/*
    * 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.IOException;
  import java.io.InputStream;
  import java.util.List;
  import java.util.Vector;
  
  import org.apache.commons.lang3.StringUtils;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import ubic.basecode.dataStructure.matrix.Matrix2D;
  
  /**
   * Abstract class representing an object that can read in a {@link Matrix2D}from a file.
   * 
   * @author Paul Pavlidis
   * 
   */
  public abstract class AbstractMatrixReader<M extends Matrix2D<String, String, V>, V> {
  
      protected static Logger log = LoggerFactory.getLogger( AbstractMatrixReader.class );
  
      public abstract M read( InputStream stream ) throws IOException;
  
      public abstract M read( String filename ) throws IOException;
  
      public abstract M read( String filename, int maxRows ) throws IOException;
  
      /**
       * @param dis
       * @param skipColumns how many data columns shoul be ignored
       * @return
       * @throws IOException
       */
      protected List<String> readHeader( BufferedReader dis, int skipColumns ) throws IOException {
          List<String> headerVec = new Vector<String>();
          String header = null;
  
          /*
           * Read past comments.
           */
          while ( ( header = dis.readLine() ) != null ) {
              if ( header.startsWith( "#" ) || header.startsWith( "!" ) || StringUtils.isBlank( header ) ) {
                  continue;
              }
              break;
          }
  
          if ( header == null ) return headerVec;
  
          if ( header.startsWith( "\t" ) ) header = "c" + header;
  
          String[] tokens = StringUtils.splitPreserveAllTokens( header, "\t" );
          // delims.
  
          String previousToken = "";
          int columnNumber = 0;
  
          for ( int i = 0; i < tokens.length; i++ ) {
              String s = StringUtils.strip( tokens[i], " " );
              boolean missing = false;
  
              if ( s.compareTo( "\t" ) == 0 ) {
  
                  if ( previousToken.compareTo( "\t" ) == 0 ) { /* two tabs in a row */
                      missing = true;
                  } else if ( i == tokens.length - 1 ) { // at end of line.
                      missing = true;
                  } else {
                      previousToken = s;
                      continue;
                  }
              } else if ( StringUtils.isBlank( s ) ) {
                  missing = true;
              }
  
              if ( missing ) {
                  throw new IOException( "Missing values are not allowed in the header (column " + columnNumber + " at '"
                          + header + "')" );
             }
             if ( columnNumber > 0 ) {
 
                 if ( skipColumns > 0 && columnNumber <= skipColumns ) {
 
                     // ignore, but count it.
                 } else {
                     headerVec.add( s );
                 }
             } else {
                 // corner string.
             }
             columnNumber++;
 
             previousToken = s;
         }
 
         return headerVec;
 
     }
 }