public class TaxaSimilarityMain
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.lang.String[] |
RANKS |
Constructor and Description |
---|
TaxaSimilarityMain(java.util.List<java.lang.String> selectedRanks) |
Modifier and Type | Method and Description |
---|---|
void |
calPairwiseSimilaritye(java.lang.String taxonFile,
java.lang.String trainSeqFile,
java.lang.String testSeqFile) |
void |
calSabSimilarity(java.lang.String taxonFile,
java.lang.String trainSeqFile,
java.lang.String testSeqFile) |
void |
createPlot(java.lang.String plotTitle,
java.io.File outdir) |
java.util.HashMap<java.lang.String,HierarchyTree> |
getAncestorNodes(HierarchyTree root,
java.lang.String seqName,
java.util.List<java.lang.String> ancestors) |
static void |
main(java.lang.String[] args)
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.
|
static java.util.List<java.lang.String> |
readRanks(java.lang.String rankFile) |
public TaxaSimilarityMain(java.util.List<java.lang.String> selectedRanks)
public static java.util.List<java.lang.String> readRanks(java.lang.String rankFile) throws java.io.IOException
java.io.IOException
public java.util.HashMap<java.lang.String,HierarchyTree> getAncestorNodes(HierarchyTree root, java.lang.String seqName, java.util.List<java.lang.String> ancestors)
public void calSabSimilarity(java.lang.String taxonFile, java.lang.String trainSeqFile, java.lang.String testSeqFile) throws java.io.IOException
java.io.IOException
public void calPairwiseSimilaritye(java.lang.String taxonFile, java.lang.String trainSeqFile, java.lang.String testSeqFile) throws java.io.IOException, edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
java.io.IOException
edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
public void createPlot(java.lang.String plotTitle, java.io.File outdir) throws java.io.IOException
java.io.IOException
public static void main(java.lang.String[] args) throws java.io.IOException, edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
args
- java.io.IOException
edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException