Package chemaxon.formats.recognizer

Class PeptideRecognizer

  • @PublicAPI
@Deprecated
public class PeptideRecognizer
extends Recognizer
    Deprecated.
    as of Marvin 2014.07.21.0 intended for internal use only
    Peptide format recognizer.
    Since:
    Marvin 5.0, 06/07/2007

    • Constructor Detail

      • PeptideRecognizer

        public PeptideRecognizer()
        Deprecated.

    • Method Detail

      • tryToRecognize

        public chemaxon.common.util.Pair<Boolean,​Collection<String>> tryToRecognize​(String line,
                                                                                  int lineNumber)
        Deprecated.
        Description copied from class: Recognizer
        Checks whether the parameter line can be part of a valid (format specified) file on the given file position.
        Overrides:
        tryToRecognize in class Recognizer
        Parameters:
        line - the line string
        lineNumber - the position of the line
        Returns:
        a Pair of which second parameter gives the format name collection that is:
        • Recognized to be excluded if the first parameter is false
        • Positively recognized if the first parameter is true

      • canBe1LetterPeptide

        public static boolean canBe1LetterPeptide​(String s)
        Deprecated.
        Tests whether a string can be one-letter-abbreviated peptide name.
        A valid name contains only uppercase letters.
        Parameters:
        s - the input string
        Returns:
        true if it can be, false if it cannot be one-letter-abbreviated peptide name

      • guessPeptideFormat

        @Deprecated
public static String guessPeptideFormat​(String header)
        Deprecated.
        as of Marvin 2014.07.21.0 intended for internal use
        Tries to distinguish between one letter and two letter peptides.
        Parameters:
        header - first few chars of the input stream
        Returns:
        "peptide:1" or "peptide:3" if it was able to find out the format, using "peptide:1" as default (ie for tryalatyr it will give "peptide:1")

      • canBe3LetterPeptide

        public static boolean canBe3LetterPeptide​(String s)
        Deprecated.
        Tests whether a string can be three-letter-abbreviated peptide name.
        Each peptide's first letter must be uppercase and the other two are lowercase.
        e.g. ValAlaTyr
        Parameters:
        s - the input string
        Returns:
        true if it can be, false if it cannot be three-letter-abbreviated peptide name

      • guessFormat

        public String guessFormat​(String line)
        Deprecated.
        Description copied from class: Recognizer
        Tries to guess the format of the given line. It is useful for single line formats.
        Overrides:
        guessFormat in class Recognizer
        Parameters:
        line - the line
        Returns:
        the name of the most likely format, that this recognizer can recognize, or null the format could not be decided