public class SearchParameters
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Class and Description |
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static class |
SearchParameters.PrecursorAccuracyType
Possible mass accuracy types.
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Constructor and Description |
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SearchParameters()
Constructor.
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Modifier and Type | Method and Description |
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void |
correctPrecursorMass(java.lang.Boolean correctPrecursorMass)
Sets whether the precursor mass shall be corrected (TagDB setting).
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boolean |
equals(SearchParameters otherSearchParameters)
Returns true of the search parameter objects have identical settings.
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java.lang.Boolean |
generateQuery()
Returns a boolean indicating whether a blast query shall be generated.
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java.lang.Boolean |
getDiscardLowQualitySpectra()
Returns a boolean indicating whether low quality spectra shall be
discarded.
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Enzyme |
getEnzyme()
Returns the enzyme used for digestion.
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java.io.File |
getFastaFile()
Returns the sequence database file used for identification.
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static java.lang.String[] |
getForwardIons()
Returns the list of forward ions.
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java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> |
getFractionMolecularWeightRanges()
Returns the user provided molecular weight ranges for the fractions.
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java.util.HashMap<java.lang.String,java.lang.Double> |
getFractionMolecularWeights()
Deprecated.
use getFractionMolecularWeightRanges instead
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java.lang.String |
getFragmentationModel()
Returns the name of the fragmentation model.
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java.lang.Double |
getFragmentIonAccuracy()
Returns the MS2 ion m/z tolerance.
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java.lang.Integer |
getHitListLength()
Returns the length of the hit list for OMSSA.
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static SearchParameters |
getIdentificationParameters(java.io.File file)
Loads the identification parameters from a serialized file.
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static java.lang.String[] |
getIons()
Getter for the list of ion symbols used.
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java.lang.Integer |
getIonSearched1()
Getter for the first kind of ion searched.
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java.lang.Integer |
getIonSearched2()
Getter for the second kind of ion searched.
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Charge |
getMaxChargeSearched()
Returns the maximal charge searched.
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java.lang.Double |
getMaxEValue()
Returns the maximal e-value searched for.
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java.lang.Integer |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
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Charge |
getMinChargeSearched()
Returns the minimal charge searched.
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Charge |
getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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java.lang.Integer |
getMinPeptideLength()
Sets the minimal peptide length allowed.
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ModificationProfile |
getModificationProfile()
Returns the modification profile of the project.
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java.lang.Integer |
getnMissedCleavages()
Returns the allowed number of missed cleavages.
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java.io.File |
getParametersFile()
Returns the parameters file loaded.
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java.lang.Double |
getPrecursorAccuracy()
Returns the precursor tolerance.
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SearchParameters.PrecursorAccuracyType |
getPrecursorAccuracyType()
Returns the precursor accuracy type.
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static java.lang.String[] |
getRewindIons()
Returns the list of rewind ions.
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java.lang.Boolean |
isCorrectPrecursorMass()
Returns a boolean indicating whether the precursor mass shall be
corrected (TagDB setting).
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java.lang.Boolean |
isEstimateCharge()
Indicates whether the precursor charge shall be estimated for OMSSA.
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java.lang.Boolean |
isPrecursorAccuracyTypePpm()
Returns true if the current precursor accuracy type is ppm.
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java.lang.Boolean |
isRemovePrecursor()
Indicates whether the precursor shall be removed for OMSSA.
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java.lang.Boolean |
isScalePrecursor()
Indicates whether the precursor shall be scaled for OMSSA.
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static void |
saveIdentificationParameters(SearchParameters identificationParameters,
java.io.File file)
Saves the identification parameters to a serialized file.
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void |
setDiscardLowQualitySpectra(java.lang.Boolean discardLowQualitySpectra)
Sets whether low quality spectra shall be discarded.
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void |
setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion.
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void |
setEstimateCharge(java.lang.Boolean estimateCharge)
Sets whether the precursor charge shall be estimated for OMSSA.
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void |
setFastaFile(java.io.File fastaFile)
Sets the sequence database file used for identification.
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void |
setFractionMolecularWeightRanges(java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)
Set the user provided molecular weight ranges for the fractions.
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void |
setFractionMolecularWeights(java.util.HashMap<java.lang.String,java.lang.Double> fractionMolecularWeights)
Deprecated.
use setFractionMolecularWeightRanges instead
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void |
setFragmentationModel(java.lang.String fragmentationModel)
Sets the name of the fragmentation model.
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void |
setFragmentIonAccuracy(java.lang.Double fragmentIonMZTolerance)
Sets the fragment ion m/z tolerance.
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void |
setGenerateQuery(java.lang.Boolean generateQuery)
Sets a boolean indicating whether a blast query shall be generated.
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void |
setHitListLength(java.lang.Integer hitListLength)
Sets the length of the hit list for OMSSA.
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void |
setIonSearched1(java.lang.String ionSearched1)
Setter for the first kind of ion searched, indexed by its single letter
code, for example "a".
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void |
setIonSearched2(java.lang.String ionSearched2)
Setter for the second kind of ion searched, indexed by its single letter
code, for example "a".
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void |
setMaxChargeSearched(Charge maxChargeSearched)
Sets the maximal charge searched.
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void |
setMaxEValue(java.lang.Double maxEValue)
Sets the maximal e-value searched for.
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void |
setMaxPeptideLength(java.lang.Integer maxPeptideLength)
Sets the maximal peptide length allowed.
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void |
setMinChargeSearched(Charge minChargeSearched)
Sets the minimal charge searched.
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void |
setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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void |
setMinPeptideLength(java.lang.Integer minPeptideLength)
Sets the minimal peptide length allowed.
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void |
setModificationProfile(ModificationProfile modificationProfile)
Sets the modification profile of the project.
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void |
setnMissedCleavages(java.lang.Integer nMissedCleavages)
Sets the allowed number of missed cleavages.
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void |
setParametersFile(java.io.File parametersFile)
Sets the parameter file loaded.
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void |
setPrecursorAccuracy(java.lang.Double precursorTolerance)
Sets the precursor tolerance.
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void |
setPrecursorAccuracyType(SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType)
Sets the precursor accuracy type.
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void |
setRemovePrecursor(java.lang.Boolean removePrecursor)
Sets whether the precursor shall be removed for OMSSA
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void |
setScalePrecursor(java.lang.Boolean scalePrecursor)
Sets whether the precursor shall be scaled for OMSSA.
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public ModificationProfile getModificationProfile()
public void setModificationProfile(ModificationProfile modificationProfile)
modificationProfile
- The modification profilepublic java.lang.Double getFragmentIonAccuracy()
public void setFragmentIonAccuracy(java.lang.Double fragmentIonMZTolerance)
fragmentIonMZTolerance
- public Enzyme getEnzyme()
public void setEnzyme(Enzyme enzyme)
enzyme
- the enzyme used for digestionpublic java.io.File getParametersFile()
public void setParametersFile(java.io.File parametersFile)
parametersFile
- the parameter file loadedpublic java.io.File getFastaFile()
public void setFastaFile(java.io.File fastaFile)
fastaFile
- the sequence database file used for identificationpublic java.lang.Integer getnMissedCleavages()
public void setnMissedCleavages(java.lang.Integer nMissedCleavages)
nMissedCleavages
- the allowed number of missed cleavagespublic java.lang.Integer getIonSearched1()
public void setIonSearched1(java.lang.String ionSearched1)
ionSearched1
- the first kind of ion searchedpublic java.lang.Integer getIonSearched2()
public void setIonSearched2(java.lang.String ionSearched2)
ionSearched2
- the second kind of ion searchedpublic static java.lang.String[] getIons()
public static java.lang.String[] getForwardIons()
public static java.lang.String[] getRewindIons()
public java.lang.Double getPrecursorAccuracy()
public void setPrecursorAccuracy(java.lang.Double precursorTolerance)
precursorTolerance
- the precursor tolerancepublic SearchParameters.PrecursorAccuracyType getPrecursorAccuracyType()
public void setPrecursorAccuracyType(SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType)
currentPrecursorAccuracyType
- the precursor accuracy typepublic java.lang.Boolean isPrecursorAccuracyTypePpm()
public java.util.HashMap<java.lang.String,java.lang.Double> getFractionMolecularWeights()
public void setFractionMolecularWeights(java.util.HashMap<java.lang.String,java.lang.Double> fractionMolecularWeights)
fractionMolecularWeights
- the fractionMolecularWeights to setpublic java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> getFractionMolecularWeightRanges()
public void setFractionMolecularWeightRanges(java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)
fractionMolecularWeightRanges
- the fractionMolecularWeightRanges to
setpublic Charge getMaxChargeSearched()
public void setMaxChargeSearched(Charge maxChargeSearched)
maxChargeSearched
- the maximal charge searchedpublic Charge getMinChargeSearched()
public void setMinChargeSearched(Charge minChargeSearched)
minChargeSearched
- the minimal charge searchedpublic java.lang.Double getMaxEValue()
public void setMaxEValue(java.lang.Double maxEValue)
maxEValue
- the maximal e-value searched forpublic java.lang.Integer getHitListLength()
public void setHitListLength(java.lang.Integer hitListLength)
hitListLength
- the length of the hit list for OMSSApublic Charge getMinimalChargeForMultipleChargedFragments()
public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
minimalChargeForMultipleChargedFragments
- the minimal precursor
charge to account for multiply charged fragments in OMSSApublic java.lang.Integer getMaxPeptideLength()
public void setMaxPeptideLength(java.lang.Integer maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic java.lang.Integer getMinPeptideLength()
public void setMinPeptideLength(java.lang.Integer minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic java.lang.Boolean isEstimateCharge()
public void setEstimateCharge(java.lang.Boolean estimateCharge)
estimateCharge
- a boolean indicating whether the precursor charge
shall be estimated for OMSSApublic java.lang.Boolean isRemovePrecursor()
public void setRemovePrecursor(java.lang.Boolean removePrecursor)
removePrecursor
- a boolean indicating whether the precursor shall
be removed for OMSSApublic java.lang.Boolean isScalePrecursor()
public void setScalePrecursor(java.lang.Boolean scalePrecursor)
scalePrecursor
- a boolean indicating whether the precursor shall be
scaled for OMSSApublic static SearchParameters getIdentificationParameters(java.io.File file) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
file
- the filejava.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public static void saveIdentificationParameters(SearchParameters identificationParameters, java.io.File file) throws java.io.FileNotFoundException, java.io.IOException, java.lang.ClassNotFoundException
identificationParameters
- file
- the filejava.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public boolean equals(SearchParameters otherSearchParameters)
otherSearchParameters
- the parameters to compare topublic java.lang.Boolean isCorrectPrecursorMass()
public void correctPrecursorMass(java.lang.Boolean correctPrecursorMass)
correctPrecursorMass
- a boolean indicating whether the precursor
mass shall be corrected (TagDB setting)public java.lang.Boolean getDiscardLowQualitySpectra()
public void setDiscardLowQualitySpectra(java.lang.Boolean discardLowQualitySpectra)
discardLowQualitySpectra
- a boolean indicating whether low quality
spectra shall be discardedpublic java.lang.String getFragmentationModel()
public void setFragmentationModel(java.lang.String fragmentationModel)
fragmentationModel
- the name of the fragmentation modelpublic java.lang.Boolean generateQuery()
public void setGenerateQuery(java.lang.Boolean generateQuery)
generateQuery
- a boolean indicating whether a blast query shall be
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