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java.lang.Objectorg.biojava.bio.program.abi.ABITrace
public class ABITrace
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.
Copyright (c) 2001
Constructor Summary | |
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ABITrace(byte[] ABIFileData)
The byte[] constructor parses an ABI file represented as a byte array. |
|
ABITrace(java.io.File ABIFile)
The File constructor opens a local ABI file and parses the content. |
|
ABITrace(java.net.URL ABIFile)
The URL constructor opens an ABI file from any URL. |
Method Summary | |
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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). |
java.awt.image.BufferedImage |
getImage(int imageHeight,
int widthScale)
Returns a BufferedImage that represents the entire trace. |
SymbolList |
getSequence()
Returns the original programatically determined (unedited) sequence as a SymbolList . |
int |
getSequenceLength()
Returns the length of the sequence (number of bases) in this trace. |
int[] |
getTrace(AtomicSymbol 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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ABITrace(java.io.File ABIFile) throws java.io.IOException
ABIFile
- is a java.io.File
on the local file system.
java.io.IOException
- if there is a problem reading the file.
java.lang.IllegalArgumentException
- if the file is not a valid ABI file.public ABITrace(java.net.URL ABIFile) throws java.io.IOException
ABIFile
- is a java.net.URL
for an ABI trace file.
java.io.IOException
- if there is a problem reading from the URL.
java.lang.IllegalArgumentException
- if the URL does not contain a valid ABI file.public ABITrace(byte[] ABIFileData)
byte[]
constructor parses an ABI file represented as a byte array.
java.lang.IllegalArgumentException
- if the data does not represent a valid ABI file.Method Detail |
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public int getSequenceLength()
public int getTraceLength()
public int[] getBasecalls()
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).
public SymbolList getSequence() throws BioError
SymbolList
.
BioError
public int[] getTrace(AtomicSymbol base) throws IllegalSymbolException
base
- the DNA AttomicSymbol to retrieve the trace values for
IllegalSymbolException
- if the base is not validpublic java.awt.image.BufferedImage getImage(int imageHeight, int widthScale)
getTraceLength()
). The entire trace is represented
in the returned image.
imageHeight
- is the desired height of the image in pixels.widthScale
- indiates how many horizontal pixels to use to represent a single x-coordinate (try 2).
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