAttribute(name = "colour") + protected String colour; + + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + + @XmlAttribute(name = "outlineColour") + protected Integer outlineColour; + + @XmlAttribute(name = "displayBoxes") + protected Boolean displayBoxes; + + @XmlAttribute(name = "displayText") + protected Boolean displayText; + + @XmlAttribute(name = "colourText") + protected Boolean colourText; + + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + + @XmlAttribute(name = "id") + protected String id; + + /** + * Gets the value of the seq property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the seq property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getSeq().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getSeq() + { + if (seq == null) + { + seq = new ArrayList(); + } + return this.seq; + } + + /** + * Gets the value of the annotationColours property. + * + * @return possible object is {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() + { + return annotationColours; + } + + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) + { + this.annotationColours = value; + } + + /** + * Gets the value of the start property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStart() + { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStart(Integer value) + { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setEnd(Integer value) + { + this.end = value; + } + + /** + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setName(String value) + { + this.name = value; + } + + /** + * Gets the value of the colour property. + * + * @return possible object is {@link String } + * + */ + public String getColour() + { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setColour(String value) + { + this.colour = value; + } + + /** + * Gets the value of the consThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getConsThreshold() + { + return consThreshold; + } + + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setConsThreshold(Integer value) + { + this.consThreshold = value; + } + + /** + * Gets the value of the pidThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getPidThreshold() + { + return pidThreshold; + } + + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setPidThreshold(Integer value) + { + this.pidThreshold = value; + } + + /** + * Gets the value of the outlineColour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getOutlineColour() + { + return outlineColour; + } + + /** + * Sets the value of the outlineColour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setOutlineColour(Integer value) + { + this.outlineColour = value; + } + + /** + * Gets the value of the displayBoxes property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isDisplayBoxes() + { + return displayBoxes; + } + + /** + * Sets the value of the displayBoxes property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setDisplayBoxes(Boolean value) + { + this.displayBoxes = value; + } + + /** + * Gets the value of the displayText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isDisplayText() + { + return displayText; + } + + /** + * Sets the value of the displayText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setDisplayText(Boolean value) + { + this.displayText = value; + } + + /** + * Gets the value of the colourText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isColourText() + { + return colourText; + } + + /** + * Sets the value of the colourText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourText(Boolean value) + { + this.colourText = value; + } + + /** + * Gets the value of the textCol1 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol1() + { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol1(Integer value) + { + this.textCol1 = value; + } + + /** + * Gets the value of the textCol2 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol2() + { + return textCol2; + } + + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol2(Integer value) + { + this.textCol2 = value; + } + + /** + * Gets the value of the textColThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextColThreshold() + { + return textColThreshold; + } + + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextColThreshold(Integer value) + { + this.textColThreshold = value; + } + + /** + * Gets the value of the showUnconserved property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowUnconserved() + { + return showUnconserved; + } + + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) + { + this.showUnconserved = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() + { + if (ignoreGapsinConsensus == null) + { + return true; + } + else + { + return ignoreGapsinConsensus; + } + } + + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) + { + this.ignoreGapsinConsensus = value; + } + + /** + * Gets the value of the showConsensusHistogram property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() + { + if (showConsensusHistogram == null) + { + return true; + } + else + { + return showConsensusHistogram; + } + } + + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) + { + this.showConsensusHistogram = value; + } + + /** + * Gets the value of the showSequenceLogo property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowSequenceLogo() + { + if (showSequenceLogo == null) + { + return false; + } + else + { + return showSequenceLogo; + } + } + + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) + { + this.showSequenceLogo = value; + } + + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() + { + if (normaliseSequenceLogo == null) + { + return false; + } + else + { + return normaliseSequenceLogo; + } + } + + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) + { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org}pdbentry">
+   *                 <sequence>
+   *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+   *                     <complexType>
+   *                       <simpleContent>
+   *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         </extension>
+   *                       </simpleContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="secondaryStructure" maxOccurs="unbounded">
+   *                     <complexType>
+   *                       <complexContent>
+   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         </restriction>
+   *                       </complexContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "features", "pdbids", "hiddenSequences", "rnaViewer" }) + public static class JSeq + { + + @XmlElement(namespace = "www.jalview.org") + protected List features; + + @XmlElement(namespace = "www.jalview.org") + protected List pdbids; + + @XmlElement(namespace = "www.jalview.org", type = Integer.class) + protected List hiddenSequences; + + @XmlElement(namespace = "www.jalview.org") + protected List rnaViewer; + + @XmlAttribute(name = "colour") + protected Integer colour; + + @XmlAttribute(name = "start", required = true) + protected int start; + + @XmlAttribute(name = "end", required = true) + protected int end; + + @XmlAttribute(name = "id", required = true) + protected String id; + + @XmlAttribute(name = "hidden") + protected Boolean hidden; + + @XmlAttribute(name = "viewreference") + protected Boolean viewreference; + + /** + * Gets the value of the features property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the features property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getFeatures().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link Feature } + * + * + */ + public List getFeatures() + { + if (features == null) + { + features = new ArrayList(); + } + return this.features; + } + + /** + * Gets the value of the pdbids property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the pdbids property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getPdbids().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.Pdbids } + * + * + */ + public List getPdbids() + { + if (pdbids == null) + { + pdbids = new ArrayList(); + } + return this.pdbids; + } + + /** + * Gets the value of the hiddenSequences property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the hiddenSequences property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getHiddenSequences().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getHiddenSequences() + { + if (hiddenSequences == null) + { + hiddenSequences = new ArrayList(); + } + return this.hiddenSequences; + } + + /** + * Gets the value of the rnaViewer property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the rnaViewer property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getRnaViewer().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.RnaViewer } + * + * + */ + public List getRnaViewer() + { + if (rnaViewer == null) + { + rnaViewer = new ArrayList(); + } + return this.rnaViewer; + } + + /** + * Gets the value of the colour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getColour() + { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setColour(Integer value) + { + this.colour = value; + } + + /** + * Gets the value of the start property. + * + */ + public int getStart() + { + return start; + } + + /** + * Sets the value of the start property. + * + */ + public void setStart(int value) + { + this.start = value; + } + + /** + * Gets the value of the end property. + * + */ + public int getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) + { + this.end = value; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + /** + * Gets the value of the hidden property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isHidden() + { + return hidden; + } + + /** + * Sets the value of the hidden property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setHidden(Boolean value) + { + this.hidden = value; + } + + /** + * Gets the value of the viewreference property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isViewreference() + { + return viewreference; + } + + /** + * Sets the value of the viewreference property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setViewreference(Boolean value) + { + this.viewreference = value; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <extension base="{www.jalview.org}pdbentry">
+     *       <sequence>
+     *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <simpleContent>
+     *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </extension>
+     *             </simpleContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </extension>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "structureState" }) + public static class Pdbids //extends Pdbentry + { + + @XmlElement(namespace = "www.jalview.org") + protected List structureState; + + /** + * Gets the value of the structureState property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the structureState property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+       * getStructureState().add(newItem);
+       *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.Pdbids.StructureState } + * + * + */ + public List getStructureState() + { + if (structureState == null) + { + structureState = new ArrayList(); + } + return this.structureState; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+       * <complexType>
+       *   <simpleContent>
+       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+       *       <attGroup ref="{www.jalview.org}swingwindow"/>
+       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </extension>
+       *   </simpleContent>
+       * </complexType>
+       *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class StructureState + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "visible") + protected Boolean visible; + + @XmlAttribute(name = "viewId") + protected String viewId; + + @XmlAttribute(name = "alignwithAlignPanel") + protected Boolean alignwithAlignPanel; + + @XmlAttribute(name = "colourwithAlignPanel") + protected Boolean colourwithAlignPanel; + + @XmlAttribute(name = "colourByJmol") + protected Boolean colourByJmol; + + @XmlAttribute(name = "type") + protected String type; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } + + /** + * Gets the value of the visible property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isVisible() + { + return visible; + } + + /** + * Sets the value of the visible property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setVisible(Boolean value) + { + this.visible = value; + } + + /** + * Gets the value of the viewId property. + * + * @return possible object is {@link String } + * + */ + public String getViewId() + { + return viewId; + } + + /** + * Sets the value of the viewId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setViewId(String value) + { + this.viewId = value; + } + + /** + * Gets the value of the alignwithAlignPanel property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isAlignwithAlignPanel() + { + if (alignwithAlignPanel == null) + { + return true; + } + else + { + return alignwithAlignPanel; + } + } + + /** + * Sets the value of the alignwithAlignPanel property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setAlignwithAlignPanel(Boolean value) + { + this.alignwithAlignPanel = value; + } + + /** + * Gets the value of the colourwithAlignPanel property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isColourwithAlignPanel() + { + if (colourwithAlignPanel == null) + { + return false; + } + else + { + return colourwithAlignPanel; + } + } + + /** + * Sets the value of the colourwithAlignPanel property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourwithAlignPanel(Boolean value) + { + this.colourwithAlignPanel = value; + } + + /** + * Gets the value of the colourByJmol property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isColourByJmol() + { + if (colourByJmol == null) + { + return true; + } + else + { + return colourByJmol; + } + } + + /** + * Sets the value of the colourByJmol property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourByJmol(Boolean value) + { + this.colourByJmol = value; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } + + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } + + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="secondaryStructure" maxOccurs="unbounded">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "secondaryStructure" }) + public static class RnaViewer + { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List secondaryStructure; + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "viewId") + protected String viewId; + + @XmlAttribute(name = "dividerLocation") + protected Integer dividerLocation; + + @XmlAttribute(name = "selectedRna") + protected Integer selectedRna; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the secondaryStructure property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the secondaryStructure property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+       * getSecondaryStructure().add(newItem);
+       *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } + * + * + */ + public List getSecondaryStructure() + { + if (secondaryStructure == null) + { + secondaryStructure = new ArrayList(); + } + return this.secondaryStructure; + } + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the viewId property. + * + * @return possible object is {@link String } + * + */ + public String getViewId() + { + return viewId; + } + + /** + * Sets the value of the viewId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setViewId(String value) + { + this.viewId = value; + } + + /** + * Gets the value of the dividerLocation property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getDividerLocation() + { + return dividerLocation; + } + + /** + * Sets the value of the dividerLocation property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setDividerLocation(Integer value) + { + this.dividerLocation = value; + } + + /** + * Gets the value of the selectedRna property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getSelectedRna() + { + return selectedRna; + } + + /** + * Sets the value of the selectedRna property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setSelectedRna(Integer value) + { + this.selectedRna = value; + } + + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+       * <complexType>
+       *   <complexContent>
+       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </restriction>
+       *   </complexContent>
+       * </complexType>
+       *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SecondaryStructure + { + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "annotationId", required = true) + protected String annotationId; + + @XmlAttribute(name = "gapped") + protected Boolean gapped; + + @XmlAttribute(name = "viewerState") + protected String viewerState; + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the annotationId property. + * + * @return possible object is {@link String } + * + */ + public String getAnnotationId() + { + return annotationId; + } + + /** + * Sets the value of the annotationId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setAnnotationId(String value) + { + this.annotationId = value; + } + + /** + * Gets the value of the gapped property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isGapped() + { + return gapped; + } + + /** + * Sets the value of the gapped property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setGapped(Boolean value) + { + this.gapped = value; + } + + /** + * Gets the value of the viewerState property. + * + * @return possible object is {@link String } + * + */ + public String getViewerState() + { + return viewerState; + } + + /** + * Sets the value of the viewerState property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setViewerState(String value) + { + this.viewerState = value; + } + + } + + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence minOccurs="0">
+   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "title", "newick" }) + public static class Tree + { + + @XmlElement(namespace = "www.jalview.org") + protected String title; + + @XmlElement(namespace = "www.jalview.org") + protected String newick; + + @XmlAttribute(name = "fontName") + protected String fontName; + + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + + @XmlAttribute(name = "threshold") + protected Float threshold; + + @XmlAttribute(name = "showBootstrap") + protected Boolean showBootstrap; + + @XmlAttribute(name = "showDistances") + protected Boolean showDistances; + + @XmlAttribute(name = "markUnlinked") + protected Boolean markUnlinked; + + @XmlAttribute(name = "fitToWindow") + protected Boolean fitToWindow; + + @XmlAttribute(name = "currentTree") + protected Boolean currentTree; + + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the newick property. + * + * @return possible object is {@link String } + * + */ + public String getNewick() + { + return newick; + } + + /** + * Sets the value of the newick property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setNewick(String value) + { + this.newick = value; + } + + /** + * Gets the value of the fontName property. + * + * @return possible object is {@link String } + * + */ + public String getFontName() + { + return fontName; + } + + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFontName(String value) + { + this.fontName = value; + } + + /** + * Gets the value of the fontSize property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontSize() + { + return fontSize; + } + + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontSize(Integer value) + { + this.fontSize = value; + } + + /** + * Gets the value of the fontStyle property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontStyle() + { + return fontStyle; + } + + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontStyle(Integer value) + { + this.fontStyle = value; + } + + /** + * Gets the value of the threshold property. + * + * @return possible object is {@link Float } + * + */ + public Float getThreshold() + { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setThreshold(Float value) + { + this.threshold = value; + } + + /** + * Gets the value of the showBootstrap property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowBootstrap() + { + return showBootstrap; + } + + /** + * Sets the value of the showBootstrap property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowBootstrap(Boolean value) + { + this.showBootstrap = value; + } + + /** + * Gets the value of the showDistances property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowDistances() + { + return showDistances; + } + + /** + * Sets the value of the showDistances property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowDistances(Boolean value) + { + this.showDistances = value; + } + + /** + * Gets the value of the markUnlinked property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isMarkUnlinked() + { + return markUnlinked; + } + + /** + * Sets the value of the markUnlinked property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setMarkUnlinked(Boolean value) + { + this.markUnlinked = value; + } + + /** + * Gets the value of the fitToWindow property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isFitToWindow() + { + return fitToWindow; + } + + /** + * Sets the value of the fitToWindow property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFitToWindow(Boolean value) + { + this.fitToWindow = value; + } + + /** + * Gets the value of the currentTree property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isCurrentTree() + { + return currentTree; + } + + /** + * Sets the value of the currentTree property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCurrentTree(Boolean value) + { + this.currentTree = value; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+   *       </sequence>
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "userColourScheme" }) + public static class UserColours + { + + @XmlElement( + name = "UserColourScheme", + namespace = "www.jalview.org", + required = true) + protected Object/*JalviewUserColours*/ userColourScheme; + + @XmlAttribute(name = "id") + protected String id; + + /** + * Gets the value of the userColourScheme property. + * + * @return possible object is {@link JalviewUserColours } + * + */ + public Object/*JalviewUserColours*/ getUserColourScheme() + { + return userColourScheme; + } + + /** + * Sets the value of the userColourScheme property. + * + * @param value + * allowed object is {@link JalviewUserColours } + * + */ + public void setUserColourScheme(Object/*JalviewUserColours*/ value) + { + this.userColourScheme = value; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+   *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "annotationColours", "hiddenColumns", "calcIdParam" }) + public static class Viewport + { + + @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + + @XmlElement(namespace = "www.jalview.org") + protected List hiddenColumns; + + @XmlElement(namespace = "www.jalview.org") + protected List calcIdParam; + + @XmlAttribute(name = "conservationSelected") + protected Boolean conservationSelected; + + @XmlAttribute(name = "pidSelected") + protected Boolean pidSelected; + + @XmlAttribute(name = "bgColour") + protected String bgColour; + + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "showFullId") + protected Boolean showFullId; + + @XmlAttribute(name = "rightAlignIds") + protected Boolean rightAlignIds; + + @XmlAttribute(name = "showText") + protected Boolean showText; + + @XmlAttribute(name = "showColourText") + protected Boolean showColourText; + + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + + @XmlAttribute(name = "showBoxes") + protected Boolean showBoxes; + + @XmlAttribute(name = "wrapAlignment") + protected Boolean wrapAlignment; + + @XmlAttribute(name = "renderGaps") + protected Boolean renderGaps; + + @XmlAttribute(name = "showSequenceFeatures") + protected Boolean showSequenceFeatures; + + @XmlAttribute(name = "showNPfeatureTooltip") + protected Boolean showNPfeatureTooltip; + + @XmlAttribute(name = "showDbRefTooltip") + protected Boolean showDbRefTooltip; + + @XmlAttribute(name = "followHighlight") + protected Boolean followHighlight; + + @XmlAttribute(name = "followSelection") + protected Boolean followSelection; + + @XmlAttribute(name = "showAnnotation") + protected Boolean showAnnotation; + + @XmlAttribute(name = "centreColumnLabels") + protected Boolean centreColumnLabels; + + @XmlAttribute(name = "showGroupConservation") + protected Boolean showGroupConservation; + + @XmlAttribute(name = "showGroupConsensus") + protected Boolean showGroupConsensus; + + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + + @XmlAttribute(name = "startRes") + protected Integer startRes; + + @XmlAttribute(name = "startSeq") + protected Integer startSeq; + + @XmlAttribute(name = "fontName") + protected String fontName; + + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + + @XmlAttribute(name = "scaleProteinAsCdna") + protected Boolean scaleProteinAsCdna; + + @XmlAttribute(name = "viewName") + protected String viewName; + + @XmlAttribute(name = "sequenceSetId") + protected String sequenceSetId; + + @XmlAttribute(name = "gatheredViews") + protected Boolean gatheredViews; + + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + + @XmlAttribute(name = "complementId") + protected String complementId; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the annotationColours property. + * + * @return possible object is {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() + { + return annotationColours; + } + + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) + { + this.annotationColours = value; + } + + /** + * Gets the value of the hiddenColumns property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the hiddenColumns property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getHiddenColumns().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport.HiddenColumns } + * + * + */ + public List getHiddenColumns() + { + if (hiddenColumns == null) + { + hiddenColumns = new ArrayList(); + } + return this.hiddenColumns; + } + + /** + * Gets the value of the calcIdParam property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the calcIdParam property. + * + *

+ * For example, to add a new item, do as follows: + * + * 

+     * getCalcIdParam().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport.CalcIdParam } + * + * + */ + public List getCalcIdParam() + { + if (calcIdParam == null) + { + calcIdParam = new ArrayList(); + } + return this.calcIdParam; + } + + /** + * Gets the value of the conservationSelected property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isConservationSelected() + { + return conservationSelected; + } + + /** + * Sets the value of the conservationSelected property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setConservationSelected(Boolean value) + { + this.conservationSelected = value; + } + + /** + * Gets the value of the pidSelected property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isPidSelected() + { + return pidSelected; + } + + /** + * Sets the value of the pidSelected property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setPidSelected(Boolean value) + { + this.pidSelected = value; + } + + /** + * Gets the value of the bgColour property. + * + * @return possible object is {@link String } + * + */ + public String getBgColour() + { + return bgColour; + } + + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setBgColour(String value) + { + this.bgColour = value; + } + + /** + * Gets the value of the consThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getConsThreshold() + { + return consThreshold; + } + + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setConsThreshold(Integer value) + { + this.consThreshold = value; + } + + /** + * Gets the value of the pidThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getPidThreshold() + { + return pidThreshold; + } + + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setPidThreshold(Integer value) + { + this.pidThreshold = value; + } + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the showFullId property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowFullId() + { + return showFullId; + } + + /** + * Sets the value of the showFullId property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowFullId(Boolean value) + { + this.showFullId = value; + } + + /** + * Gets the value of the rightAlignIds property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isRightAlignIds() + { + return rightAlignIds; + } + + /** + * Sets the value of the rightAlignIds property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setRightAlignIds(Boolean value) + { + this.rightAlignIds = value; + } + + /** + * Gets the value of the showText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowText() + { + return showText; + } + + /** + * Sets the value of the showText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowText(Boolean value) + { + this.showText = value; + } + + /** + * Gets the value of the showColourText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowColourText() + { + return showColourText; + } + + /** + * Sets the value of the showColourText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowColourText(Boolean value) + { + this.showColourText = value; + } + + /** + * Gets the value of the showUnconserved property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowUnconserved() + { + if (showUnconserved == null) + { + return false; + } + else + { + return showUnconserved; + } + } + + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) + { + this.showUnconserved = value; + } + + /** + * Gets the value of the showBoxes property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowBoxes() + { + return showBoxes; + } + + /** + * Sets the value of the showBoxes property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowBoxes(Boolean value) + { + this.showBoxes = value; + } + + /** + * Gets the value of the wrapAlignment property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isWrapAlignment() + { + return wrapAlignment; + } + + /** + * Sets the value of the wrapAlignment property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setWrapAlignment(Boolean value) + { + this.wrapAlignment = value; + } + + /** + * Gets the value of the renderGaps property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isRenderGaps() + { + return renderGaps; + } + + /** + * Sets the value of the renderGaps property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setRenderGaps(Boolean value) + { + this.renderGaps = value; + } + + /** + * Gets the value of the showSequenceFeatures property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowSequenceFeatures() + { + return showSequenceFeatures; + } + + /** + * Sets the value of the showSequenceFeatures property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowSequenceFeatures(Boolean value) + { + this.showSequenceFeatures = value; + } + + /** + * Gets the value of the showNPfeatureTooltip property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowNPfeatureTooltip() + { + return showNPfeatureTooltip; + } + + /** + * Sets the value of the showNPfeatureTooltip property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowNPfeatureTooltip(Boolean value) + { + this.showNPfeatureTooltip = value; + } + + /** + * Gets the value of the showDbRefTooltip property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowDbRefTooltip() + { + return showDbRefTooltip; + } + + /** + * Sets the value of the showDbRefTooltip property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowDbRefTooltip(Boolean value) + { + this.showDbRefTooltip = value; + } + + /** + * Gets the value of the followHighlight property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isFollowHighlight() + { + if (followHighlight == null) + { + return true; + } + else + { + return followHighlight; + } + } + + /** + * Sets the value of the followHighlight property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFollowHighlight(Boolean value) + { + this.followHighlight = value; + } + + /** + * Gets the value of the followSelection property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isFollowSelection() + { + if (followSelection == null) + { + return true; + } + else + { + return followSelection; + } + } + + /** + * Sets the value of the followSelection property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFollowSelection(Boolean value) + { + this.followSelection = value; + } + + /** + * Gets the value of the showAnnotation property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowAnnotation() + { + return showAnnotation; + } + + /** + * Sets the value of the showAnnotation property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowAnnotation(Boolean value) + { + this.showAnnotation = value; + } + + /** + * Gets the value of the centreColumnLabels property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isCentreColumnLabels() + { + if (centreColumnLabels == null) + { + return false; + } + else + { + return centreColumnLabels; + } + } + + /** + * Sets the value of the centreColumnLabels property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCentreColumnLabels(Boolean value) + { + this.centreColumnLabels = value; + } + + /** + * Gets the value of the showGroupConservation property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowGroupConservation() + { + if (showGroupConservation == null) + { + return false; + } + else + { + return showGroupConservation; + } + } + + /** + * Sets the value of the showGroupConservation property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowGroupConservation(Boolean value) + { + this.showGroupConservation = value; + } + + /** + * Gets the value of the showGroupConsensus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowGroupConsensus() + { + if (showGroupConsensus == null) + { + return false; + } + else + { + return showGroupConsensus; + } + } + + /** + * Sets the value of the showGroupConsensus property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowGroupConsensus(Boolean value) + { + this.showGroupConsensus = value; + } + + /** + * Gets the value of the showConsensusHistogram property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() + { + if (showConsensusHistogram == null) + { + return true; + } + else + { + return showConsensusHistogram; + } + } + + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) + { + this.showConsensusHistogram = value; + } + + /** + * Gets the value of the showSequenceLogo property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowSequenceLogo() + { + if (showSequenceLogo == null) + { + return false; + } + else + { + return showSequenceLogo; + } + } + + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) + { + this.showSequenceLogo = value; + } + + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() + { + if (normaliseSequenceLogo == null) + { + return false; + } + else + { + return normaliseSequenceLogo; + } + } + + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) + { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() + { + if (ignoreGapsinConsensus == null) + { + return true; + } + else + { + return ignoreGapsinConsensus; + } + } + + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) + { + this.ignoreGapsinConsensus = value; + } + + /** + * Gets the value of the startRes property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStartRes() + { + return startRes; + } + + /** + * Sets the value of the startRes property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStartRes(Integer value) + { + this.startRes = value; + } + + /** + * Gets the value of the startSeq property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStartSeq() + { + return startSeq; + } + + /** + * Sets the value of the startSeq property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStartSeq(Integer value) + { + this.startSeq = value; + } + + /** + * Gets the value of the fontName property. + * + * @return possible object is {@link String } + * + */ + public String getFontName() + { + return fontName; + } + + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFontName(String value) + { + this.fontName = value; + } + + /** + * Gets the value of the fontSize property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontSize() + { + return fontSize; + } + + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontSize(Integer value) + { + this.fontSize = value; + } + + /** + * Gets the value of the fontStyle property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontStyle() + { + return fontStyle; + } + + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontStyle(Integer value) + { + this.fontStyle = value; + } + + /** + * Gets the value of the scaleProteinAsCdna property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isScaleProteinAsCdna() + { + if (scaleProteinAsCdna == null) + { + return true; + } + else + { + return scaleProteinAsCdna; + } + } + + /** + * Sets the value of the scaleProteinAsCdna property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setScaleProteinAsCdna(Boolean value) + { + this.scaleProteinAsCdna = value; + } + + /** + * Gets the value of the viewName property. + * + * @return possible object is {@link String } + * + */ + public String getViewName() + { + return viewName; + } + + /** + * Sets the value of the viewName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setViewName(String value) + { + this.viewName = value; + } + + /** + * Gets the value of the sequenceSetId property. + * + * @return possible object is {@link String } + * + */ + public String getSequenceSetId() + { + return sequenceSetId; + } + + /** + * Sets the value of the sequenceSetId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setSequenceSetId(String value) + { + this.sequenceSetId = value; + } + + /** + * Gets the value of the gatheredViews property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isGatheredViews() + { + return gatheredViews; + } + + /** + * Sets the value of the gatheredViews property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setGatheredViews(Boolean value) + { + this.gatheredViews = value; + } + + /** + * Gets the value of the textCol1 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol1() + { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol1(Integer value) + { + this.textCol1 = value; + } + + /** + * Gets the value of the textCol2 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol2() + { + return textCol2; + } + + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol2(Integer value) + { + this.textCol2 = value; + } + + /** + * Gets the value of the textColThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextColThreshold() + { + return textColThreshold; + } + + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextColThreshold(Integer value) + { + this.textColThreshold = value; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + /** + * Gets the value of the complementId property. + * + * @return possible object is {@link String } + * + */ + public String getComplementId() + { + return complementId; + } + + /** + * Sets the value of the complementId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setComplementId(String value) + { + this.complementId = value; + } + + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </extension>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class CalcIdParam extends WebServiceParameterSet + { + + @XmlAttribute(name = "calcId", required = true) + protected String calcId; + + @XmlAttribute(name = "needsUpdate") + protected Boolean needsUpdate; + + @XmlAttribute(name = "autoUpdate", required = true) + protected boolean autoUpdate; + + /** + * Gets the value of the calcId property. + * + * @return possible object is {@link String } + * + */ + public String getCalcId() + { + return calcId; + } + + /** + * Sets the value of the calcId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setCalcId(String value) + { + this.calcId = value; + } + + /** + * Gets the value of the needsUpdate property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isNeedsUpdate() + { + if (needsUpdate == null) + { + return false; + } + else + { + return needsUpdate; + } + } + + /** + * Sets the value of the needsUpdate property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setNeedsUpdate(Boolean value) + { + this.needsUpdate = value; + } + + /** + * Gets the value of the autoUpdate property. + * + */ + public boolean isAutoUpdate() + { + return autoUpdate; + } + + /** + * Sets the value of the autoUpdate property. + * + */ + public void setAutoUpdate(boolean value) + { + this.autoUpdate = value; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class HiddenColumns + { + + @XmlAttribute(name = "start") + protected Integer start; + + @XmlAttribute(name = "end") + protected Integer end; + + /** + * Gets the value of the start property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStart() + { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStart(Integer value) + { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setEnd(Integer value) + { + this.end = value; + } + + } + + } + +} diff --git a/src/jalview/xml/binding/jalviewBH/SequenceSet.java b/src/jalview/xml/binding/jalviewBH/SequenceSet.java new file mode 100644 index 0000000..d78c585 --- /dev/null +++ b/src/jalview/xml/binding/jalviewBH/SequenceSet.java @@ -0,0 +1,324 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 04:36:20 PM BST +// + + +package jalview.xml.binding.jalviewBH; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "sequence", + "annotation", + "sequenceSetProperties", + "alcodonFrame" +}) +@XmlRootElement(name = "SequenceSet") +public class SequenceSet { + + // BH testing here + private class Sequence {} + private class Annotation {} + private class AlcodonFrame {} + // + + @XmlElement(name = "Sequence") + protected List sequence; + @XmlElement(name = "Annotation") + protected List annotation; + protected List sequenceSetProperties; + @XmlElement(name = "AlcodonFrame") + protected List alcodonFrame; + @XmlAttribute(name = "gapChar", required = true) + protected String gapChar; + @XmlAttribute(name = "datasetId") + protected String datasetId; + + /** + * Gets the value of the sequence property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequence property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getSequence().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Sequence } + * + * + */ + public List getSequence() { + if (sequence == null) { + sequence = new ArrayList(); + } + return this.sequence; + } + + /** + * Gets the value of the annotation property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the annotation property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAnnotation().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Annotation } + * + * + */ + public List getAnnotation() { + if (annotation == null) { + annotation = new ArrayList(); + } + return this.annotation; + } + + /** + * Gets the value of the sequenceSetProperties property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequenceSetProperties property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getSequenceSetProperties().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link SequenceSet.SequenceSetProperties } + * + * + */ + public List getSequenceSetProperties() { + if (sequenceSetProperties == null) { + sequenceSetProperties = new ArrayList(); + } + return this.sequenceSetProperties; + } + + /** + * Gets the value of the alcodonFrame property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the alcodonFrame property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAlcodonFrame().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame } + * + * + */ + public List getAlcodonFrame() { + if (alcodonFrame == null) { + alcodonFrame = new ArrayList(); + } + return this.alcodonFrame; + } + + /** + * Gets the value of the gapChar property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getGapChar() { + return gapChar; + } + + /** + * Sets the value of the gapChar property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setGapChar(String value) { + this.gapChar = value; + } + + /** + * Gets the value of the datasetId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDatasetId() { + return datasetId; + } + + /** + * Sets the value of the datasetId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDatasetId(String value) { + this.datasetId = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SequenceSetProperties { + + @XmlAttribute(name = "key") + protected String key; + @XmlAttribute(name = "value") + protected String value; + + /** + * Gets the value of the key property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getKey() { + return key; + } + + /** + * Sets the value of the key property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setKey(String value) { + this.key = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalviewBH/VAMSAS.java b/src/jalview/xml/binding/jalviewBH/VAMSAS.java new file mode 100644 index 0000000..c10f7df --- /dev/null +++ b/src/jalview/xml/binding/jalviewBH/VAMSAS.java @@ -0,0 +1,109 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 04:36:20 PM BST +// + + +package jalview.xml.binding.jalviewBH; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for VAMSAS complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="VAMSAS">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "VAMSAS", propOrder = { + "tree", + "sequenceSet" +}) +public class VAMSAS { + + @XmlElement(name = "Tree") + protected List tree; + @XmlElement(name = "SequenceSet") + protected List sequenceSet; + + /** + * Gets the value of the tree property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the tree property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getTree().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getTree() { + if (tree == null) { + tree = new ArrayList(); + } + return this.tree; + } + + /** + * Gets the value of the sequenceSet property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequenceSet property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getSequenceSet().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link SequenceSet } + * + * + */ + public List getSequenceSet() { + if (sequenceSet == null) { + sequenceSet = new ArrayList(); + } + return this.sequenceSet; + } + +} -- 1.7.10.2