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kMutageneclaude
kMutagene
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claude
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refactor: rename Project/Sample -> BioProject/BioSample for INSDC clarity
In INSDC terminology, BioProject and BioSample are the cross-archive entity names (visible to data submitters via the PRJ*/SAM* accession prefixes), while the SRA/ENA XML schema uses `Project` and `Sample` internally. Rename to the cross-archive names so the library surface matches what biology users already know. Substitution rules added to typename-substitutions.txt: E) Names starting with `Project` -> `BioProject*`; names starting with `Sample` -> `BioSample*`, EXCEPT `SampleGroup*` which is a distinct entity (the ENA.sample_group.xsd schema). F) Collapse the trivially duplicated stems that the schema element names introduced, before the Bio prefix: ProjectProjectAttributes -> BioProjectAttributes SampleSampleName -> BioSampleName (etc. for Links/Name/Attributes pairs) F# IO layer follows: - module BioProject now exposes `type BioProject` (was `type Project`) - module Sample renamed to module BioSample (file Sample.fs -> BioSample.fs); exposes `type BioSample` (was `type Sample`) - Tests.fs updated to construct BioProject.BioProject() / BioSample.BioSample() SampleGroup, SampleRef inside other entities (e.g. AnalysisSampleRef), and non-leading occurrences of "Project"/"Sample" are intentionally unchanged. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
1 parent 58b8159 commit 65a876c

31 files changed

Lines changed: 175 additions & 165 deletions

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/Project.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProject.cs

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@@ -19,7 +19,7 @@ namespace BioFSharp.FileFormats.INSDC
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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[System.Xml.Serialization.XmlRootAttribute("PROJECT", Namespace="")]
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public partial class Project : BioFSharp.FileFormats.INSDC.Object
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public partial class BioProject : BioFSharp.FileFormats.INSDC.Object
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{
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/// <summary>
@@ -83,12 +83,12 @@ public bool CollaboratorsSpecified
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}
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/// <summary>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="Project" /> class.</para>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="BioProject" /> class.</para>
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/// </summary>
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public Project()
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public BioProject()
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{
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this._collaborators = new System.Collections.ObjectModel.Collection<string>();
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this._relatedProjects = new System.Collections.ObjectModel.Collection<ProjectRelatedProjectsRelatedProject>();
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this._relatedProjects = new System.Collections.ObjectModel.Collection<BioProjectRelatedProjectsRelatedProject>();
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this._projectLinks = new System.Collections.ObjectModel.Collection<BioFSharp.FileFormats.INSDC.Link>();
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this._projectAttributes = new System.Collections.ObjectModel.Collection<BioFSharp.FileFormats.INSDC.Attribute>();
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}
@@ -98,25 +98,25 @@ public Project()
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/// </summary>
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[System.ComponentModel.DescriptionAttribute("A project for grouping submitted data together.")]
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[System.Xml.Serialization.XmlElementAttribute("SUBMISSION_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public ProjectSubmissionProject SubmissionProject { get; set; }
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public BioProjectSubmissionProject SubmissionProject { get; set; }
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/// <summary>
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/// <para>A project for grouping other projects together.</para>
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/// </summary>
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[System.ComponentModel.DescriptionAttribute("A project for grouping other projects together.")]
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[System.Xml.Serialization.XmlElementAttribute("UMBRELLA_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public ProjectUmbrellaProject UmbrellaProject { get; set; }
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public BioProjectUmbrellaProject UmbrellaProject { get; set; }
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[System.Xml.Serialization.XmlIgnoreAttribute()]
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private System.Collections.ObjectModel.Collection<ProjectRelatedProjectsRelatedProject> _relatedProjects;
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private System.Collections.ObjectModel.Collection<BioProjectRelatedProjectsRelatedProject> _relatedProjects;
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/// <summary>
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/// <para>Other projects related to this project.</para>
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/// </summary>
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[System.ComponentModel.DescriptionAttribute("Other projects related to this project.")]
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[System.Xml.Serialization.XmlArrayAttribute("RELATED_PROJECTS", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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[System.Xml.Serialization.XmlArrayItemAttribute("RELATED_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public System.Collections.ObjectModel.Collection<ProjectRelatedProjectsRelatedProject> RelatedProjects
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public System.Collections.ObjectModel.Collection<BioProjectRelatedProjectsRelatedProject> RelatedProjects
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{
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get
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{

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectProjectAttributes.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectAttributes.cs

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@@ -15,10 +15,10 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectProjectAttributes", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectAttributes", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectProjectAttributes
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public partial class BioProjectAttributes
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{
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[System.Xml.Serialization.XmlIgnoreAttribute()]
@@ -39,9 +39,9 @@ private set
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}
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/// <summary>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="ProjectProjectAttributes" /> class.</para>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="BioProjectAttributes" /> class.</para>
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/// </summary>
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public ProjectProjectAttributes()
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public BioProjectAttributes()
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{
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this._projectAttribute = new System.Collections.ObjectModel.Collection<BioFSharp.FileFormats.INSDC.Attribute>();
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}

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectCollaborators.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectCollaborators.cs

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@@ -15,10 +15,10 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectCollaborators", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectCollaborators", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectCollaborators
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public partial class BioProjectCollaborators
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{
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[System.Xml.Serialization.XmlIgnoreAttribute()]
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}
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/// <summary>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="ProjectCollaborators" /> class.</para>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="BioProjectCollaborators" /> class.</para>
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/// </summary>
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public ProjectCollaborators()
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public BioProjectCollaborators()
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{
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this._collaborator = new System.Collections.ObjectModel.Collection<string>();
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}

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectProjectLinks.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectLinks.cs

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@@ -15,10 +15,10 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectProjectLinks", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectLinks", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectProjectLinks
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public partial class BioProjectLinks
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{
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[System.Xml.Serialization.XmlIgnoreAttribute()]
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}
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/// <summary>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="ProjectProjectLinks" /> class.</para>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="BioProjectLinks" /> class.</para>
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/// </summary>
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public ProjectProjectLinks()
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public BioProjectLinks()
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{
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this._projectLink = new System.Collections.ObjectModel.Collection<BioFSharp.FileFormats.INSDC.Link>();
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}

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectRelatedProjects.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectRelatedProjects.cs

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@@ -15,18 +15,18 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectRelatedProjects", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectRelatedProjects", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectRelatedProjects
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public partial class BioProjectRelatedProjects
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{
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[System.Xml.Serialization.XmlIgnoreAttribute()]
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private System.Collections.ObjectModel.Collection<ProjectRelatedProjectsRelatedProject> _relatedProject;
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private System.Collections.ObjectModel.Collection<BioProjectRelatedProjectsRelatedProject> _relatedProject;
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[System.ComponentModel.DataAnnotations.RequiredAttribute(AllowEmptyStrings=true)]
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[System.Xml.Serialization.XmlElementAttribute("RELATED_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public System.Collections.ObjectModel.Collection<ProjectRelatedProjectsRelatedProject> RelatedProject
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public System.Collections.ObjectModel.Collection<BioProjectRelatedProjectsRelatedProject> RelatedProject
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{
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get
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{
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}
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/// <summary>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="ProjectRelatedProjects" /> class.</para>
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/// <para xml:lang="en">Initializes a new instance of the <see cref="BioProjectRelatedProjects" /> class.</para>
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/// </summary>
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public ProjectRelatedProjects()
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public BioProjectRelatedProjects()
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{
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this._relatedProject = new System.Collections.ObjectModel.Collection<ProjectRelatedProjectsRelatedProject>();
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this._relatedProject = new System.Collections.ObjectModel.Collection<BioProjectRelatedProjectsRelatedProject>();
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}
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}
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}

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectRelatedProjectsRelatedProject.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectRelatedProjectsRelatedProject.cs

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@@ -15,19 +15,19 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectRelatedProjectsRelatedProject", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectRelatedProjectsRelatedProject", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectRelatedProjectsRelatedProject
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public partial class BioProjectRelatedProjectsRelatedProject
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{
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[System.Xml.Serialization.XmlElementAttribute("PARENT_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public ProjectRelatedProjectsRelatedProjectParentProject ParentProject { get; set; }
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public BioProjectRelatedProjectsRelatedProjectParentProject ParentProject { get; set; }
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[System.Xml.Serialization.XmlElementAttribute("CHILD_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public ProjectRelatedProjectsRelatedProjectChildProject ChildProject { get; set; }
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public BioProjectRelatedProjectsRelatedProjectChildProject ChildProject { get; set; }
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[System.Xml.Serialization.XmlElementAttribute("PEER_PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public ProjectRelatedProjectsRelatedProjectPeerProject PeerProject { get; set; }
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public BioProjectRelatedProjectsRelatedProjectPeerProject PeerProject { get; set; }
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}
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}

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectRelatedProjectsRelatedProjectPeerProject.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectRelatedProjectsRelatedProjectChildProject.cs

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@@ -15,10 +15,10 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectRelatedProjectsRelatedProjectPeerProject", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectRelatedProjectsRelatedProjectChildProject", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectRelatedProjectsRelatedProjectPeerProject
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public partial class BioProjectRelatedProjectsRelatedProjectChildProject
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{
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/// <summary>

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectRelatedProjectsRelatedProjectParentProject.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectRelatedProjectsRelatedProjectParentProject.cs

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@@ -15,10 +15,10 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectRelatedProjectsRelatedProjectParentProject", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectRelatedProjectsRelatedProjectParentProject", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectRelatedProjectsRelatedProjectParentProject
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public partial class BioProjectRelatedProjectsRelatedProjectParentProject
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{
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/// <summary>

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectRelatedProjectsRelatedProjectChildProject.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectRelatedProjectsRelatedProjectPeerProject.cs

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@@ -15,10 +15,10 @@ namespace BioFSharp.FileFormats.INSDC
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[System.CodeDom.Compiler.GeneratedCodeAttribute("XmlSchemaClassGenerator", "3.0.1270.0")]
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[System.SerializableAttribute()]
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[System.Xml.Serialization.XmlTypeAttribute("ProjectRelatedProjectsRelatedProjectChildProject", Namespace="", AnonymousType=true)]
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[System.Xml.Serialization.XmlTypeAttribute("BioProjectRelatedProjectsRelatedProjectPeerProject", Namespace="", AnonymousType=true)]
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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public partial class ProjectRelatedProjectsRelatedProjectChildProject
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public partial class BioProjectRelatedProjectsRelatedProjectPeerProject
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{
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/// <summary>

src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/ProjectSet.cs renamed to src/BioFSharp.FileFormats.INSDC/Generated/BioFSharp.FileFormats.INSDC/BioProjectSet.cs

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@@ -19,15 +19,15 @@ namespace BioFSharp.FileFormats.INSDC
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[System.Diagnostics.DebuggerStepThroughAttribute()]
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[System.ComponentModel.DesignerCategoryAttribute("code")]
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[System.Xml.Serialization.XmlRootAttribute("PROJECT_SET", Namespace="")]
22-
public partial class ProjectSet
22+
public partial class BioProjectSet
2323
{
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[System.Xml.Serialization.XmlIgnoreAttribute()]
26-
private System.Collections.ObjectModel.Collection<Project> _project;
26+
private System.Collections.ObjectModel.Collection<BioProject> _project;
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[System.ComponentModel.DataAnnotations.RequiredAttribute(AllowEmptyStrings=true)]
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[System.Xml.Serialization.XmlElementAttribute("PROJECT", Form=System.Xml.Schema.XmlSchemaForm.Unqualified)]
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public System.Collections.ObjectModel.Collection<Project> Project
30+
public System.Collections.ObjectModel.Collection<BioProject> Project
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{
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get
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{
@@ -40,11 +40,11 @@ private set
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}
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/// <summary>
43-
/// <para xml:lang="en">Initializes a new instance of the <see cref="ProjectSet" /> class.</para>
43+
/// <para xml:lang="en">Initializes a new instance of the <see cref="BioProjectSet" /> class.</para>
4444
/// </summary>
45-
public ProjectSet()
45+
public BioProjectSet()
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{
47-
this._project = new System.Collections.ObjectModel.Collection<Project>();
47+
this._project = new System.Collections.ObjectModel.Collection<BioProject>();
4848
}
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}
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}

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