Package org.biojava.bio.chromatogram

Class ChromatogramFactory

  • public class ChromatogramFactory
extends java.lang.Object
    A factory that creates Chromatogram objects from files or streams. In either case, the type of object to create is determined from the first four bytes of the stream (the magic number).
    Since:
    1.3
    Author:
    Rhett Sutphin (UI CBCB), Matthew Pocock

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int ABI_MAGIC
      The magic number for ABIF files.
      static int SCF_MAGIC
      The magic number for SCF files.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Chromatogram create​(java.io.File f)
      Creates a new Chromatogram object from the named file.
      static Chromatogram create​(java.io.InputStream in)
      Creates a new Chromatogram object from the supplied stream.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • SCF_MAGIC

        public static final int SCF_MAGIC
        The magic number for SCF files.
        See Also:
        Constant Field Values

      • ABI_MAGIC

        public static final int ABI_MAGIC
        The magic number for ABIF files.
        See Also:
        Constant Field Values

    • Constructor Detail

      • ChromatogramFactory

        public ChromatogramFactory()

    • Method Detail

      • create

        public static Chromatogram create​(java.io.File f)
                           throws java.io.IOException,
                                  UnsupportedChromatogramFormatException
        Creates a new Chromatogram object from the named file.
        Parameters:
        f - the file to read
        Returns:
        a new Chromatogram
        Throws:
        java.io.IOException - when the file can't be read or some other I/O error occurs
        UnsupportedChromatogramFormatException - when the file doesn't contain a chromatogram in a supported format

      • create

        public static Chromatogram create​(java.io.InputStream in)
                           throws java.io.IOException,
                                  UnsupportedChromatogramFormatException
        Creates a new Chromatogram object from the supplied stream. Note that for some chromatogram formats, this can be much more memory-intensive than reading from a file.

        Note also that if the provided stream is a CachingInputStream, it will be seeked back to 0 before being passed to the parser. This is because the parsers that use CachingInputStream assume that the "file" starts at 0.

        Parameters:
        in - the stream from which to read the chromatogram.
        Returns:
        a new Chromatogram
        Throws:
        java.io.IOException - when there's a problem with the stream
        UnsupportedChromatogramFormatException - when the file doesn't contain a chromatogram in a supported format