com.compomics.util.experiment.identification
Class SearchParameters

java.lang.Object
  extended by com.compomics.util.experiment.identification.SearchParameters
All Implemented Interfaces:
Serializable

public class SearchParameters
extends Object
implements Serializable

This class groups the parameters used for identification.

Author:
Marc Vaudel
See Also:
Serialized Form

Nested Class Summary
static class SearchParameters.PrecursorAccuracyType
          Possible mass accuracy types.
 
Constructor Summary
SearchParameters()
          Constructor.
 
Method Summary
 void correctPrecursorMass(Boolean correctPrecursorMass)
          Sets whether the precursor mass shall be corrected (TagDB setting).
 boolean equals(SearchParameters otherSearchParameters)
          Returns true of the search parameter objects have identical settings.
 Boolean generateQuery()
          Returns a boolean indicating whether a blast query shall be generated.
 Boolean getDiscardLowQualitySpectra()
          Returns a boolean indicating whether low quality spectra shall be discarded.
 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
 String getFragmentationModel()
          Returns the name of the fragmentation model.
 Double getFragmentIonAccuracy()
          Returns the MS2 ion m/z tolerance.
 Integer getHitListLength()
          Returns the length of the hit list for OMSSA.
 Integer getHitListLengthDeNovo()
          Returns the length of the hit list for PepNovo+.
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()
          Returns the maximal e-value searched for.
 Integer getMaxPeptideLength()
          Returns the maximal peptide length allowed.
 Charge getMinChargeSearched()
          Returns the minimal charge searched.
 Charge getMinimalChargeForMultipleChargedFragments()
          Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.
 Integer getMinPeptideLength()
          Sets the minimal peptide length allowed.
 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.
 Double getPrecursorAccuracy()
          Returns the precursor tolerance.
 SearchParameters.PrecursorAccuracyType getPrecursorAccuracyType()
          Returns the precursor accuracy type.
static String[] getRewindIons()
          Returns the list of rewind ions.
 Boolean isCorrectPrecursorMass()
          Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
 Boolean isEstimateCharge()
          Indicates whether the precursor charge shall be estimated for OMSSA.
 Boolean isPrecursorAccuracyTypePpm()
          Returns true if the current precursor accuracy type is ppm.
 Boolean isRemovePrecursor()
          Indicates whether the precursor shall be removed for OMSSA.
 Boolean isScalePrecursor()
          Indicates whether the precursor shall be scaled for OMSSA.
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)
          Sets whether low quality spectra shall be discarded.
 void setEnzyme(Enzyme enzyme)
          Sets the enzyme used for digestion.
 void setEstimateCharge(Boolean estimateCharge)
          Sets whether the precursor charge shall be estimated for OMSSA.
 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 setFragmentationModel(String fragmentationModel)
          Sets the name of the fragmentation model.
 void setFragmentIonAccuracy(Double fragmentIonMZTolerance)
          Sets the fragment ion m/z tolerance.
 void setGenerateQuery(Boolean generateQuery)
          Sets a boolean indicating whether a blast query shall be generated.
 void setHitListLength(Integer hitListLength)
          Sets the length of the hit list for OMSSA.
 void setHitListLengthDeNovo(Integer hitListLengthDeNovo)
          Sets the length of the hit list for PepNovo.
 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)
          Sets the maximal e-value searched for.
 void setMaxPeptideLength(Integer maxPeptideLength)
          Sets the maximal peptide length allowed.
 void setMinChargeSearched(Charge minChargeSearched)
          Sets the minimal charge searched.
 void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
          Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.
 void setMinPeptideLength(Integer minPeptideLength)
          Sets the minimal peptide length allowed.
 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 setPrecursorAccuracy(Double precursorTolerance)
          Sets the precursor tolerance.
 void setPrecursorAccuracyType(SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType)
          Sets the precursor accuracy type.
 void setRemovePrecursor(Boolean removePrecursor)
          Sets whether the precursor shall be removed for OMSSA
 void setScalePrecursor(Boolean scalePrecursor)
          Sets whether the precursor shall be scaled for OMSSA.
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SearchParameters

public SearchParameters()
Constructor.

Method Detail

getModificationProfile

public ModificationProfile getModificationProfile()
Returns the modification profile of the project.

Returns:
the modification profile of the project

setModificationProfile

public void setModificationProfile(ModificationProfile modificationProfile)
Sets the modification profile of the project.

Parameters:
modificationProfile - The modification profile

getFragmentIonAccuracy

public Double getFragmentIonAccuracy()
Returns the MS2 ion m/z tolerance.

Returns:
the MS2 ion m/z tolerance

setFragmentIonAccuracy

public void setFragmentIonAccuracy(Double fragmentIonMZTolerance)
Sets the fragment ion m/z tolerance.

Parameters:
fragmentIonMZTolerance -

getEnzyme

public Enzyme getEnzyme()
Returns the enzyme used for digestion.

Returns:
the enzyme used for digestion

setEnzyme

public void setEnzyme(Enzyme enzyme)
Sets the enzyme used for digestion.

Parameters:
enzyme - the enzyme used for digestion

getParametersFile

public File getParametersFile()
Returns the parameters file loaded.

Returns:
the parameters file loaded

setParametersFile

public void setParametersFile(File parametersFile)
Sets the parameter file loaded.

Parameters:
parametersFile - the parameter file loaded

getFastaFile

public File getFastaFile()
Returns the sequence database file used for identification.

Returns:
the sequence database file used for identification

setFastaFile

public void setFastaFile(File fastaFile)
Sets the sequence database file used for identification.

Parameters:
fastaFile - the sequence database file used for identification

getnMissedCleavages

public Integer getnMissedCleavages()
Returns the allowed number of missed cleavages.

Returns:
the allowed number of missed cleavages

setnMissedCleavages

public void setnMissedCleavages(Integer nMissedCleavages)
Sets the allowed number of missed cleavages.

Parameters:
nMissedCleavages - the allowed number of missed cleavages

getIonSearched1

public Integer getIonSearched1()
Getter for the first kind of ion searched.

Returns:
the first kind of ion searched as an integer (see static fields of the PeptideFragmentIon class)

setIonSearched1

public void setIonSearched1(String ionSearched1)
Setter for the first kind of ion searched, indexed by its single letter code, for example "a".

Parameters:
ionSearched1 - the first kind of ion searched

getIonSearched2

public Integer getIonSearched2()
Getter for the second kind of ion searched.

Returns:
the second kind of ion searched as an integer (see static fields of the PeptideFragmentIon class)

setIonSearched2

public void setIonSearched2(String ionSearched2)
Setter for the second kind of ion searched, indexed by its single letter code, for example "a".

Parameters:
ionSearched2 - the second kind of ion searched

getIons

public static String[] getIons()
Getter for the list of ion symbols used.

Returns:
the list of ion symbols used

getForwardIons

public static String[] getForwardIons()
Returns the list of forward ions.

Returns:
the forwardIons

getRewindIons

public static String[] getRewindIons()
Returns the list of rewind ions.

Returns:
the rewindIons

getPrecursorAccuracy

public Double getPrecursorAccuracy()
Returns the precursor tolerance.

Returns:
the precursor tolerance

setPrecursorAccuracy

public void setPrecursorAccuracy(Double precursorTolerance)
Sets the precursor tolerance.

Parameters:
precursorTolerance - the precursor tolerance

getPrecursorAccuracyType

public SearchParameters.PrecursorAccuracyType getPrecursorAccuracyType()
Returns the precursor accuracy type.

Returns:
the precursor accuracy type

setPrecursorAccuracyType

public void setPrecursorAccuracyType(SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType)
Sets the precursor accuracy type.

Parameters:
currentPrecursorAccuracyType - the precursor accuracy type

isPrecursorAccuracyTypePpm

public Boolean isPrecursorAccuracyTypePpm()
Returns true if the current precursor accuracy type is ppm.

Returns:
true if the current precursor accuracy type is ppm

getFractionMolecularWeights

public HashMap<String,Double> getFractionMolecularWeights()
Deprecated. use getFractionMolecularWeightRanges instead

Returns the user provided molecular weights of the fractions. The key is the fraction file path.

Returns:
the user provided molecular weights of the fractions

setFractionMolecularWeights

public void setFractionMolecularWeights(HashMap<String,Double> fractionMolecularWeights)
Deprecated. use setFractionMolecularWeightRanges instead

Set the user provided molecular weights of the fractions. The key is the fraction file path.

Parameters:
fractionMolecularWeights - the fractionMolecularWeights to set

getFractionMolecularWeightRanges

public HashMap<String,no.uib.jsparklines.data.XYDataPoint> getFractionMolecularWeightRanges()
Returns the user provided molecular weight ranges for the fractions. The key is the fraction file path.

Returns:
the user provided molecular weight ranges of the fractions

setFractionMolecularWeightRanges

public void setFractionMolecularWeightRanges(HashMap<String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)
Set the user provided molecular weight ranges for the fractions. The key is the fraction file path.

Parameters:
fractionMolecularWeightRanges - the fractionMolecularWeightRanges to set

getMaxChargeSearched

public Charge getMaxChargeSearched()
Returns the maximal charge searched.

Returns:
the maximal charge searched

setMaxChargeSearched

public void setMaxChargeSearched(Charge maxChargeSearched)
Sets the maximal charge searched.

Parameters:
maxChargeSearched - the maximal charge searched

getMinChargeSearched

public Charge getMinChargeSearched()
Returns the minimal charge searched.

Returns:
the minimal charge searched

setMinChargeSearched

public void setMinChargeSearched(Charge minChargeSearched)
Sets the minimal charge searched.

Parameters:
minChargeSearched - the minimal charge searched

getMaxEValue

public Double getMaxEValue()
Returns the maximal e-value searched for.

Returns:
the maximal e-value searched for

setMaxEValue

public void setMaxEValue(Double maxEValue)
Sets the maximal e-value searched for.

Parameters:
maxEValue - the maximal e-value searched for

getHitListLength

public Integer getHitListLength()
Returns the length of the hit list for OMSSA.

Returns:
the length of the hit list for OMSSA

setHitListLength

public void setHitListLength(Integer hitListLength)
Sets the length of the hit list for OMSSA.

Parameters:
hitListLength - the length of the hit list for OMSSA

getHitListLengthDeNovo

public Integer getHitListLengthDeNovo()
Returns the length of the hit list for PepNovo+.

Returns:
the length of the hit list for OMSSA

setHitListLengthDeNovo

public void setHitListLengthDeNovo(Integer hitListLengthDeNovo)
Sets the length of the hit list for PepNovo.

Parameters:
hitListLengthDeNovo - the length of the hit list for PepNovo

getMinimalChargeForMultipleChargedFragments

public Charge getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.

Returns:
the minimal precursor charge to account for multiply charged fragments in OMSSA

setMinimalChargeForMultipleChargedFragments

public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.

Parameters:
minimalChargeForMultipleChargedFragments - the minimal precursor charge to account for multiply charged fragments in OMSSA

getMaxPeptideLength

public Integer getMaxPeptideLength()
Returns the maximal peptide length allowed.

Returns:
the maximal peptide length allowed

setMaxPeptideLength

public void setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.

Parameters:
maxPeptideLength - the maximal peptide length allowed

getMinPeptideLength

public Integer getMinPeptideLength()
Sets the minimal peptide length allowed.

Returns:
the minimal peptide length allowed

setMinPeptideLength

public void setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.

Parameters:
minPeptideLength - the minimal peptide length allowed

isEstimateCharge

public Boolean isEstimateCharge()
Indicates whether the precursor charge shall be estimated for OMSSA.

Returns:
a boolean indicating whether the precursor charge shall be estimated for OMSSA

setEstimateCharge

public void setEstimateCharge(Boolean estimateCharge)
Sets whether the precursor charge shall be estimated for OMSSA.

Parameters:
estimateCharge - a boolean indicating whether the precursor charge shall be estimated for OMSSA

isRemovePrecursor

public Boolean isRemovePrecursor()
Indicates whether the precursor shall be removed for OMSSA.

Returns:
a boolean indicating whether the precursor shall be removed for OMSSA

setRemovePrecursor

public void setRemovePrecursor(Boolean removePrecursor)
Sets whether the precursor shall be removed for OMSSA

Parameters:
removePrecursor - a boolean indicating whether the precursor shall be removed for OMSSA

isScalePrecursor

public Boolean isScalePrecursor()
Indicates whether the precursor shall be scaled for OMSSA.

Returns:
a boolean indicating whether the precursor shall be scaled for OMSSA

setScalePrecursor

public void setScalePrecursor(Boolean scalePrecursor)
Sets whether the precursor shall be scaled for OMSSA.

Parameters:
scalePrecursor - a boolean indicating whether the precursor shall be scaled for OMSSA

getIdentificationParameters

public static SearchParameters getIdentificationParameters(File file)
                                                    throws FileNotFoundException,
                                                           IOException,
                                                           ClassNotFoundException
Loads the identification parameters from a serialized file.

Parameters:
file - the file
Returns:
the modification file
Throws:
FileNotFoundException
IOException
ClassNotFoundException

saveIdentificationParameters

public static void saveIdentificationParameters(SearchParameters identificationParameters,
                                                File file)
                                         throws FileNotFoundException,
                                                IOException,
                                                ClassNotFoundException
Saves the identification parameters to a serialized file.

Parameters:
identificationParameters -
file - the file
Throws:
FileNotFoundException
IOException
ClassNotFoundException

saveIdentificationParametersAsTextFile

public void saveIdentificationParametersAsTextFile(File file)
                                            throws FileNotFoundException,
                                                   IOException,
                                                   ClassNotFoundException
Saves the identification parameters as a human readable text file.

Parameters:
file - the file
Throws:
FileNotFoundException
IOException
ClassNotFoundException

toString

public String toString()
Overrides:
toString in class Object

equals

public boolean equals(SearchParameters otherSearchParameters)
Returns true of the search parameter objects have identical settings.

Parameters:
otherSearchParameters - the parameters to compare to
Returns:
true of the search parameter objects have identical settings

isCorrectPrecursorMass

public Boolean isCorrectPrecursorMass()
Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).

Returns:
a boolean indicating whether the precursor mass shall be corrected (TagDB setting)

correctPrecursorMass

public void correctPrecursorMass(Boolean correctPrecursorMass)
Sets whether the precursor mass shall be corrected (TagDB setting).

Parameters:
correctPrecursorMass - a boolean indicating whether the precursor mass shall be corrected (TagDB setting)

getDiscardLowQualitySpectra

public Boolean getDiscardLowQualitySpectra()
Returns a boolean indicating whether low quality spectra shall be discarded.

Returns:
a boolean indicating whether low quality spectra shall be discarded

setDiscardLowQualitySpectra

public void setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
Sets whether low quality spectra shall be discarded.

Parameters:
discardLowQualitySpectra - a boolean indicating whether low quality spectra shall be discarded

getFragmentationModel

public String getFragmentationModel()
Returns the name of the fragmentation model.

Returns:
the name of the fragmentation model

setFragmentationModel

public void setFragmentationModel(String fragmentationModel)
Sets the name of the fragmentation model.

Parameters:
fragmentationModel - the name of the fragmentation model

generateQuery

public Boolean generateQuery()
Returns a boolean indicating whether a blast query shall be generated.

Returns:
a boolean indicating whether a blast query shall be generated

setGenerateQuery

public void setGenerateQuery(Boolean generateQuery)
Sets a boolean indicating whether a blast query shall be generated.

Parameters:
generateQuery - a boolean indicating whether a blast query shall be generated


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