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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,154 @@ | ||
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| ```java | ||
| package com.bio4j.model; | ||
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| import com.bio4j.angulillos.*; | ||
| import java.util.Set; | ||
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| // TODO move to angulillos | ||
| public abstract class LinkGraph< | ||
| G extends LinkGraph<G,RV,RE>, | ||
| RV,RE | ||
| > | ||
| extends TypedGraph<G,RV,RE> { | ||
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| protected LinkGraph(UntypedGraph<RV,RE> raw) { super(raw); } | ||
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| // TODO these two classes are duplicated here because of them being private in angulillos | ||
| private abstract class FunnyElement< | ||
| F extends FunnyElement<F,FT, RF>, | ||
| FT extends FunnyElementType<F,FT, RF>, | ||
| RF | ||
| > implements TypedElement<F,FT, G,RF> { | ||
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| private final RF raw; | ||
| private final FT type; | ||
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| @Override public final RF raw() { return this.raw; } | ||
| @Override public final FT type() { return this.type; } | ||
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| // NOTE: we cannot do the same to `self`, because `super()` constructor cannot refer to `this` | ||
| protected FunnyElement(RF raw, FT type) { | ||
| this.raw = raw; | ||
| this.type = type; | ||
| } | ||
| } | ||
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| private abstract class FunnyElementType< | ||
| F extends FunnyElement<F,FT, RF>, | ||
| FT extends FunnyElementType<F,FT, RF>, | ||
| RF | ||
| > implements TypedElement.Type<F,FT, G,RF> { | ||
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| @Override public final G graph() { return LinkGraph.this.self(); } | ||
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| public abstract F fromRaw(RF raw); | ||
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| protected abstract FT self(); | ||
| ``` | ||
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| This set stores all properties that are defined on this element type | ||
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| ```java | ||
| private final Set<AnyProperty> properties = new java.util.HashSet<>(); | ||
| public final Set<AnyProperty> properties() { return this.properties; } | ||
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| // public abstract class Property<X> | ||
| // implements com.bio4j.angulillos.Property<FT,X> { | ||
| // // NOTE: this initializer block will be inherited and will add each vertex type to the set | ||
| // { | ||
| // if ( | ||
| // ElementType.this.properties.removeIf( (AnyProperty p) -> | ||
| // p._label().equals( this._label() ) | ||
| // ) | ||
| // ) { | ||
| // throw new IllegalArgumentException( | ||
| // "Element type [" + | ||
| // ElementType.this._label() + | ||
| // "] contains duplicate property: " + | ||
| // this._label() | ||
| // ); | ||
| // } | ||
| // ElementType.this.properties.add(this); | ||
| // } | ||
| // | ||
| // private final Class<X> valueClass; | ||
| // | ||
| // @Override public final FT elementType() { return self(); } | ||
| // @Override public final Class<X> valueClass() { return this.valueClass; } | ||
| // | ||
| // protected Property(Class<X> valueClass) { | ||
| // this.valueClass = valueClass; | ||
| // } | ||
| // } | ||
| } | ||
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| public abstract class LinkEdge< | ||
| SG extends TypedGraph<SG,RV,RE>, | ||
| S extends TypedGraph<SG,RV,RE>.Vertex<S>, | ||
| E extends LinkEdge<SG,S,E,TG,T>, | ||
| TG extends TypedGraph<TG,RV,RE>, | ||
| T extends TypedGraph<TG,RV,RE>.Vertex<T> | ||
| > extends FunnyElement<E,LinkEdgeType<SG,S,E,TG,T>,RE> | ||
| implements TypedEdge< | ||
| S, TypedGraph<SG,RV,RE>.VertexType<S>, | ||
| E, LinkEdgeType<SG,S,E,TG,T>, | ||
| T, TypedGraph<TG,RV,RE>.VertexType<T>, | ||
| G,RV,RE | ||
| > | ||
| { | ||
| protected LinkEdge(RE raw, LinkEdgeType<SG,S,E,TG,T> type) { super(raw, type); } | ||
| } | ||
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| // TODO initializer block missing | ||
| public abstract class LinkEdgeType< | ||
| SG extends TypedGraph<SG,RV,RE>, | ||
| S extends TypedGraph<SG,RV,RE>.Vertex<S>, | ||
| E extends LinkEdge<SG,S,E,TG,T>, | ||
| TG extends TypedGraph<TG,RV,RE>, | ||
| T extends TypedGraph<TG,RV,RE>.Vertex<T> | ||
| > extends FunnyElementType<E, LinkEdgeType<SG,S,E,TG,T>, RE> | ||
| implements TypedEdge.Type< | ||
| S, TypedGraph<SG,RV,RE>.VertexType<S>, | ||
| E, LinkEdgeType<SG,S,E,TG,T>, | ||
| T, TypedGraph<TG,RV,RE>.VertexType<T>, | ||
| G,RV,RE | ||
| > | ||
| { | ||
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| protected LinkEdgeType<SG,S,E,TG,T> self() { return this; } | ||
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| private final TypedGraph<SG,RV,RE>.VertexType<S> sourceType; | ||
| private final TypedGraph<TG,RV,RE>.VertexType<T> targetType; | ||
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| @Override public final TypedGraph<SG,RV,RE>.VertexType<S> sourceType() { return this.sourceType; } | ||
| @Override public final TypedGraph<TG,RV,RE>.VertexType<T> targetType() { return this.targetType; } | ||
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| protected LinkEdgeType(TypedGraph<SG,RV,RE>.VertexType<S> sourceType, TypedGraph<TG,RV,RE>.VertexType<T> targetType) { | ||
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| this.sourceType = sourceType; | ||
| this.targetType = targetType; | ||
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| // private access in angulillos | ||
| // sourceType.outEdges.add( self() ); | ||
| // targetType.inEdges.add( self() ); | ||
| } | ||
| } | ||
| } | ||
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| ``` | ||
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| [main/java/com/bio4j/model/UniProtGraph.java]: UniProtGraph.java.md | ||
| [main/java/com/bio4j/model/UniProtENZYMEGraph.java]: UniProtENZYMEGraph.java.md | ||
| [main/java/com/bio4j/model/NCBITaxonomyGraph.java]: NCBITaxonomyGraph.java.md | ||
| [main/java/com/bio4j/model/UniRefGraph.java]: UniRefGraph.java.md | ||
| [main/java/com/bio4j/model/ENZYMEGraph.java]: ENZYMEGraph.java.md | ||
| [main/java/com/bio4j/model/UniProtNCBITaxonomyGraph.java]: UniProtNCBITaxonomyGraph.java.md | ||
| [main/java/com/bio4j/model/GOGraph.java]: GOGraph.java.md | ||
| [main/java/com/bio4j/model/UniProtGOGraph.java]: UniProtGOGraph.java.md | ||
| [main/java/com/bio4j/model/LinkGraph.java]: LinkGraph.java.md |
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