org.biojava.bio.chromatogram

Class ChromatogramTools

java.lang.Object

org.biojava.bio.chromatogram.ChromatogramTools

public class ChromatogramTools
extends Object

Utility class for dealing with Chromatograms.

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

Method Summary

Methods

Modifier and Type	Method and Description
static SymbolList	getDNASequence(Chromatogram chromat) Get the called DNA sequence from a chromatogram.
static int	getIntFromSymbolList(SymbolList list, int which) Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.
static int	getTraceOffset(Chromatogram chromat, int which) Get a specific value from the trace offset sequence in the given chromatogram and extract its int value.
static int[]	getTraceOffsetArray(Chromatogram chromat) Converts the peak offsets list of the given chromatogram into a new int array.
static SymbolList	getTraceOffsets(Chromatogram chromat) Get the peak offsets for the called bases of a chromatogram.

Methods inherited from class java.lang.Object

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

Method Detail

getDNASequence

public static final SymbolList getDNASequence(Chromatogram chromat)

Get the called DNA sequence from a chromatogram. A synonym for chromat.getBaseCalls().symbolListForLabel(Chromatogram.DNA).

Parameters:

chromat - the Chromatogram to process

Returns:

a SymbolList containing the DNA

getTraceOffsets

public static final SymbolList getTraceOffsets(Chromatogram chromat)

Get the peak offsets for the called bases of a chromatogram. A synonym for chromat.getBaseCalls().symbolListForLabel(Chromatogram.OFFSETS).

Parameters:

chromat - the Chromatogram to process

Returns:

a SymbolList of offsets

getTraceOffsetArray

public static final int[] getTraceOffsetArray(Chromatogram chromat)

Converts the peak offsets list of the given chromatogram into a new int array.

The array is, of course, allocated and initialized at each call, so using this method like this:

 for (int i = m ; i < n ; i++)
    doSomething(getTraceOffsetArray(c)[i]);
 

is not recommended.

Parameters:

chromat - the Chromatogram to process

Returns:

an array of integers representing peak offsets

getTraceOffset

public static final int getTraceOffset(Chromatogram chromat,
                 int which)

Get a specific value from the trace offset sequence in the given chromatogram and extract its int value.

Parameters:

chromat - the chromatogram to examine

which - which symbol in the trace offset sequence to get. 1-based index.

Returns:

the offset for that peak

getIntFromSymbolList

public static final int getIntFromSymbolList(SymbolList list,
                       int which)

Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.

Parameters:

list - the target list

which - which symbol to unwrap and return. 1-based index.

Returns:

the integer represented by the symbol at that position