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- keys and tags have their own classes now
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417 changes: 211 additions & 206 deletions
417
...n/java/org/broadinstitute/hellbender/tools/coveragemodel/CoverageModelEMComputeBlock.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -13,32 +13,32 @@ | |
| * | ||
| * @author Mehrtash Babadi <[email protected]> | ||
| */ | ||
| abstract class CacheNode { | ||
| public abstract class CacheNode { | ||
| /** | ||
| * A string identifier for the cache node | ||
| * A key for identifying this cache node | ||
| */ | ||
| private final String key; | ||
| private final NodeKey key; | ||
|
|
||
| /** | ||
| * The collection of string identifiers of the immediate parents of this node (can be empty) | ||
| * The collection of lookup keys for parents of this node (can be empty) | ||
| */ | ||
| private final Collection<String> parents; | ||
| private final Collection<NodeKey> parents; | ||
|
|
||
| /** | ||
| * The collection of string identifiers of the tags associated to this node (can be empty) | ||
| * The collection of tags associated to this node (can be empty) | ||
| */ | ||
| private final Collection<String> tags; | ||
| private final Collection<NodeTag> tags; | ||
|
|
||
| /** | ||
| * Public constructor | ||
| * | ||
| * @param key string identifier of the cache node | ||
| * @param key lookup key of the cache node | ||
| * @param tags the tags associated to this cache node | ||
| * @param parents immediate parents of this cache node | ||
| * @param parents lookup keys of the parents of this cache node | ||
| */ | ||
| CacheNode(@Nonnull final String key, | ||
| @Nonnull final Collection<String> tags, | ||
| @Nonnull final Collection<String> parents) { | ||
| CacheNode(@Nonnull final NodeKey key, | ||
| @Nonnull final Collection<NodeTag> tags, | ||
| @Nonnull final Collection<NodeKey> parents) { | ||
| this.key = Utils.nonNull(key, "The key of a cache node can not be null"); | ||
| this.tags = Collections.unmodifiableCollection(Utils.nonNull(tags, "The tag collection of a cache node can not be null")); | ||
| this.parents = Collections.unmodifiableCollection(Utils.nonNull(parents, "The immediate parents of a cache node can not be null")); | ||
|
|
@@ -47,10 +47,10 @@ abstract class CacheNode { | |
| /** | ||
| * Get the value stored in the node | ||
| * | ||
| * @param parents parent values (as a map from their string identifiers to their values) | ||
| * @param parents parent values (as a map from their keys to their values) | ||
| * @return a {@link Duplicable}; possibly by reference | ||
| */ | ||
| abstract Duplicable get(@Nonnull final Map<String, Duplicable> parents); | ||
| abstract Duplicable get(@Nonnull final Map<NodeKey, Duplicable> parents); | ||
|
|
||
| /** | ||
| * Set the value of the node | ||
|
|
@@ -95,27 +95,27 @@ abstract class CacheNode { | |
| * Get the string identifier of the node | ||
| * @return a non-null {@link String} | ||
| */ | ||
| final String getKey() { | ||
| final NodeKey getKey() { | ||
| return key; | ||
| } | ||
|
|
||
| /** | ||
| * Get the collection of string identifier of the parents of this node (can be empty) | ||
| * Get the collection of keys of the parents of this node (can be empty) | ||
| */ | ||
| final Collection<String> getParents() { | ||
| final Collection<NodeKey> getParents() { | ||
| return Collections.unmodifiableCollection(parents); | ||
| } | ||
|
|
||
| /** | ||
| * Get the collection of string identifier of the tags associated to this node (can be empty) | ||
| * Get the collection of tags associated to this node (can be empty) | ||
| */ | ||
| final Collection<String> getTags() { | ||
| final Collection<NodeTag> getTags() { | ||
| return Collections.unmodifiableCollection(tags); | ||
| } | ||
|
|
||
| @Override | ||
| public final String toString() { | ||
| return key; | ||
| return key.toString(); | ||
| } | ||
|
|
||
| /** | ||
|
|
@@ -136,4 +136,66 @@ public final boolean equals(Object other) { | |
| public final int hashCode() { | ||
| return key.hashCode(); | ||
| } | ||
|
|
||
| /** | ||
| * This class represents a node key. It is a wrapper around a String. | ||
| */ | ||
| public static class NodeKey { | ||
| private final String key; | ||
|
|
||
| public NodeKey(final String key) { | ||
| this.key = Utils.nonNull(key, "Node key must be non-null"); | ||
| } | ||
|
|
||
| @Override | ||
| public String toString() { | ||
| return key; | ||
| } | ||
|
|
||
| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
|
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| NodeKey nodeKey = (NodeKey) o; | ||
|
|
||
| return key.equals(nodeKey.key); | ||
| } | ||
|
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||
| @Override | ||
| public int hashCode() { | ||
| return key.hashCode(); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * This class represents a node tag. It is a wrapper around a String. | ||
| */ | ||
| public static class NodeTag { | ||
| private final String tag; | ||
|
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||
| public NodeTag(final String tag) { | ||
| this.tag = Utils.nonNull(tag, "Node tag must be non-null"); | ||
| } | ||
|
|
||
| @Override | ||
| public String toString() { | ||
| return tag; | ||
| } | ||
|
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||
| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
|
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| NodeTag nodeTag = (NodeTag) o; | ||
|
|
||
| return tag.equals(nodeTag.tag); | ||
| } | ||
|
|
||
| @Override | ||
| public int hashCode() { | ||
| return tag.hashCode(); | ||
| } | ||
| } | ||
| } | ||
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