Overview  Package   Class  Use  Deprecated  Index
Home >> All >> edu >> mit >> wi >> omnigene >> service >> analysis >> [ pedtool overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

edu.mit.wi.omnigene.service.analysis.pedtool
Class PedFileParser  

java.lang.Object
  edu.mit.wi.omnigene.service.analysis.pedtool.PedFileParser

---

public class PedFileParser

extends java.lang.Object

Title: PedFileParser.java

Description: Uses it to parse a pedigree file and store the data in object PedFile. The format of pedigree file is: column 1: familyID column 2: individual ID column 3: dad ID column 4: mom ID column 5: gender ( 1 is male, 2 is female ) column 6: affected status (1 is unaffected, 2 is affected ) column 7: (optional) libility column 8 and 9: marker 1 (seperated by space) column 2n and 2n+1: marker n (seperated by space) Columns are seperated by tab except between one set of marker. Family ID plus individual ID is unique and "0" stands for data missing.

Version:

$Revision 1.2 $

---

Field Summary
static int	PEDFILE
static int	PEDFILE_WITHHEADER

 

Constructor Summary

PedFileParser()

 

Method Summary
static PedFile	parse(java.io.File in, int type)           Parses input file to object PedFile

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

PEDFILE

public static final int PEDFILE

See Also:

Constant Field Values

---

PEDFILE_WITHHEADER

public static final int PEDFILE_WITHHEADER

See Also:

Constant Field Values

Constructor Detail

PedFileParser

public PedFileParser()

Method Detail

parse

public static PedFile parse(java.io.File in,
                            int type)
                     throws CheckDataException

Parses input file to object PedFile

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> edu >> mit >> wi >> omnigene >> service >> analysis >> [ pedtool overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---