public class MsAmandaParameters extends Object implements IdentificationAlgorithmParameter
Modifier and Type | Field and Description |
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static int |
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
The maximum allowed length of the FASTA file name.
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Constructor and Description |
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MsAmandaParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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boolean |
generateDecoy()
Returns whether a decoy database shall be created and searched against.
|
Advocate |
getAlgorithm()
Returns the identification algorithm.
|
String |
getInstrumentID()
Return the instrument ID.
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Integer |
getMaxRank()
Returns the maximum rank.
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boolean |
isLowMemoryMode()
Returns whether the low memory mode is used.
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boolean |
isMonoIsotopic()
Returns whether monoisotopic mass values shall be used (in contrast to
average mass values).
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void |
setGenerateDecoyDatabase(boolean generateDecoy)
Set whether a decoy database shall be created and searched against.
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void |
setInstrumentID(String instrumentID)
Set the instrument ID.
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void |
setLowMemoryMode(boolean lowMemoryMode)
Set whether the low memory mode is used.
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void |
setMaxRank(Integer maxRank)
Set the maximum rank.
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void |
setMonoIsotopic(boolean monoisotopic)
Set whether monoisotopic mass values shall be used (in contrast to
average mass values).
|
String |
toString(boolean html)
Returns the parameters as a string.
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public static final int MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
public Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingpublic boolean generateDecoy()
public void setGenerateDecoyDatabase(boolean generateDecoy)
generateDecoy
- the generateDecoy to setpublic boolean isMonoIsotopic()
public void setMonoIsotopic(boolean monoisotopic)
monoisotopic
- the monoisotopic to setpublic String getInstrumentID()
public void setInstrumentID(String instrumentID)
instrumentID
- the instrumentID to setpublic Integer getMaxRank()
public void setMaxRank(Integer maxRank)
maxRank
- the maxRank to setpublic boolean isLowMemoryMode()
public void setLowMemoryMode(boolean lowMemoryMode)
lowMemoryMode
- the lowMemoryMode to setCopyright © 2016. All rights reserved.