trans.tpmap
Class TPMapLine

java.lang.Object
  trans.tpmap.TPMapLine

All Implemented Interfaces:

java.lang.Comparable

public class TPMapLine

extends java.lang.Object

implements java.lang.Comparable

Minimal tpmap line, chrom, start, nothing else.

Constructor Summary

TPMapLine(java.lang.String line)

TPMapLine(java.lang.String[] items)
For parsing from an Agilent data file.

TPMapLine(java.lang.String[] items, boolean trueFalse)
For parsing from an Nimblegen NDF data file.

TPMapLine(java.lang.String chr, int pos, int row, int column, java.lang.String sequence)
Coordinates are zero based!

TPMapLine(java.lang.String chr, int pos, int row, int column, java.lang.String sequence, boolean hybridizesForwardStrand)
Coordinates are zero based!

TPMapLine(java.lang.String chrNum, java.lang.String row, java.lang.String column, java.lang.String sequence)
For parsing from an Agilent promoter array data file.

Method Summary

int	compareTo(java.lang.Object obj)
java.lang.String	getChromosome()
java.lang.String	getLine()
int	getPmX()
int	getPmY()
int	getStart()
static boolean	saveTPMap(TPMapLine[] sortedTPMap, java.io.File tpmapFile)

Methods inherited from class java.lang.Object

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

Constructor Detail

TPMapLine

public TPMapLine(java.lang.String[] items)

For parsing from an Agilent data file.

TPMapLine

public TPMapLine(java.lang.String chrNum,
                 java.lang.String row,
                 java.lang.String column,
                 java.lang.String sequence)

For parsing from an Agilent promoter array data file. Note there isn't a sequence for the oligo!

TPMapLine

public TPMapLine(java.lang.String chr,
                 int pos,
                 int row,
                 int column,
                 java.lang.String sequence)

Coordinates are zero based!

TPMapLine

public TPMapLine(java.lang.String chr,
                 int pos,
                 int row,
                 int column,
                 java.lang.String sequence,
                 boolean hybridizesForwardStrand)

Coordinates are zero based!

TPMapLine

public TPMapLine(java.lang.String[] items,
                 boolean trueFalse)

For parsing from an Nimblegen NDF data file.

TPMapLine

public TPMapLine(java.lang.String line)

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

saveTPMap

public static boolean saveTPMap(TPMapLine[] sortedTPMap,
                                java.io.File tpmapFile)

getLine

public java.lang.String getLine()

getChromosome

public java.lang.String getChromosome()

getPmX

public int getPmX()

getPmY

public int getPmY()

getStart

public int getStart()