public class SearchParameters extends Object implements Serializable
Modifier and Type | Class and Description |
---|---|
static class |
SearchParameters.MassAccuracyType
Possible mass accuracy types.
|
static class |
SearchParameters.PrecursorAccuracyType
Deprecated.
use MassAccuracyType
|
Constructor and Description |
---|
SearchParameters()
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
correctPrecursorMass(Boolean correctPrecursorMass)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
boolean |
equals(SearchParameters otherSearchParameters)
Returns true of the search parameter objects have identical settings.
|
Boolean |
generateQuery()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Set<Integer> |
getAlgorithms()
Returns the algorithms for which specific parameters are stored.
|
HashMap<Integer,IdentificationAlgorithmParameter> |
getAlgorithmSpecificParameters()
Returns the algorithm specific parameters in a map: algorithm as indexed
in the Advocate class > parameters.
|
Boolean |
getDiscardLowQualitySpectra()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Enzyme |
getEnzyme()
Returns the enzyme used for digestion.
|
File |
getFastaFile()
Returns the sequence database file used for identification.
|
static String[] |
getForwardIons()
Returns the list of forward ions.
|
HashMap<String,no.uib.jsparklines.data.XYDataPoint> |
getFractionMolecularWeightRanges()
Returns the user provided molecular weight ranges for the fractions.
|
HashMap<String,Double> |
getFractionMolecularWeights()
Deprecated.
use getFractionMolecularWeightRanges instead
|
SearchParameters.MassAccuracyType |
getFragmentAccuracyType()
Returns the fragment accuracy type.
|
String |
getFragmentationModel()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Double |
getFragmentIonAccuracy()
Returns the MS2 ion m/z tolerance.
|
Integer |
getHitListLength()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Integer |
getHitListLengthDeNovo()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
IdentificationAlgorithmParameter |
getIdentificationAlgorithmParameter(int algorithmID)
Returns the algorithm specific parameters, null if not found.
|
static SearchParameters |
getIdentificationParameters(File file)
Loads the identification parameters from a serialized file.
|
static String[] |
getIons()
Getter for the list of ion symbols used.
|
Integer |
getIonSearched1()
Getter for the first kind of ion searched.
|
Integer |
getIonSearched2()
Getter for the second kind of ion searched.
|
Charge |
getMaxChargeSearched()
Returns the maximal charge searched.
|
Double |
getMaxEValue()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Integer |
getMaxPeptideLength()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Charge |
getMinChargeSearched()
Returns the minimal charge searched.
|
Charge |
getMinimalChargeForMultipleChargedFragments()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Integer |
getMinPeptideLength()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
ModificationProfile |
getModificationProfile()
Returns the modification profile of the project.
|
Integer |
getnMissedCleavages()
Returns the allowed number of missed cleavages.
|
File |
getParametersFile()
Returns the parameters file loaded.
|
Map<String,String> |
getPepNovoPtmMap()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Double |
getPrecursorAccuracy()
Returns the precursor tolerance.
|
Double |
getPrecursorAccuracyDalton()
Returns the precursor tolerance in Dalton (for de novo searches).
|
SearchParameters.MassAccuracyType |
getPrecursorAccuracyType()
Returns the precursor accuracy type.
|
static String[] |
getRewindIons()
Returns the list of rewind ions.
|
Boolean |
isCorrectPrecursorMass()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Boolean |
isEstimateCharge()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Boolean |
isPrecursorAccuracyTypePpm()
Returns true if the current precursor accuracy type is ppm.
|
Boolean |
isRemovePrecursor()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
Boolean |
isScalePrecursor()
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
static void |
saveIdentificationParameters(SearchParameters identificationParameters,
File file)
Saves the identification parameters to a serialized file.
|
void |
saveIdentificationParametersAsTextFile(File file)
Saves the identification parameters as a human readable text file.
|
void |
setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion.
|
void |
setEstimateCharge(Boolean estimateCharge)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setFastaFile(File fastaFile)
Sets the sequence database file used for identification.
|
void |
setFractionMolecularWeightRanges(HashMap<String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)
Set the user provided molecular weight ranges for the fractions.
|
void |
setFractionMolecularWeights(HashMap<String,Double> fractionMolecularWeights)
Deprecated.
use setFractionMolecularWeightRanges instead
|
void |
setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType)
Sets the fragment accuracy type.
|
void |
setFragmentationModel(String fragmentationModel)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setFragmentIonAccuracy(Double fragmentIonMZTolerance)
Sets the fragment ion m/z tolerance.
|
void |
setGenerateQuery(Boolean generateQuery)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setHitListLength(Integer hitListLength)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setHitListLengthDeNovo(Integer hitListLengthDeNovo)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setIdentificationAlgorithmParameter(int algorithmID,
IdentificationAlgorithmParameter identificationAlgorithmParameter)
Adds identification algorithm specific parameters.
|
void |
setIonSearched1(String ionSearched1)
Setter for the first kind of ion searched, indexed by its single letter
code, for example "a".
|
void |
setIonSearched2(String ionSearched2)
Setter for the second kind of ion searched, indexed by its single letter
code, for example "a".
|
void |
setMaxChargeSearched(Charge maxChargeSearched)
Sets the maximal charge searched.
|
void |
setMaxEValue(Double maxEValue)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setMaxPeptideLength(Integer maxPeptideLength)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setMinChargeSearched(Charge minChargeSearched)
Sets the minimal charge searched.
|
void |
setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setMinPeptideLength(Integer minPeptideLength)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setModificationProfile(ModificationProfile modificationProfile)
Sets the modification profile of the project.
|
void |
setnMissedCleavages(Integer nMissedCleavages)
Sets the allowed number of missed cleavages.
|
void |
setParametersFile(File parametersFile)
Sets the parameter file loaded.
|
void |
setPepNovoPtmMap(Map<String,String> pepNovoPtmMap)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setPrecursorAccuracy(Double precursorTolerance)
Sets the precursor tolerance.
|
void |
setPrecursorAccuracyDalton(Double precursorToleranceDalton)
Sets the precursor tolerance in Dalton (for de novo searches).
|
void |
setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType)
Sets the precursor accuracy type.
|
void |
setRemovePrecursor(Boolean removePrecursor)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
void |
setScalePrecursor(Boolean scalePrecursor)
Deprecated.
use the appropriated IdentificationAlgorithmParameters
instead
|
String |
toString() |
String |
toString(boolean html)
Returns the search parameters as a string.
|
public ModificationProfile getModificationProfile()
public void setModificationProfile(ModificationProfile modificationProfile)
modificationProfile
- The modification profilepublic Double getFragmentIonAccuracy()
public void setFragmentIonAccuracy(Double fragmentIonMZTolerance)
fragmentIonMZTolerance
- public Enzyme getEnzyme()
public void setEnzyme(Enzyme enzyme)
enzyme
- the enzyme used for digestionpublic File getParametersFile()
public void setParametersFile(File parametersFile)
parametersFile
- the parameter file loadedpublic File getFastaFile()
public void setFastaFile(File fastaFile)
fastaFile
- the sequence database file used for identificationpublic Integer getnMissedCleavages()
public void setnMissedCleavages(Integer nMissedCleavages)
nMissedCleavages
- the allowed number of missed cleavagespublic Integer getIonSearched1()
public void setIonSearched1(String ionSearched1)
ionSearched1
- the first kind of ion searchedpublic Integer getIonSearched2()
public void setIonSearched2(String ionSearched2)
ionSearched2
- the second kind of ion searchedpublic static String[] getIons()
public static String[] getForwardIons()
public static String[] getRewindIons()
public Double getPrecursorAccuracy()
public void setPrecursorAccuracy(Double precursorTolerance)
precursorTolerance
- the precursor tolerancepublic Double getPrecursorAccuracyDalton()
public void setPrecursorAccuracyDalton(Double precursorToleranceDalton)
precursorToleranceDalton
- the precursor tolerancepublic SearchParameters.MassAccuracyType getPrecursorAccuracyType()
public void setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType)
precursorAccuracyType
- the precursor accuracy typepublic SearchParameters.MassAccuracyType getFragmentAccuracyType()
public void setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType)
fragmentAccuracyType
- the fragment accuracy typepublic Boolean isPrecursorAccuracyTypePpm()
public HashMap<String,Double> getFractionMolecularWeights()
public void setFractionMolecularWeights(HashMap<String,Double> fractionMolecularWeights)
fractionMolecularWeights
- the fractionMolecularWeights to setpublic HashMap<String,no.uib.jsparklines.data.XYDataPoint> getFractionMolecularWeightRanges()
public void setFractionMolecularWeightRanges(HashMap<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 Double getMaxEValue()
public void setMaxEValue(Double maxEValue)
maxEValue
- the maximal e-value searched forpublic Integer getHitListLength()
public void setHitListLength(Integer hitListLength)
hitListLength
- the length of the hit list for OMSSApublic Integer getHitListLengthDeNovo()
public void setHitListLengthDeNovo(Integer hitListLengthDeNovo)
hitListLengthDeNovo
- the length of the hit list for PepNovopublic Charge getMinimalChargeForMultipleChargedFragments()
public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
minimalChargeForMultipleChargedFragments
- the minimal precursor
charge to account for multiply charged fragments in OMSSApublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic Integer getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic Boolean isEstimateCharge()
public void setEstimateCharge(Boolean estimateCharge)
estimateCharge
- a boolean indicating whether the precursor charge
shall be estimated for OMSSApublic Boolean isRemovePrecursor()
public void setRemovePrecursor(Boolean removePrecursor)
removePrecursor
- a boolean indicating whether the precursor shall
be removed for OMSSApublic Boolean isScalePrecursor()
public void setScalePrecursor(Boolean scalePrecursor)
scalePrecursor
- a boolean indicating whether the precursor shall be
scaled for OMSSApublic HashMap<Integer,IdentificationAlgorithmParameter> getAlgorithmSpecificParameters()
public IdentificationAlgorithmParameter getIdentificationAlgorithmParameter(int algorithmID)
algorithmID
- the index of the search engine as indexed in the
Advocate classpublic void setIdentificationAlgorithmParameter(int algorithmID, IdentificationAlgorithmParameter identificationAlgorithmParameter)
algorithmID
- the algorithm id as indexed in the Advocate classidentificationAlgorithmParameter
- the specific parameterspublic Set<Integer> getAlgorithms()
public static SearchParameters getIdentificationParameters(File file) throws FileNotFoundException, IOException, ClassNotFoundException
file
- the fileFileNotFoundException
IOException
ClassNotFoundException
public static void saveIdentificationParameters(SearchParameters identificationParameters, File file) throws FileNotFoundException, IOException, ClassNotFoundException
identificationParameters
- file
- the fileFileNotFoundException
IOException
ClassNotFoundException
public void saveIdentificationParametersAsTextFile(File file) throws FileNotFoundException, IOException, ClassNotFoundException
file
- the fileFileNotFoundException
IOException
ClassNotFoundException
public String toString(boolean html)
html
- use HTML formattingpublic boolean equals(SearchParameters otherSearchParameters)
otherSearchParameters
- the parameters to compare topublic Boolean isCorrectPrecursorMass()
public void correctPrecursorMass(Boolean correctPrecursorMass)
correctPrecursorMass
- a boolean indicating whether the precursor
mass shall be corrected (TagDB setting)public Boolean getDiscardLowQualitySpectra()
public void setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
discardLowQualitySpectra
- a boolean indicating whether low quality
spectra shall be discardedpublic String getFragmentationModel()
public void setFragmentationModel(String fragmentationModel)
fragmentationModel
- the name of the fragmentation modelpublic Boolean generateQuery()
public void setGenerateQuery(Boolean generateQuery)
generateQuery
- a boolean indicating whether a blast query shall be
generatedpublic Map<String,String> getPepNovoPtmMap()
Copyright © 2014. All rights reserved.