/*
    * 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 cern.colt.matrix.ObjectMatrix1D;
  import cern.colt.matrix.impl.DenseObjectMatrix2D;
  
  /**
   * Matrix that can hold any type of object
   * 
   * @author pavlidis
   * 
   */
  public class ObjectMatrixImpl<R, C, V> extends AbstractMatrix<R, C, V> implements ObjectMatrix<R, C, V> {
  
      private static final long serialVersionUID = -902358802107186038L;
      private DenseObjectMatrix2D matrix;
  
      public ObjectMatrixImpl( int x, int y ) {
          super();
          matrix = new DenseObjectMatrix2D( x, y );
      }
  
      /**
       * @param columns
       * @return
       */
      @Override
      public ObjectMatrixImpl<R, C, V> subsetColumns( List<C> columns ) {
          ObjectMatrixImpl<R, C, V> returnval = new ObjectMatrixImpl<R, C, V>( 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;
      }
  
      /**
       * @return
       */
      @Override
      public int columns() {
          return matrix.columns();
      }
  
      /**
       * @param row
       * @param column
       * @return
       */
      @SuppressWarnings("unchecked")
      @Override
      public V get( int row, int column ) {
          return ( V ) matrix.getQuick( row, column );
      }
  
      /*
       * (non-Javadoc)
       * 
       * @see ubic.basecode.dataStructure.matrix.NamedObjectMatrix#get(java.lang.Object, java.lang.Object)
       */
      public Object get( R row, C column ) {
          return get( getRowIndexByName( row ), getColIndexByName( column ) );
      }
  
      @Override
      public V getByKeys( R r, C c ) {
          return this.get( getRowIndexByName( r ), getColIndexByName( c ) );
     }
 
     @Override
     @SuppressWarnings("unchecked")
     public V[] getColumn( int col ) {
         V[] result = ( V[] ) new Object[rows()]; // this is how they do it in ArrayList
         for ( int i = 0; i < rows(); i++ ) {
             result[i] = get( i, col );
         }
 
         return result;
     }
 
     @Override
     public V getEntry( int row, int column ) {
         return get( row, column );
     }
 
     @Override
     @SuppressWarnings("unchecked")
     public V[] getRow( int row ) {
         Object[] ro = viewRow( row ).toArray();
         V[] result = ( V[] ) new Object[columns()]; // this is how they do it in ArrayList
         System.arraycopy( ro, 0, result, 0, ro.length );
         return result;
     }
 
     @Override
     public boolean isMissing( int i, int j ) {
         return get( i, j ) == "";
     }
 
     /**
      * @return
      */
 
     @Override
     public int rows() {
         return matrix.rows();
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see ubic.basecode.dataStructure.matrix.NamedMatrix#set(int, int, java.lang.Object)
      */
     @Override
     public void set( int row, int column, V value ) {
         matrix.setQuick( row, column, value );
     }
 
     /*
      * (non-Javadoc)
      * 
      * @see ubic.basecode.dataStructure.matrix.NamedMatrix#set(java.lang.Object, java.lang.Object, java.lang.Object)
      */
     @Override
     public void setByKeys( R r, C c, V v ) {
         this.set( getRowIndexByName( r ), getColIndexByName( c ), v );
     }
 
     /**
      * @return
      */
     @Override
     public int size() {
         return matrix.size();
     }
 
     @Override
     public ObjectMatrix<R, C, V> subset( int startRow, int startCol, int numRow, int numCol ) {
         int endRow = startRow + numRow - 1;
         super.checkRowRange( startRow, endRow );
         int endCol = startCol + numCol - 1;
         super.checkColRange( startCol, endCol );
         ObjectMatrix<R, C, V> result = new ObjectMatrixImpl<R, C, V>( numRow, numCol );
         int r = 0;
         for ( int i = startRow; i < endRow; i++ ) {
             int c = 0;
             for ( int j = startCol; j < endCol; j++ ) {
                 result.set( r, c++, this.get( i, j ) );
             }
             r++;
         }
         /*
          * FIXME set up the row/column names.
          */
         return result;
 
     }
 
     @Override
     public String toString() {
         StringBuffer buf = new StringBuffer();
         buf.append( "label" );
         for ( int i = 0; i < columns(); i++ ) {
             buf.append( "\t" + getColName( i ) );
         }
         buf.append( "\n" );
 
         for ( int i = 0; i < rows(); i++ ) {
             buf.append( getRowName( i ) );
             for ( int j = 0; j < columns(); j++ ) {
                 V v = get( i, j );
 
                 if ( v instanceof Double ) {
                     buf.append( String.format( "\t%.3g", v ) );
 
                 } else {
                     buf.append( "\t" + v );
                 }
             }
             buf.append( "\n" );
         }
         return buf.toString();
     }
 
     /**
      * @param column
      * @return
      */
     public ObjectMatrix1D viewColumn( int column ) {
         return matrix.viewColumn( column );
     }
 
     /**
      * @param row
      * @return
      */
     public ObjectMatrix1D viewRow( int row ) {
         return matrix.viewRow( row );
     }
 }