Package org.biojava.bio.chromatogram

Class ChromatogramTools

    • 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