/*
    * 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.io.reader;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.InputStreamReader;
  import java.text.DecimalFormat;
  import java.text.NumberFormat;
  import java.text.ParseException;
  import java.util.*;
  
  import org.apache.commons.lang3.StringUtils;
  
  import ubic.basecode.dataStructure.matrix.DoubleMatrix;
  import ubic.basecode.dataStructure.matrix.DoubleMatrixFactory;
  import ubic.basecode.util.FileTools;
  import cern.colt.list.DoubleArrayList;
  
  /**
   * Reader for {@link basecode.dataStructure.matrix.DoubleMatrix}. Lines beginning with "#" or "!" will be ignored.
   *
   * @author Paul Pavlidis
   *
   */
  public class DoubleMatrixReader extends AbstractMatrixReader<DoubleMatrix<String, String>, Double> {
  
      private List<String> colNames;
      private int numHeadings;
  
      /**
       * @param stream InputStream stream to read from
       * @return NamedMatrix object constructed from the data file
       * @throws IOException
       */
      @Override
      public DoubleMatrix<String, String> read( InputStream stream ) throws IOException {
          return read( stream, null, 0 );
      }
  
      /**
       * @param stream InputStream
       * @param wantedRowNames Set
       * @return <code>read( stream, wantedRowNames, createEmptyRows )</code> with <code>createEmptyRows</code> set to
       *         true.
       * @throws IOException
       */
      public DoubleMatrix<String, String> read( InputStream stream, Collection<String> wantedRowNames )
              throws IOException {
          return read( stream, wantedRowNames, true, 0, -1 );
      }
  
      /**
       * @param stream InputStream
       * @param wantedRowNames Set
       * @param createEmptyRows if a row contained in <code>wantedRowNames</code> is not found in the file, create an
       *        empty row filled with Double.NaN iff this param is true.
       * @param maxRows
       * @return matrix
       * @throws IOException
       */
      @SuppressWarnings("resource")
      public DoubleMatrix<String, String> read( InputStream stream, Collection<String> wantedRowNames,
              boolean createEmptyRows, int skipColumns, int maxRows ) throws IOException {
  
          NumberFormat nf = NumberFormat.getInstance( Locale.ENGLISH );
          if ( nf instanceof DecimalFormat ) {
              // ( ( DecimalFormat ) nf ).setDecimalSeparatorAlwaysShown( true );
          }
  
          BufferedReader dis = new BufferedReader( new InputStreamReader( stream ) );
  
          List<DoubleArrayList> MTemp = new Vector<DoubleArrayList>();
  
          List<String> rowNames = new Vector<String>();
          String row;
  
          //
          // We need to keep track of which row names we actually found in the file
          // because will want to add empty rows for each row name we didn't find
          // (if createEmptyRows == true).
         //
         Collection<String> wantedRowsFound = new HashSet<String>();
 
         colNames = readHeader( dis, skipColumns );
 
         numHeadings = colNames.size();
 
         int rowNumber = 0;
 
         while ( ( row = dis.readLine() ) != null ) {
 
             if ( StringUtils.isBlank( row ) ) {
                 continue;
             }
 
             String rowName = parseRow( row, rowNames, MTemp, wantedRowNames, skipColumns, nf );
 
             if ( rowName == null ) {
                 // signals a blank or skipped row.
                 continue;
             }
 
             if ( wantedRowNames != null ) {
 
                 // if we already have all the rows we want, then bail out
                 if ( wantedRowsFound.size() >= wantedRowNames.size() ) {
                     assert wantedRowsFound.containsAll( wantedRowNames );
                     log.info( "Found all rows needed" );
                     return createMatrix( MTemp, rowNames, colNames );
                 }
 
                 if ( wantedRowNames.contains( rowName ) ) {
                     wantedRowsFound.add( rowName );
                 }
             }
 
             if ( maxRows > 0 && ++rowNumber == maxRows ) break;
 
         }
         stream.close();
 
         //
         // Add empty rows for each row name we didn't find in the file
         //
         if ( wantedRowNames != null && wantedRowNames.size() != wantedRowsFound.size() && createEmptyRows ) {
             Iterator<String> iterator = wantedRowNames.iterator();
             while ( iterator.hasNext() ) {
                 String s = iterator.next();
                 if ( !wantedRowsFound.contains( s ) ) {
                     if ( log.isDebugEnabled() ) log.debug( s + " was not found, adding empty row" );
                     DoubleArrayList emptyRow = createEmptyRow( numHeadings );
                     rowNames.add( s );
                     MTemp.add( emptyRow );
                 }
             }
         }
         assert rowNames.size() == MTemp.size();
         return createMatrix( MTemp, rowNames, colNames );
 
     }
 
     /**
      * @param stream
      * @param wantedRowNames
      * @param numberOfColumnsToSkip
      * @return
      * @throws IOException
      */
     public DoubleMatrix<String, String> read( InputStream stream, Collection<String> wantedRowNames,
             int numberOfColumnsToSkip ) throws IOException {
         return read( stream, wantedRowNames, true, numberOfColumnsToSkip, -1 );
     }
 
     /**
      * @param filename data file to read from (can be compressed)
      * @return NamedMatrix object constructed from the data file
      * @throws IOException
      */
     @Override
     public DoubleMatrix<String, String> read( String filename ) throws IOException {
         return read( filename, null, -1 );
     }
 
     /**
      * Read a matrix from a file, subject to filtering criteria.
      *
      * @param filename data file to read from (can be compressed)
      * @param wantedRowNames contains names of rows we want to get
      * @return NamedMatrix object constructed from the data file
      * @throws IOException
      */
     @SuppressWarnings("resource")
     public DoubleMatrix<String, String> read( String filename, Collection<String> wantedRowNames ) throws IOException {
         File infile = new File( filename );
         if ( !infile.exists() || !infile.canRead() ) {
             throw new IOException( "Could not read from file " + filename );
         }
         InputStream stream = FileTools.getInputStreamFromPlainOrCompressedFile( filename );
         return read( stream, wantedRowNames, -1 );
     } // end read
 
     /**
      * @param fileName
      * @param wantedRowNames if null, takes all rows
      * @param numberOfColumnsToSkip how many columns to skip -- not counting the first column. So if you set this to 4,
      *        the first four data columns will be skipped. If you set it to zero, only the first column will be skipped.
      * @return
      * @throws IOException
      */
     @SuppressWarnings("resource")
     public DoubleMatrix<String, String> read( String fileName, Collection<String> wantedRowNames,
             int numberOfColumnsToSkip ) throws IOException {
         File infile = new File( fileName );
         if ( !infile.exists() || !infile.canRead() ) {
             throw new IOException( "Could not read from file " + fileName );
         }
         InputStream stream = FileTools.getInputStreamFromPlainOrCompressedFile( fileName );
         return read( stream, wantedRowNames, true, numberOfColumnsToSkip, -1 );
     }
 
     @Override
     public DoubleMatrix<String, String> read( String filename, int maxRows ) throws IOException {
         return read( filename, null, maxRows );
     }
 
     protected DoubleArrayList createEmptyRow( int numColumns ) {
 
         DoubleArrayList row = new DoubleArrayList();
         for ( int i = 0; i < numColumns; i++ ) {
             row.add( Double.NaN );
         }
         return row;
     }
 
     // -----------------------------------------------------------------
     // protected methods
     // -----------------------------------------------------------------
 
     protected DoubleMatrix<String, String> createMatrix( List<DoubleArrayList> MTemp, List<String> rowNames,
             List<String> colNames1 ) {
 
         if ( MTemp.isEmpty() ) {
             throw new IllegalArgumentException( "Must provide vectors" );
         }
         DoubleMatrix<String, String> matrix = DoubleMatrixFactory.fastrow( MTemp.size(), MTemp.get( 0 ).size() );
 
         for ( int i = 0; i < matrix.rows(); i++ ) {
             for ( int j = 0; j < matrix.columns(); j++ ) {
                 if ( MTemp.get( i ).size() < j + 1 ) {
                     matrix.set( i, j, Double.NaN );
                     // this allows the input file to have ragged ends.
                     // todo I'm not sure allowing ragged inputs is a good idea -PP
                 } else {
                     matrix.set( i, j, MTemp.get( i ).elements()[j] );
                 }
             }
         }
 
         assert matrix.rows() == MTemp.size();
         assert matrix.rows() == rowNames.size();
         assert matrix.columns() == colNames.size() : "Got " + matrix.columns() + " != " + colNames.size();
 
         matrix.setRowNames( rowNames );
         matrix.setColumnNames( colNames1 );
         return matrix;
 
     } // end createMatrix
 
     /**
      * @param row
      * @param rowNames
      * @param MTemp
      * @param wantedRowNames
      * @param skipColumns the number of columns after the first to ignore (for example, Gemma output that includes gene
      *        information as well as numeric data)
      * @return
      * @throws IOException
      */
     private String parseRow( String row, Collection<String> rowNames, List<DoubleArrayList> MTemp,
             Collection<String> wantedRowNames, int skipColumns, NumberFormat nf ) throws IOException {
 
         if ( row.startsWith( "#" ) || row.startsWith( "!" ) ) {
             return null;
         }
 
         String[] tokens = StringUtils.splitPreserveAllTokens( row, "\t" );
 
         DoubleArrayList rowTemp = new DoubleArrayList();
         int columnNumber = 0;
         String previousToken = "";
         String currentRowName = null;
         for ( int i = 0; i < tokens.length; i++ ) {
             String tok = tokens[i];
             boolean missing = false;
 
             if ( tok.compareTo( "\t" ) == 0 ) {
                 /* two tabs in a row */
                 if ( previousToken.compareTo( "\t" ) == 0 ) {
                     missing = true;
                 } else if ( i == tokens.length - 1 ) { // at end of line.
                     missing = true;
                 } else {
                     previousToken = tok;
                     continue;
                 }
             } else if ( StringUtils.isBlank( tok ) || tok.compareTo( "NaN" ) == 0 || tok.compareTo( "NA" ) == 0 ) {
                 missing = true;
             }
 
             if ( columnNumber > 0 ) {
 
                 if ( skipColumns > 0 && columnNumber <= skipColumns ) {
                     // skip.
                 } else if ( missing ) {
                     rowTemp.add( Double.NaN );
                 } else {
                     try {
                         /*
                          * NumberFormat.parse thinks things like 9101001_at are okay. Try to catch such cases. Note that
                          * we can't use Double.parseDouble because that doesn't seem to handle locale-specific number
                          * formats like european decimals (0,001 etc.)
                          */
                         // if ( tok.matches( ".*[a-zA-Z_=].*" ) ) {
                         // throw new NumberFormatException( "Unexpected non-numeric value found in column "
                         // + columnNumber + ": " + tok );
                         // }
                         rowTemp.add( nf.parse( tok.toUpperCase() ).doubleValue() );
                     } catch ( ParseException e ) {
                         throw new RuntimeException( e );
                     }
                 }
             } else {
                 // First field is the row label.
 
                 if ( missing ) {
                     throw new IOException( "Missing values not allowed for row labels ("
                             + StringUtils.abbreviate( row, 20 ) + ")" );
                 }
 
                 currentRowName = tok;
 
                 // Skip rows. Return the row name anyway.
                 if ( wantedRowNames != null && !wantedRowNames.contains( currentRowName ) ) {
                     return currentRowName;
                 }
 
                 rowNames.add( currentRowName );
             }
 
             columnNumber++;
             previousToken = tok;
         } // end while (st.hasMoreTokens())
           // done parsing one row -- no more tokens
 
         if ( rowTemp.size() > numHeadings ) {
             throw new IOException( "Too many values (" + rowTemp.size() + ") in row  (based on headings count of "
                     + numHeadings + ")" );
         }
 
         MTemp.add( rowTemp );
         return currentRowName;
 
     }
 
 } // end class DoubleMatrixReader