org.biojava.nbio.core.sequence.io

Class ABITrace

java.lang.Object

org.biojava.nbio.core.sequence.io.ABITrace

public class ABITrace
extends Object

Title: ABITrace

ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types. It can also return an image corresponding to the trace. It has three constructors with input types File, URL, and byte[].

ABI files contain two sets of basecall and sequence data, one that was originally created programatically and the other, which is an editable copy. This version of this object only references the original unedited data.

Constructor Summary

Constructors

Constructor and Description
ABITrace(byte[] ABIFileData) The byte[] constructor parses an ABI file represented as a byte array.
ABITrace(File ABIFile) The File constructor opens a local ABI file and parses the content.
ABITrace(URL ABIFile) The URL constructor opens an ABI file from any URL.

Method Summary

Modifier and Type	Method and Description
int[]	getBasecalls() Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
BufferedImage	getImage(int imageHeight, int widthScale) Returns a BufferedImage that represents the entire trace.
int[]	getQcalls() Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location).
AbstractSequence<NucleotideCompound>	getSequence() Returns the original programmatically determined (unedited) sequence as a AbstractSequence.
int	getSequenceLength() Returns the length of the sequence (number of bases) in this trace.
int[]	getTrace(String base) Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
int	getTraceLength() Returns the length of the trace (number of x-coordinate points in the graph).

Methods inherited from class java.lang.Object

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

Constructor Detail

ABITrace

public ABITrace(File ABIFile)
         throws IOException

The File constructor opens a local ABI file and parses the content.

Parameters:

ABIFile - is a java.io.File on the local file system.

Throws:

IOException - if there is a problem reading the file.

IllegalArgumentException - if the file is not a valid ABI file.

ABITrace

public ABITrace(URL ABIFile)
         throws IOException

The URL constructor opens an ABI file from any URL.

Parameters:

ABIFile - is a java.net.URL for an ABI trace file.

Throws:

IOException - if there is a problem reading from the URL.

IllegalArgumentException - if the URL does not contain a valid ABI file.

ABITrace

public ABITrace(byte[] ABIFileData)

The byte[] constructor parses an ABI file represented as a byte array.

Parameters:

ABIFileData - - byte array

Throws:

IllegalArgumentException - if the data does not represent a valid ABI file.

Method Detail

getSequenceLength

public int getSequenceLength()

Returns the length of the sequence (number of bases) in this trace.

Returns:

int seqLength

getTraceLength

public int getTraceLength()

Returns the length of the trace (number of x-coordinate points in the graph).

Returns:

int traceLength

getBasecalls

public int[] getBasecalls()

Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).

Returns:

int[] Basecalls

getQcalls

public int[] getQcalls()

Returns an int[] array that represents the quality - each int in the array corresponds to an quality value 90-255) in the graph at a base location).

Returns:

int[] qCalls

getSequence

public AbstractSequence<NucleotideCompound> getSequence()
                                                 throws CompoundNotFoundException

Returns the original programmatically determined (unedited) sequence as a AbstractSequence.

Returns:

AbstractSequence sequence

Throws:

CompoundNotFoundException

getTrace

public int[] getTrace(String base)
               throws CompoundNotFoundException

Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.

Parameters:

base - - the DNA String to retrieve the trace values for

Returns:

an array of ints giving the entire trace for that base

Throws:

CompoundNotFoundException - if the base is not valid

getImage

public BufferedImage getImage(int imageHeight,
                              int widthScale)

Returns a BufferedImage that represents the entire trace. The height can be set precisely in pixels, the width in pixels is determined by the scaling factor times the number of points in the trace (getTraceLength()). The entire trace is represented in the returned image.

Parameters:

imageHeight - - desired height of the image in pixels.

widthScale - - how many horizontal pixels to use to represent a single x-coordinate (try 2).

Returns:

BufferedImage image