/*
    * 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 org.apache.commons.lang3.StringUtils;
  
  import cern.colt.matrix.ObjectMatrix1D;
  import cern.colt.matrix.impl.DenseObjectMatrix2D;
  
  /**
   * A NamedMatrix containing String objects.
   * 
   * @author Paul Pavlidis
   * 
   */
  public class StringMatrix<R, C> extends AbstractMatrix<R, C, String> implements ObjectMatrix<R, C, String> {
  
      /**
       * @param columns
       * @return
       */
      @Override
      public ObjectMatrix<R, C, String> subsetColumns( List<C> columns ) {
          StringMatrix<R, C> returnval = new StringMatrix<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;
      }
  
      /**
       * 
       */
      private static final long serialVersionUID = -7369003979104984162L;
      private DenseObjectMatrix2D matrix;
  
      public StringMatrix( int x, int y ) {
          super();
          matrix = new DenseObjectMatrix2D( x, y );
      }
  
      /**
       * @return
       */
      @Override
      public int columns() {
          return matrix.columns();
      }
  
      /**
       * @param row
       * @param column
       * @return
       */
      @Override
      public String get( int row, int column ) {
          return ( String ) matrix.get( row, column );
      }
  
      /*
       * (non-Javadoc)
       * 
       * @see ubic.basecode.dataStructure.matrix.NamedObjectMatrix#get(java.lang.Object, java.lang.Object)
       */
      public String get( R row, C column ) {
          return this.get( this.getRowIndexByName( row ), this.getColIndexByName( column ) );
      }
  
      @Override
     public String getByKeys( R r, C c ) {
         return this.get( getRowIndexByName( r ), getColIndexByName( c ) );
     }
 
     public String[] getColObj( int col ) {
         String[] result = new String[rows()];
         for ( int i = 0; i < rows(); i++ ) {
             result[i] = get( i, col );
         }
         return result;
     }
 
     @Override
     public String[] getColumn( int col ) {
         String[] result = new String[rows()];
         for ( int i = 0; i < rows(); i++ ) {
             result[i] = get( i, col );
         }
         return result;
     }
 
     @Override
     public String getEntry( int row, int column ) {
         return get( row, column );
     }
 
     public String getObject( int row, int col ) {
         return get( row, col );
     }
 
     @Override
     public String[] getRow( int row ) {
         String[] result = new String[columns()];
         for ( int i = 0; i < columns(); i++ ) {
             result[i] = get( row, i );
         }
         return result;
     }
 
     /**
      * Strings are considered missing if they are whitespace, null or empty.
      */
     @Override
     public boolean isMissing( int i, int j ) {
         return StringUtils.isBlank( get( i, j ) );
     }
 
     /**
      * @return
      */
     @Override
     public int rows() {
         return matrix.rows();
     }
 
     /**
      * @param row
      * @param column
      * @param value
      */
     @Override
     public void set( int row, int column, String value ) {
         matrix.set( 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, String v ) {
         this.set( getRowIndexByName( r ), getColIndexByName( c ), v );
     }
 
     /**
      * @return
      */
     @Override
     public int size() {
         return matrix.size();
     }
 
     @Override
     public ObjectMatrix<R, C, String> 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, String> result = new StringMatrix<R, C>( numRow, numCol );
         int r = 0;
         for ( int i = startRow; i <= endRow; i++ ) {
             int c = 0;
             result.setRowName( this.getRowName( i ), r );
             for ( int j = startCol; j <= endCol; j++ ) {
                 if ( r == 0 ) {
                     result.setColumnName( this.getColName( j ), c );
                 }
                 result.set( r, c++, this.get( i, j ) );
             }
             r++;
         }
 
         return result;
 
     }
 
     /**
      * @return java.lang.String
      */
     @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++ ) {
                 buf.append( "\t" + get( i, j ) );
             }
             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 );
     }
 
 }