statalign.model.ext.plugins.structalign
Class Funcs

java.lang.Object
  statalign.model.ext.plugins.structalign.Funcs

public class Funcs
extends java.lang.Object

Constructor Summary

Funcs()

Method Summary

static java.util.ArrayList<java.lang.Integer>	collectLeaves(Vertex v)
static java.util.ArrayList<java.lang.Integer>	findRefSubtrees(Tree tree, int refInd)
static double[][]	getRowSub(double[][] coord, java.util.ArrayList<java.lang.Integer> rows)
static double[][]	getSubMatrix(double[][] matrix, int[] rows, int[] cols)
static void	initLSRotations(Tree tree, double[][][] coords, double[][] xlats, double[][] axes, double[] angles)
static org.apache.commons.math3.linear.RealVector	meanVector(org.apache.commons.math3.linear.RealMatrix A) For an n X 3 coordinate matrix, calculate the 1 X 3 mean vector
static void	moveDown(Vertex v, java.util.List<java.lang.Integer> inds)
static void	moveUp(Vertex v, java.util.List<java.lang.Integer> inds)
static Vertex	sampleVertex(Tree tree)
static void	writeRotationFiles(Tree tree, double[][][] coords, double[][] xlats, double[][] axes, double[] angles)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Funcs

public Funcs()

Method Detail

getSubMatrix

public static double[][] getSubMatrix(double[][] matrix,
                                      int[] rows,
                                      int[] cols)

meanVector

public static org.apache.commons.math3.linear.RealVector meanVector(org.apache.commons.math3.linear.RealMatrix A)

For an n X 3 coordinate matrix, calculate the 1 X 3 mean vector

Parameters:

A - - coordinate matrix

Returns:

mean vector

sampleVertex

public static Vertex sampleVertex(Tree tree)

findRefSubtrees

public static java.util.ArrayList<java.lang.Integer> findRefSubtrees(Tree tree,
                                                                     int refInd)

moveUp

public static void moveUp(Vertex v,
                          java.util.List<java.lang.Integer> inds)

collectLeaves

public static java.util.ArrayList<java.lang.Integer> collectLeaves(Vertex v)

moveDown

public static void moveDown(Vertex v,
                            java.util.List<java.lang.Integer> inds)

writeRotationFiles

public static void writeRotationFiles(Tree tree,
                                      double[][][] coords,
                                      double[][] xlats,
                                      double[][] axes,
                                      double[] angles)

initLSRotations

public static void initLSRotations(Tree tree,
                                   double[][][] coords,
                                   double[][] xlats,
                                   double[][] axes,
                                   double[] angles)

getRowSub

public static double[][] getRowSub(double[][] coord,
                                   java.util.ArrayList<java.lang.Integer> rows)