content: package aliview.importer;
  
  import java.io.BufferedReader;
  import java.io.File;
  import java.io.FileReader;
  import java.util.ArrayList;
  import java.util.List;
  
  import org.apache.commons.lang.StringUtils;
  import org.apache.log4j.Logger;
  
  import aliview.NucleotideUtilities;
  import aliview.sequences.FileSequence;
  
  public class NotUsed_IndexFileReader {
  	private static final Logger logger = Logger.getLogger(NotUsed_IndexFileReader.class);
  	/*
  	public static ArrayList<FileSequence> createSequences(File indexFile, FileMMSequenceList seqList) {
  
  			long startTime = System.currentTimeMillis();
  			ArrayList<FileSequence> sequences = new ArrayList<FileSequence>();
  
  			try {
  				BufferedReader r = new BufferedReader(new FileReader(indexFile));
  				String line;
  				int nLine = 0;
  				int seqIndex = 0;
  		//		String[] splitted = new String[5];
  				while ((line = r.readLine()) != null) {
  
  					line = line.trim();
  
  					if(line.length() > 0){
  
  						String[] splitted = StringUtils.split(line, '\t');
  					//	String[] splitted = line.split("\t");//StringUtils.split(line, '\t');
  
  //						int startPos = 0;
  //						int endPos = line.indexOf('\t',startPos);
  //						
  //						splitted[0] = line.substring(startPos, endPos);
  //						startPos = endPos + 1;
  //						endPos = line.indexOf('\t',startPos);
  //						splitted[1] = line.substring(startPos, endPos);
  //						startPos = endPos + 1;
  //						endPos = line.indexOf('\t',startPos);
  //						splitted[2] = line.substring(startPos, endPos);
  //						startPos = endPos + 1;
  //						endPos = line.indexOf('\t',startPos);
  //						splitted[3] = line.substring(startPos, endPos);
  //						startPos = endPos + 1;
  //						endPos = line.indexOf('\t',startPos);
  //						splitted[4] = line.substring(startPos, endPos);
  
  						String  seqName = splitted[0];
  						int seqWithoutWhitespaceLength = Integer.parseInt(splitted[1]);
  						long seqAfterNameStartPointer = Long.parseLong(splitted[2]);
  						int lineCharLength = Integer.parseInt(splitted[3]);
  						int lineAbsoluteLength = Integer.parseInt(splitted[4]);
  
  						int nSeqFullLines = (int)Math.floor(seqWithoutWhitespaceLength/lineCharLength);
  						int lineDiff = lineAbsoluteLength - lineCharLength;
  
  
  						double partialLine = ((double)seqWithoutWhitespaceLength/(double)lineCharLength) - (double)nSeqFullLines;
  
  						int extraChars = (int)Math.floor(partialLine * lineDiff);
  
  
  						long endPointer = seqAfterNameStartPointer + seqWithoutWhitespaceLength + nSeqFullLines * lineDiff + extraChars;
  
  						FileSequence seq = new FileSequence(seqList, seqIndex, seqName, seqWithoutWhitespaceLength, seqAfterNameStartPointer, endPointer, lineCharLength, lineAbsoluteLength);
  						sequences.add(seq);
  						seqIndex ++;
  					}
  					nLine ++;
  				}
  
  			} catch (Exception e) {
  				logger.error(e);
  			}
  			long endTime = System.currentTimeMillis();
  			System.out.println("reading index took " + (endTime - startTime) + " milliseconds");
  
  			return sequences;
  		}
  
  	 */
  }
  