chemaxon.formats.recognizer

Class PeptideRecognizer

java.lang.Object

chemaxon.formats.recognizer.Recognizer

chemaxon.formats.recognizer.PeptideRecognizer

Deprecated.

as of Marvin 2014.07.21.0 intended for internal use only

@PublicAPI
 @Deprecated
public class PeptideRecognizer
extends Recognizer

Peptide format recognizer.

Since:

Marvin 5.0, 06/07/2007

Version:

5.1, 07/29/2008

Author:

Rita Vereb, Peter Csizmadia

Field Summary

Fields inherited from class chemaxon.formats.recognizer.Recognizer

needsMore

Constructor Summary

Constructors

Constructor and Description
PeptideRecognizer() Deprecated.

Method Summary

Modifier and Type	Method and Description
static boolean	canBe1LetterPeptide(java.lang.String s) Deprecated. Tests whether a string can be one-letter-abbreviated peptide name. A valid name contains only uppercase letters.
static boolean	canBe3LetterPeptide(java.lang.String s) Deprecated. Tests whether a string can be three-letter-abbreviated peptide name.
java.lang.String	guessFormat(java.lang.String line) Deprecated. Tries to guess the format of the given line.
static java.lang.String	guessPeptideFormat(java.lang.String header) Deprecated. as of Marvin 2014.07.21.0 intended for internal use
chemaxon.common.util.Pair<java.lang.Boolean,java.util.Collection<java.lang.String>>	tryToRecognize(java.lang.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

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideRecognizer

public PeptideRecognizer()

Deprecated.

Method Detail

tryToRecognize

public chemaxon.common.util.Pair<java.lang.Boolean,java.util.Collection<java.lang.String>> tryToRecognize(java.lang.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(java.lang.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 java.lang.String guessPeptideFormat(java.lang.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(java.lang.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 java.lang.String guessFormat(java.lang.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