Class TaxaSimilarityMain
java.lang.Object
edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
calPairwiseSimilaritye
(String taxonFile, String trainSeqFile, String testSeqFile) void
calSabSimilarity
(String taxonFile, String trainSeqFile, String testSeqFile) void
createPlot
(String plotTitle, File outdir) getAncestorNodes
(HierarchyTree root, String seqName, List<String> ancestors) static void
This calculates the average similarity (Sab score or pairwise alignment) between taxa at given ranks and plot the box and whisker plot and accumulation curve.
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Field Details
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RANKS
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Constructor Details
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TaxaSimilarityMain
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Method Details
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readRanks
- Throws:
IOException
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getAncestorNodes
public HashMap<String,HierarchyTree> getAncestorNodes(HierarchyTree root, String seqName, List<String> ancestors) -
calSabSimilarity
public void calSabSimilarity(String taxonFile, String trainSeqFile, String testSeqFile) throws IOException - Throws:
IOException
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calPairwiseSimilaritye
public void calPairwiseSimilaritye(String taxonFile, String trainSeqFile, String testSeqFile) throws IOException, edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException - Throws:
IOException
edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
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createPlot
- Throws:
IOException
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main
public static void main(String[] args) throws IOException, edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException This calculates the average similarity (Sab score or pairwise alignment) between taxa at given ranks and plot the box and whisker plot and accumulation curve. The distances associate to a given rank contains the distances between different child taxa. It does not include the distances within the same child taxa. For example, if a query and it's closest match are from the same genus, the distance value is added to that genus. If there are from different genera but the same family, the distance value is added to that family, etc.- Parameters:
args
-- Throws:
IOException
edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
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