/*
    * The baseCode project
    * 
    * Copyright (c) 2006 University of British Columbia
    * 
    * Licensed under the Apache License, Version 2.0 (the "License");
    * you may not use this file except in compliance with the License.
    * You may obtain a copy of the License at
    *
   *       http://www.apache.org/licenses/LICENSE-2.0
   *
   * Unless required by applicable law or agreed to in writing, software
   * distributed under the License is distributed on an "AS IS" BASIS,
   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   * See the License for the specific language governing permissions and
   * limitations under the License.
   *
   */
  package ubic.basecode.dataStructure.matrix;
  
  import java.util.List;
  
  import no.uib.cipr.matrix.DenseMatrix;
  import no.uib.cipr.matrix.sparse.FlexCompRowMatrix;
  import no.uib.cipr.matrix.sparse.SparseVector;
  import cern.colt.list.DoubleArrayList;
  import cern.colt.matrix.DoubleMatrix1D;
  
  /**
   * Supports sparse matrices (where sparse means most values are zero, not that they are missing).
   * 
   * @author xwan
   * @see no.uib.cipr.matrix.sparse.FlexCompRowMatrix for how this is implemented under the hood.
   * 
   */
  public class CompressedSparseDoubleMatrix<R, C> extends DoubleMatrix<R, C> {
  
      private static final long serialVersionUID = 5771918031750038719L;
  
      /*
       * FlexCompRowMatrix isn't serializable, so either is this in any useful way, despite claim.
       */
      private transient FlexCompRowMatrix matrix;
  
      /**
       * @param mat
       */
      public CompressedSparseDoubleMatrix( double[][] mat ) {
          super();
          matrix = new FlexCompRowMatrix( new DenseMatrix( mat ) );
          matrix.compact();
      }
  
      /**
       * @param rows int
       * @param cols int
       */
      public CompressedSparseDoubleMatrix( int rows, int cols ) {
          super();
          matrix = new FlexCompRowMatrix( rows, cols );
          matrix.compact();
      }
  
      /**
       * @return double[][]
       */
      @Override
      public double[][] asArray() {
          double[][] result = new double[rows()][];
          for ( int i = 0; i < rows(); i++ ) {
              result[i] = getRow( i );
          }
          return result;
      }
  
      /**
       * @return
       */
      public int cardinality() {
          int total = 0;
          for ( int i = 0; i < matrix.numRows(); i++ ) {
              total = total + matrix.getRow( i ).getUsed();
          }
  
          return total;
      }
  
      /**
       * @return
       */
      @Override
      public int columns() {
          return matrix.numColumns();
      }
  
      /*
       * (non-Javadoc)
       * 
       * @see ubic.basecode.dataStructure.matrix.DoubleMatrixNamed#copy()
      */
     @Override
     public DoubleMatrix<R, C> copy() {
         DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( this.rows(), this.columns() );
 
         for ( int i = 0; i < this.rows(); i++ ) {
             returnval.setRowName( this.getRowName( i ), i );
             for ( int j = 0; j < this.columns(); j++ ) {
                 if ( i == 0 ) {
                     returnval.setColumnName( this.getColName( j ), j );
                 }
                 returnval.set( i, j, this.get( i, j ) );
             }
         }
         return returnval;
 
     }
 
     /**
      * @param row
      * @param column
      * @return
      */
     @Override
     public double get( int row, int column ) {
         return matrix.get( row, column );
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see ubic.basecode.dataStructure.matrix.NamedPrimitiveMatrix#getColObj(int)
      */
     @Override
     public Double[] getColObj( int col ) {
         Double[] result = new Double[rows()];
         for ( int i = 0; i < rows(); i++ ) {
             result[i] = new Double( get( i, col ) );
         }
         return result;
     }
 
     @Override
     public DoubleMatrix<R, C> getColRange( int startCol, int endCol ) {
         super.checkColRange( startCol, endCol );
 
         DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( this.rows(), 1 + endCol - startCol );
         int k = 0;
         for ( int i = startCol; i <= endCol; i++ ) {
             C colName = this.getColName( i );
             if ( colName != null ) {
                 returnval.setColumnName( colName, i );
             }
             for ( int j = 0, m = this.rows(); j < m; j++ ) {
                 if ( i == startCol ) {
                     R rowName = this.getRowName( j );
                     returnval.setRowName( rowName, j );
                 }
                 returnval.set( j, k, this.get( j, i ) );
             }
             k++;
         }
         return returnval;
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see basecode.dataStructure.matrix.DoubleMatrixNamed#getColumn(int)
      */
     @Override
     public double[] getColumn( int col ) {
         double[] result = new double[rows()];
         for ( int i = 0; i < rows(); i++ ) {
             result[i] = get( i, col );
         }
         return result;
     }
 
     @Override
     public Double getObject( int row, int col ) {
         return new Double( get( row, col ) );
     }
 
     /**
      * Return a reference to a specific row.
      * 
      * @param row int
      * @return double[]
      */
     @Override
     public double[] getRow( int row ) {
         SparseVector vector = this.matrix.getRow( row );
         double[] data = vector.getData();
         int[] indices = vector.getIndex();
         double[] values = new double[columns()];
         assert data.length == indices.length;
         for ( int j = 0; j < data.length; j++ ) {
             if ( indices[j] == 0 && j > 0 ) break;
             values[indices[j]] = data[j];
         }
         return values;
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see basecode.dataStructure.matrix.AbstractNamedDoubleMatrix#getRowArrayList(int)
      */
     @Override
     public DoubleArrayList getRowArrayList( int i ) {
         return new DoubleArrayList( getRow( i ) );
     }
 
     /**
      * @param s String
      * @return double[]
      */
     @Override
     public double[] getRowByName( R s ) {
         return getRow( getRowIndexByName( s ) );
     }
 
     @Override
     public Double[] getRowObj( int row ) {
         Double[] result = new Double[columns()];
         double[] values = getRow( row );
         for ( int i = 0; i < columns(); i++ ) {
             result[i] = new Double( values[i] );
         }
         return result;
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see ubic.basecode.dataStructure.matrix.Matrix2D#getRowRange(int, int)
      */
     @Override
     public DoubleMatrix<R, C> getRowRange( int startRow, int endRow ) {
         super.checkRowRange( startRow, endRow );
 
         DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( endRow + 1 - startRow, this.columns() );
         int k = 0;
         for ( int i = startRow; i <= endRow; i++ ) {
             R rowName = this.getRowName( i );
             if ( rowName != null ) {
                 returnval.setRowName( rowName, i );
             }
             for ( int j = 0, m = this.columns(); j < m; j++ ) {
                 if ( i == 0 ) {
                     C colName = this.getColName( j );
                     returnval.setColumnName( colName, j );
                 }
                 returnval.set( k, j, this.get( i, j ) );
             }
             k++;
         }
         return returnval;
     }
 
     @Override
     public boolean isMissing( int i, int j ) {
         return Double.isNaN( get( i, j ) );
     }
 
     @Override
     public int rows() {
         return matrix.numRows();
     }
 
     /**
      * @param row
      * @param column
      * @param value
      */
     @Override
     public void set( int row, int column, Double value ) {
         matrix.set( row, column, value );
     }
 
     /**
      * @return
      */
     @Override
     public int size() {
         return matrix.numColumns() * matrix.numRows();
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see ubic.basecode.dataStructure.matrix.DoubleMatrix#subsetColumns(java.util.List)
      */
     @Override
     public DoubleMatrix<R, C> subsetColumns( List<C> columns ) {
 
         DoubleMatrix<R, C> returnval = new DenseDoubleMatrix<R, C>( this.rows(), columns.size() );
         returnval.setRowNames( this.getRowNames() );
         for ( int i = 0; i < this.rows(); i++ ) {
             int currentColumn = 0;
             for ( C c : columns ) {
                 int j = this.getColIndexByName( c );
 
                 returnval.set( i, currentColumn, this.get( i, j ) );
 
                 if ( i == 0 ) {
                     returnval.setColumnName( c, currentColumn );
                 }
 
                 currentColumn++;
 
             }
 
         }
         return returnval;
     }
 
     @Override
     public DoubleMatrix<R, C> subsetRows( List<R> rowNames ) {
         DoubleMatrix<R, C> returnval = new CompressedSparseDoubleMatrix<R, C>( rowNames.size(), this.columns() );
 
         int currentRow = 0;
         for ( R rowName : rowNames ) {
 
             if ( !this.containsRowName( rowName ) ) continue;
 
             int i = this.getRowIndexByName( rowName );
             returnval.setRowName( rowName, currentRow );
             for ( int j = 0; j < this.columns(); j++ ) {
                 if ( currentRow == 0 ) {
                     returnval.setColumnName( this.getColName( j ), j );
                 }
                 returnval.set( currentRow, j, this.get( i, j ) );
             }
             currentRow++;
         }
         if ( !returnval.getRowNames().containsAll( rowNames ) ) {
             throw new IllegalArgumentException( "Invalid rows to select, some are not in the original matrix" );
         }
         return returnval;
     }
 
     @Override
     public DoubleMatrix<C, R> transpose() {
         throw new UnsupportedOperationException();
     }
 
     /**
      * 
      */
     public void trimToSize() {
 
     }
 
     /**
      * @param column
      * @return
      */
     @Override
     public DoubleMatrix1D viewColumn( int column ) {
         double[] oneColumn = new double[this.rows()];
         for ( int i = 0; i < matrix.numRows(); i++ )
             oneColumn[i] = this.get( i, column );
         return new DenseDoubleMatrix1D( oneColumn );
     }
 
     /**
      * @param row
      * @return
      */
     @Override
     public DoubleMatrix1D viewRow( int row ) {
         return new DenseDoubleMatrix1D( getRow( row ) );
     }
 
 }