org.biojava.bio.chromatogram
Class ChromatogramTools

java.lang.Object
  extended by 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
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