Extend the ZhangUnorderedTreeEditDistance to Return the Optimal Node Mapping #33
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The fields forestDistances and treeDistances are both a HashMap. A HashMap is initially empty we don't need to fill it with "-1" values to represent a empty HashMap.
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* This reduces the cognitive complexity of minCostMaxFlow method to be below a suggested threshold of 15
* this abstract method is already defined in the interface NodeMapping that the class AbstractNodeMapping implements
…odon.mamut.treesimilarity.util
* Make the reason for the Runtime exception that may occur in this method more explicit and suggest the solution for it.
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This PR nicely adds node-mapping between two given trees based on the Zhang unordered edit distance, which is a highly useful feature.
There are some open questions - cf. below. Most important question relates to the number of mappings that created in a specific test case which does not relate to the number of nodes contained in the given trees.
I created a PR that contains suggestions how to improved this PR.
- It moves all existing util classes for ZhangUnordered to separate package and makes required methods public
- It contains some javadoc improvements.
- It contains suggestions regarding the code smells detected by sonarcloud: https://sonarcloud.io/project/issues?id=mastodon-sc_mastodon-deep-lineage&pullRequest=33&resolved=false&types=CODE_SMELL
src/main/java/org/mastodon/mamut/treesimilarity/NodeMappings.java
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src/main/java/org/mastodon/mamut/treesimilarity/NodeMappings.java
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src/main/java/org/mastodon/mamut/treesimilarity/NodeMappings.java
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src/main/java/org/mastodon/mamut/treesimilarity/NodeMappings.java
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src/test/java/org/mastodon/mamut/treesimilarity/NodeMappingTest.java
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I just see that I created a PR with suggestions, mentioned it, but did not explicitly link it. Thus, you may not have seen it: |
Compute node mapping review
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The zhang unordered tree edit distance is always associated with a respective mapping between the nodes of the two trees. This PR extends the ZhangUnorderedTreeEditDistance class to also return the optimal node mapping.
This PR is required for mastodon-sc/mastodon-tomancak#26