package org.molgenis.util.plink.drivers;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.StringTokenizer;
import org.molgenis.util.TextFileUtils;
import org.molgenis.util.plink.PlinkFileParser;
import org.molgenis.util.plink.datatypes.FamEntry;
/**
* Driver to query FAM files. FAM files annotate the families of BED files. See:
* http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml
*
* Content of a FAM file: Family ID Individual ID Paternal ID Maternal ID Sex
* (1=male; 2=female; other=unknown) Phenotype
*/
public class FamFileDriver implements PlinkFileParser
{
private BufferedReader reader;
private File file;
private char separator;
private long nrElements;
/**
* Construct a FamFileDriver on this file
*
* @param famFile
* @throws Exception
*/
public FamFileDriver(File famFile)
{
this(famFile, DEFAULT_FIELD_SEPARATOR);
}
public FamFileDriver(File famFile, char separator)
{
if (famFile == null) throw new IllegalArgumentException("file is null");
this.file = famFile;
this.separator = separator;
this.nrElements = -1l;
}
/**
* Get all FAM file entries
*
* @return
* @throws Exception
*/
public List<FamEntry> getAllEntries() throws IOException
{
reset();
List<FamEntry> entryList = new ArrayList<FamEntry>();
String line;
while ((line = reader.readLine()) != null)
entryList.add(parseEntry(line));
return entryList;
}
/**
* Get a specific set of FAM file entries
*
* @param from
* = inclusive
* @param to
* = exclusive
* @return
* @throws Exception
*/
public List<FamEntry> getEntries(final long from, final long to) throws IOException
{
reset();
List<FamEntry> entryList = new ArrayList<FamEntry>();
String line;
for (int i = 0; (line = reader.readLine()) != null && i < to; ++i)
if (i >= from) entryList.add(parseEntry(line));
return entryList;
}
private FamEntry parseEntry(String line) throws IOException
{
StringTokenizer strTokenizer = new StringTokenizer(line, this.separator + "");
try
{
String family = strTokenizer.nextToken();
String individual = strTokenizer.nextToken();
String father = strTokenizer.nextToken();
String mother = strTokenizer.nextToken();
byte sex = Byte.parseByte(strTokenizer.nextToken());
double phenotype = Double.parseDouble(strTokenizer.nextToken());
return new FamEntry(family, individual, father, mother, sex, phenotype);
}
catch (NoSuchElementException e)
{
throw new IOException("error in line: " + line, e);
}
catch (IndexOutOfBoundsException e)
{
throw new IOException("error in line: " + line, e);
}
catch (NumberFormatException e)
{
throw new IOException("error in line: " + line, e);
}
}
public long getNrOfElements() throws IOException
{
if (nrElements == -1) nrElements = TextFileUtils.getNumberOfNonEmptyLines(file, FILE_ENCODING);
return nrElements;
}
@Override
public void close() throws IOException
{
if (this.reader != null) this.reader.close();
}
public void reset() throws IOException
{
if (this.reader != null) close();
this.reader = new BufferedReader(new InputStreamReader(new FileInputStream(file), FILE_ENCODING));
}
}