public class ChromatogramTools
extends Object 

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

• Method Summary

  All 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