Package chemaxon.formats.recognizer

Class PeptideRecognizer

java.lang.Object
chemaxon.formats.recognizer.Recognizer
chemaxon.formats.recognizer.PeptideRecognizer
@PublicAPI @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public class PeptideRecognizer extends Recognizer
Deprecated, for removal: This API element is subject to removal in a future version.
No longer used, will be removed.
Peptide format recognizer.
Since:
Marvin 5.0, 06/07/2007

  • Constructor Details

    • PeptideRecognizer

      public PeptideRecognizer()
      Deprecated, for removal: This API element is subject to removal in a future version.

  • Method Details

    • tryToRecognize

      public chemaxon.common.util.Pair<Boolean,Collection<String>> tryToRecognize(String line, int lineNumber)
      Deprecated, for removal: This API element is subject to removal in a future version.
      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

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean canBe1LetterPeptide(String s)
      Deprecated, for removal: This API element is subject to removal in a future version.
      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(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static String guessPeptideFormat(String header)
      Deprecated, for removal: This API element is subject to removal in a future version.
      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

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static boolean canBe3LetterPeptide(String s)
      Deprecated, for removal: This API element is subject to removal in a future version.
      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, for removal: This API element is subject to removal in a future version.
      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