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
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Field Summary
Fields inherited from class chemaxon.formats.recognizer.Recognizer
needsMore
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Constructor Summary
ConstructorDescriptionDeprecated, for removal: This API element is subject to removal in a future version. -
Method Summary
Modifier and TypeMethodDescriptionstatic boolean
Deprecated, for removal: This API element is subject to removal in a future version.static boolean
Deprecated, for removal: This API element is subject to removal in a future version.guessFormat
(String line) Deprecated, for removal: This API element is subject to removal in a future version.Tries to guess the format of the given line.static String
guessPeptideFormat
(String header) Deprecated, for removal: This API element is subject to removal in a future version.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.Checks whether the parameter line can be part of a valid (format specified) file on the given file position.Methods inherited from class chemaxon.formats.recognizer.Recognizer
getLastProcessedLineNum, isLastLine, needsMore, tryToRecognize
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Constructor Details
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PeptideRecognizer
public PeptideRecognizer()Deprecated, for removal: This API element is subject to removal in a future version.
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Method Details
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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 classRecognizer
- Parameters:
line
- the line stringlineNumber
- 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
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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
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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")
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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
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guessFormat
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 classRecognizer
- 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
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