Package org.forester.application
Class support_transfer
- java.lang.Object
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- org.forester.application.support_transfer
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public final class support_transfer extends java.lang.Object
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Constructor Summary
Constructors Constructor Description support_transfer()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
main(java.lang.String[] args)
Transfers branch length values from one Phylogeny to another.static void
moveBranchLengthsToBootstrap(Phylogeny p)
Moves the values in the branch length field to the bootstrap field, for each PhylogenyNode of this Phylogeny.static void
transferSupportValues(Phylogeny from, Phylogeny to)
Modifies Phylogeny to with the support values from Phylogeny from.
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Method Detail
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main
public static void main(java.lang.String[] args)
Transfers branch length values from one Phylogeny to another. It is mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )" of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.- Parameters:
args
- [0] Filename (String) for Phylogeny which has correct branch length valuesargs
- [1] String Filename (String) for Phylogeny to which the branch lengths of the first Phylogeny are to be copied, both Trees must only differ in their branch length values, i.e. topology and sequence names, etc. must be the sameargs
- [2] String Filename (String) for outputfileargs
- [3] String [number of tree with correct bl to use in case treefile contains more than one, default 0]
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moveBranchLengthsToBootstrap
public static final void moveBranchLengthsToBootstrap(Phylogeny p)
Moves the values in the branch length field to the bootstrap field, for each PhylogenyNode of this Phylogeny. Converts a Phylogeny originating from a phylip treefile after bootstrapping and which therefore has its bootstrap values where the branch lenghts would be.
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transferSupportValues
public static final void transferSupportValues(Phylogeny from, Phylogeny to)
Modifies Phylogeny to with the support values from Phylogeny from. Important (but obvious): The topology of both trees needs to be the same. The method is not robust, and might produce wrong results if the internal topology differs or if the external node names are not unique.- Parameters:
from
- the Phylogeny to copy the support values fromto
- the Phylogeny to copy the support values to
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