Package chemaxon.formats.recognizer
Class PeptideRecognizer
- java.lang.Object
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- chemaxon.formats.recognizer.Recognizer
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- chemaxon.formats.recognizer.PeptideRecognizer
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@PublicAPI @Deprecated public class PeptideRecognizer extends Recognizer
Deprecated.as of Marvin 2014.07.21.0 intended for internal use onlyPeptide format recognizer.- Since:
- Marvin 5.0, 06/07/2007
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Field Summary
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Fields inherited from class chemaxon.formats.recognizer.Recognizer
needsMore
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Constructor Summary
Constructors Constructor Description PeptideRecognizer()
Deprecated.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static boolean
canBe1LetterPeptide(String s)
Deprecated.Tests whether a string can be one-letter-abbreviated peptide name.
A valid name contains only uppercase letters.static boolean
canBe3LetterPeptide(String s)
Deprecated.Tests whether a string can be three-letter-abbreviated peptide name.String
guessFormat(String line)
Deprecated.Tries to guess the format of the given line.static String
guessPeptideFormat(String header)
Deprecated.as of Marvin 2014.07.21.0 intended for internal usechemaxon.common.util.Pair<Boolean,Collection<String>>
tryToRecognize(String line, int lineNumber)
Deprecated.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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Method Detail
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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 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
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
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guessPeptideFormat
@Deprecated public static String guessPeptideFormat(String header)
Deprecated.as of Marvin 2014.07.21.0 intended for internal useTries 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
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
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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 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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