Package ubic.basecode.dataStructure.matrix

Class AbstractMatrix<R,C,V>

java.lang.Object
ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,V>
All Implemented Interfaces:
Serializable, Matrix2D<R,C,V>
Direct Known Subclasses:
CompressedBitMatrix, DoubleMatrix, IntegerMatrix, ObjectMatrixImpl, StringMatrix
public abstract class AbstractMatrix<R,C,V> extends Object implements Matrix2D<R,C,V>, Serializable
Author:
pavlidis
See Also:

  • Field Details

  • Constructor Details

    • AbstractMatrix

      public AbstractMatrix()

  • Method Details

    • addColumnName

      public final void addColumnName(C s)
      Add a column name when we don't care what the index will be. The index will be set by the method. This is useful for when we need to set up a matrix before we know how many column or rows there are.
      Specified by:
      addColumnName in interface Matrix2D<R,C,V>
      Parameters:
      s -

    • addRowName

      public final void addRowName(R s)
      Add a row name when we don't care what the index will be. The index will be set by the method. This is useful for when we need to set up a matrix before we know how many column or rows there are.
      Parameters:
      s -

    • asDoubles

      public double[][] asDoubles()
      Description copied from interface: Matrix2D
      Attempt to coerce the entries into doubles.

      Numeric entries (Double, BigDecimal, Integer, BigInteger) and Strings that can be parsed as doubles are converted. Booleans are converted to 1 or 0. Dates are converted via Date.getDate(). Null entries are rendered as Double.NaN. For entries that are other types of objects, the HashCode is used.

      Specified by:
      asDoubles in interface Matrix2D<R,C,V>
      Returns:

    • assign

      public void assign(V value)
      Description copied from interface: Matrix2D
      Set all values in the matrix to the given value.
      Specified by:
      assign in interface Matrix2D<R,C,V>
      Parameters:
      value -

    • containsColumnName

      public final boolean containsColumnName(C columnName)
      Specified by:
      containsColumnName in interface Matrix2D<R,C,V>
      Parameters:
      columnName -
      Returns:

    • containsRowName

      public final boolean containsRowName(R rowName)
      Specified by:
      containsRowName in interface Matrix2D<R,C,V>
      Parameters:
      rowName -
      Returns:

    • getColIndexByName

      public final int getColIndexByName(C columnKey)
      Description copied from interface: Matrix2D
      Get the index of a column by name.
      Specified by:
      getColIndexByName in interface Matrix2D<R,C,V>
      Parameters:
      columnKey - String
      Returns:
      int

    • getColName

      public final C getColName(int i)
      Description copied from interface: Matrix2D
      Gte the column name for an index.
      Specified by:
      getColName in interface Matrix2D<R,C,V>
      Parameters:
      i - int
      Returns:
      java.lang.String

    • getColNames

      public final List<C> getColNames()
      Specified by:
      getColNames in interface Matrix2D<R,C,V>
      Returns:
      list of column names. Do not modify this list. Use the addColumnName methods.

    • getRowIndexByName

      public final int getRowIndexByName(R s)
      Description copied from interface: Matrix2D
      Get the index of a row by name..
      Specified by:
      getRowIndexByName in interface Matrix2D<R,C,V>
      Parameters:
      s - String
      Returns:
      int

    • getRowName

      public final R getRowName(int i)
      Description copied from interface: Matrix2D
      Get the row name for an index
      Specified by:
      getRowName in interface Matrix2D<R,C,V>
      Parameters:
      i - int
      Returns:
      java.lang.String

    • getRowNameMapIterator

      public final Iterator<R> getRowNameMapIterator()
      Specified by:
      getRowNameMapIterator in interface Matrix2D<R,C,V>
      Returns:
      java.util.Iterator

    • getRowNames

      public final List<R> getRowNames()
      Specified by:
      getRowNames in interface Matrix2D<R,C,V>
      Returns:

    • hasColNames

      public final boolean hasColNames()
      Description copied from interface: Matrix2D
      Check if this matrix has a valid set of column names.
      Specified by:
      hasColNames in interface Matrix2D<R,C,V>
      Returns:
      boolean

    • hasMissingValues

      public boolean hasMissingValues()
      Test for the presence of missing values (null, or in the case of numbers, NaN)
      Returns:

    • hasRow

      public final boolean hasRow(R r)
      Specified by:
      hasRow in interface Matrix2D<R,C,V>
      Parameters:
      r - Object
      Returns:
      boolean

    • hasRowNames

      public final boolean hasRowNames()
      Specified by:
      hasRowNames in interface Matrix2D<R,C,V>
      Returns:
      boolean

    • numMissing

      public final int numMissing()
      Description copied from interface: Matrix2D
      Return the number of missing values in the matrix.
      Specified by:
      numMissing in interface Matrix2D<R,C,V>
      Returns:

    • setColumnName

      public final void setColumnName(C s, int i)
      Description copied from interface: Matrix2D
      Add a column name associated with an index.
      Specified by:
      setColumnName in interface Matrix2D<R,C,V>
      Parameters:
      s - Object a column name
      i - int the column index associated with this name

    • setColumnNames

      public void setColumnNames(List<C> v)
      Specified by:
      setColumnNames in interface Matrix2D<R,C,V>
      Parameters:
      v -

    • setRowName

      public final void setRowName(R s, int i)
      Description copied from interface: Matrix2D
      Add a row name associated with a row index.
      Specified by:
      setRowName in interface Matrix2D<R,C,V>
      Parameters:
      s - Object
      i - int

    • setRowNames

      public final void setRowNames(List<R> v)
      Specified by:
      setRowNames in interface Matrix2D<R,C,V>
      Parameters:
      v -

    • size

      public abstract int size()

    • checkColRange

      protected void checkColRange(int startCol, int endCol)

    • checkRowRange

      protected void checkRowRange(int startRow, int endRow)