DistanceMatrix (net.maizegenetics:tassel 5.2.54 API)

java.lang.Object
- net.maizegenetics.taxa.distance.DistanceMatrix

All Implemented Interfaces:

TableReport

Direct Known Subclasses:

DistanceMatrixWithCounts
```
public class DistanceMatrix
extends Object
implements TableReport
```
Storage for pairwise distance matrices. Only stores half the matrix as it is symmetrical.
For best performance, iterate over matrix this way.
```
 DistanceMatrix matrix;
 for (int i = 0; i < myNumTaxa; i++) {
     for (int j = 0; j <= i; j++) {
         matrix.getDistance(i, j);
     }
 }
 
```
Author:

Korbinian Strimmer, Alexei Drummond, Terry Casstevens

Constructor Summary

Constructors
Constructor and Description
`DistanceMatrix(DistanceMatrix dm)` Constructor that clones a distance matrix.
`DistanceMatrix(DistanceMatrix dm, TaxaList subset)` Constructor that clones a distance matrix and for only the specified taxa.
`DistanceMatrix(double[][] distance, TaxaList taxa)` Constructor taking distances array and taxa list.
`DistanceMatrix(double[][] distances, TaxaList taxa, GeneralAnnotation annotations)` Use DistanceMatrixBuilder instead of this.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`absoluteDistance(DistanceMatrix mat)` compute absolute distance to second distance matrix
`GeneralAnnotation`	`annotations()`
`double[][]`	`getClonedDistances()` Returns the distances as a 2-dimensional array of doubles.
`int`	`getClosestIndex(int fromIndex, int[] exclusion)`
`int`	`getColumnCount()` Get the number of the columns
`String`	`getColumnName(int col)`
`float`	`getDistance(int row, int col)`
`double[][]`	`getDistances()` Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)
`long`	`getElementCount()` Get the total number of elements in the dataset.
`Object[]`	`getRow(long rowLong)` Returns specified row.
`long`	`getRowCount()` Get the number of rows
`int`	`getSize()` Returns the number of taxa which is also the number of rows and columns that the distance matrix has.
`Object[]`	`getTableColumnNames()` Get the names of the columns
`String`	`getTableTitle()` Get the title of the table
`TaxaList`	`getTaxaList()` Return TaxaList of this alignment.
`Taxon`	`getTaxon(int i)`
`Object`	`getValueAt(long rowIndex, int columnIndex)` Returns value at given row and column.
`static DistanceMatrix`	`hadamardProduct(DistanceMatrix m0, DistanceMatrix m1)`
`boolean`	`isSymmetric()` test whether this matrix is a symmetric distance matrix
`double`	`meanDistance()` Returns the mean pairwise distance of this matrix
`int`	`numberOfTaxa()`
`void`	`printPHYLIP(PrintWriter out)` print alignment (PHYLIP format)
`double`	`squaredDistance(DistanceMatrix mat, boolean weighted)` compute squared distance to second distance matrix
`String`	`toString()` returns representation of this alignment as a string
`int`	`whichIdNumber(String name)`
`int`	`whichIdNumber(Taxon id)`

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.maizegenetics.util.TableReport
toStringTabDelim

- Constructor Detail
  - DistanceMatrix
```
public DistanceMatrix(double[][] distance,
                      TaxaList taxa)
```
    Constructor taking distances array and taxa list. Use DistanceMatrixBuilder instead of this.
    
    See Also:
    
    DistanceMatrixBuilder
  - DistanceMatrix
```
public DistanceMatrix(double[][] distances,
                      TaxaList taxa,
                      GeneralAnnotation annotations)
```
    Use DistanceMatrixBuilder instead of this.
    
    See Also:
    
    DistanceMatrixBuilder
  - DistanceMatrix
```
public DistanceMatrix(DistanceMatrix dm)
```
    Constructor that clones a distance matrix.
  - DistanceMatrix
```
public DistanceMatrix(DistanceMatrix dm,
                      TaxaList subset)
```
    Constructor that clones a distance matrix and for only the specified taxa.
- Method Detail
  - printPHYLIP
```
public void printPHYLIP(PrintWriter out)
                 throws IOException
```
    print alignment (PHYLIP format)
    
    Throws:
    
    IOException
  - toString
```
public String toString()
```
    returns representation of this alignment as a string
    
    Overrides:
    
    toString in class Object
  - squaredDistance
```
public double squaredDistance(DistanceMatrix mat,
                              boolean weighted)
```
    compute squared distance to second distance matrix
  - absoluteDistance
```
public double absoluteDistance(DistanceMatrix mat)
```
    compute absolute distance to second distance matrix
  - getSize
```
public int getSize()
```
    Returns the number of taxa which is also the number of rows and columns that the distance matrix has.
  - getClonedDistances
```
public final double[][] getClonedDistances()
```
    Returns the distances as a 2-dimensional array of doubles. Matrix is cloned first so it can be altered freely.
  - getDistances
```
public final double[][] getDistances()
```
    Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)
  - getDistance
```
public final float getDistance(int row,
                               int col)
```
  - meanDistance
```
public double meanDistance()
```
    Returns the mean pairwise distance of this matrix
  - getTaxon
```
public Taxon getTaxon(int i)
```
  - numberOfTaxa
```
public int numberOfTaxa()
```
  - whichIdNumber
```
public int whichIdNumber(String name)
```
  - whichIdNumber
```
public int whichIdNumber(Taxon id)
```
  - getTaxaList
```
public TaxaList getTaxaList()
```
    Return TaxaList of this alignment.
  - isSymmetric
```
public boolean isSymmetric()
```
    test whether this matrix is a symmetric distance matrix
  - getClosestIndex
```
public int getClosestIndex(int fromIndex,
                           int[] exclusion)
```
    Parameters:
    
    fromIndex - the index of the thing (taxa,sequence) from which we want to find the closest (excluding self)
    
    exclusion - indexes of things that should not be considered, may be null
    
    Returns:
    
    the index of the member closes to the specified
  - hadamardProduct
```
public static DistanceMatrix hadamardProduct(DistanceMatrix m0,
                                             DistanceMatrix m1)
```
  - getTableColumnNames
```
public Object[] getTableColumnNames()
```
    Description copied from interface: TableReport
    
    Get the names of the columns
    
    Specified by:
    
    getTableColumnNames in interface TableReport
    
    Returns:
    
    columns names
  - getRow
```
public Object[] getRow(long rowLong)
```
    Returns specified row.
    
    Specified by:
    
    getRow in interface TableReport
    
    Parameters:
    
    rowLong - row number
    
    Returns:
    
    row
  - getTableTitle
```
public String getTableTitle()
```
    Description copied from interface: TableReport
    
    Get the title of the table
    
    Specified by:
    
    getTableTitle in interface TableReport
    
    Returns:
    
    title
  - getRowCount
```
public long getRowCount()
```
    Description copied from interface: TableReport
    
    Get the number of rows
    
    Specified by:
    
    getRowCount in interface TableReport
    
    Returns:
    
    number of rows
  - getElementCount
```
public long getElementCount()
```
    Description copied from interface: TableReport
    
    Get the total number of elements in the dataset. Elements = rowCount * columnCount;
    
    Specified by:
    
    getElementCount in interface TableReport
    
    Returns:
    
    number of elements
  - getColumnCount
```
public int getColumnCount()
```
    Description copied from interface: TableReport
    
    Get the number of the columns
    
    Specified by:
    
    getColumnCount in interface TableReport
    
    Returns:
    
    number of columns
  - getValueAt
```
public Object getValueAt(long rowIndex,
                         int columnIndex)
```
    Description copied from interface: TableReport
    
    Returns value at given row and column.
    
    Specified by:
    
    getValueAt in interface TableReport
    
    Parameters:
    
    rowIndex - row number
    
    columnIndex - column number
    
    Returns:
    
    data
  - getColumnName
```
public String getColumnName(int col)
```
  - annotations
```
public GeneralAnnotation annotations()
```

Class DistanceMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface net.maizegenetics.util.TableReport

Constructor Detail

DistanceMatrix

DistanceMatrix

DistanceMatrix

DistanceMatrix

Method Detail

printPHYLIP

toString

squaredDistance

absoluteDistance

getSize

getClonedDistances

getDistances

getDistance

meanDistance

getTaxon

numberOfTaxa

whichIdNumber

whichIdNumber

getTaxaList

isSymmetric

getClosestIndex

hadamardProduct

getTableColumnNames

getRow

getTableTitle

getRowCount

getElementCount

getColumnCount

getValueAt

getColumnName

annotations