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 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 invalid input: '<' 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