Class ChromatogramTools

Method Details

• 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