Package com.compomics.util.parameters.identification.tool_specific

Class OmssaParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.OmssaParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable
public class OmssaParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The OMSSA specific parameters.
Author:
Marc Vaudel
See Also:

  • Constructor Details

    • OmssaParameters

      public OmssaParameters()
      Constructor.

  • Method Details

    • 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 int getHitListLength()
      Returns the length of the hit list for OMSSA.
      Returns:
      the length of the hit list for OMSSA

    • setHitListLength

      public void setHitListLength(int hitListLength)
      Sets the length of the hit list for OMSSA.
      Parameters:
      hitListLength - the length of the hit list for OMSSA

    • getMinimalChargeForMultipleChargedFragments

      public int 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(int 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 int getMaxPeptideLength()
      Returns the maximal peptide length allowed.
      Returns:
      the maximal peptide length allowed

    • setMaxPeptideLength

      public void setMaxPeptideLength(int maxPeptideLength)
      Sets the maximal peptide length allowed.
      Parameters:
      maxPeptideLength - the maximal peptide length allowed

    • getMinPeptideLength

      public int getMinPeptideLength()
      Sets the minimal peptide length allowed.
      Returns:
      the minimal peptide length allowed

    • setMinPeptideLength

      public void setMinPeptideLength(int 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

    • getSelectedOutput

      public String getSelectedOutput()
      Returns the selected output type, omx, csv or pepXML.
      Returns:
      the selected output type

    • setSelectedOutput

      public void setSelectedOutput(String selectedOutput)
      Sets the output type, omx, csv or pepXML.
      Parameters:
      selectedOutput - the output type

    • getOmssaOutputTypes

      public static String[] getOmssaOutputTypes()
      Returns the output types available.
      Returns:
      the output types available

    • isMemoryMappedSequenceLibraries

      public boolean isMemoryMappedSequenceLibraries()
      Indicates whether sequence libraries should be mapped in memory.
      Returns:
      a boolean indicating whether sequence libraries should be mapped in memory

    • setMemoryMappedSequenceLibraries

      public void setMemoryMappedSequenceLibraries(boolean memoryMappedSequenceLibraries)
      Sets whether sequence libraries should be mapped in memory.
      Parameters:
      memoryMappedSequenceLibraries - a boolean indicating whether sequence libraries should be mapped in memory

    • getNeutronThreshold

      public double getNeutronThreshold()
      Returns the mass after which exact neutron mass should be considered in the calculation.
      Returns:
      the mass after which exact neutron mass should be considered in the calculation

    • setNeutronThreshold

      public void setNeutronThreshold(double neutronThreshold)
      Sets the mass after which exact neutron mass should be considered in the calculation.
      Parameters:
      neutronThreshold - the mass after which exact neutron mass should be considered in the calculation

    • getLowIntensityCutOff

      public double getLowIntensityCutOff()
      Returns the low intensity cut-off as percentage of the most intense ion peak.
      Returns:
      the low intensity cut-off as percentage of the most intense ion peak

    • setLowIntensityCutOff

      public void setLowIntensityCutOff(double lowIntensityCutOff)
      Sets the low intensity cut-off as percentage of the most intense ion peak.
      Parameters:
      lowIntensityCutOff - the low intensity cut-off as percentage of the most intense ion peak

    • getHighIntensityCutOff

      public double getHighIntensityCutOff()
      Returns the high intensity cut-off as percentage of the most intense ion peak.
      Returns:
      the high intensity cut-off as percentage of the most intense ion peak

    • setHighIntensityCutOff

      public void setHighIntensityCutOff(double highIntensityCutOff)
      Sets the high intensity cut-off as percentage of the most intense ion peak.
      Parameters:
      highIntensityCutOff - the high intensity cut-off as percentage of the most intense ion peak

    • getIntensityCutOffIncrement

      public double getIntensityCutOffIncrement()
      Returns the intensity cut-off increment.
      Returns:
      the intensity cut-off increment

    • setIntensityCutOffIncrement

      public void setIntensityCutOffIncrement(double intensityCutOffIncrement)
      Sets the intensity cut-off increment.
      Parameters:
      intensityCutOffIncrement - the intensity cut-off increment

    • getSingleChargeWindow

      public int getSingleChargeWindow()
      Returns the window size for singly charged ions.
      Returns:
      the window size for singly charged ions

    • setSingleChargeWindow

      public void setSingleChargeWindow(int singleChargeWindow)
      Sets the window size for singly charged ions.
      Parameters:
      singleChargeWindow - the window size for singly charged ions

    • getDoubleChargeWindow

      public int getDoubleChargeWindow()
      Returns the window size for doubly charged ions.
      Returns:
      the window size for doubly charged ions

    • setDoubleChargeWindow

      public void setDoubleChargeWindow(int doubleChargeWindow)
      Sets the window size for doubly charged ions.
      Parameters:
      doubleChargeWindow - the window size for doubly charged ions

    • getnPeaksInSingleChargeWindow

      public int getnPeaksInSingleChargeWindow()
      Returns the number of peaks in singly charged windows.
      Returns:
      the number of peaks in singly charged windows

    • setnPeaksInSingleChargeWindow

      public void setnPeaksInSingleChargeWindow(int nPeaksInSingleChargeWindow)
      Sets the number of peaks in singly charged windows.
      Parameters:
      nPeaksInSingleChargeWindow - the number of peaks in singly charged windows

    • getnPeaksInDoubleChargeWindow

      public int getnPeaksInDoubleChargeWindow()
      Returns the number of peaks in doubly charged windows.
      Returns:
      the number of peaks in doubly charged windows

    • setnPeaksInDoubleChargeWindow

      public void setnPeaksInDoubleChargeWindow(int nPeaksIndoubleChargeWindow)
      Sets the number of peaks in doubly charged windows.
      Parameters:
      nPeaksIndoubleChargeWindow - the number of peaks in doubly charged windows

    • getMaxHitsPerSpectrumPerCharge

      public int getMaxHitsPerSpectrumPerCharge()
      Returns the maximal number of hits searched per spectrum and per charge.
      Returns:
      the maximal number of hits searched per spectrum and per charge

    • setMaxHitsPerSpectrumPerCharge

      public void setMaxHitsPerSpectrumPerCharge(int maxHitsPerSpectrumPerCharge)
      Set the maximal number of hits searched per spectrum and per charge.
      Parameters:
      maxHitsPerSpectrumPerCharge - the maximal number of hits searched per spectrum and per charge

    • getnAnnotatedMostIntensePeaks

      public int getnAnnotatedMostIntensePeaks()
      Returns the minimal number of annotated most intense peaks.
      Returns:
      the minimal number of annotated most intense peaks

    • setnAnnotatedMostIntensePeaks

      public void setnAnnotatedMostIntensePeaks(int nAnnotatedMostIntensePeaks)
      Sets the minimal number of annotated most intense peaks.
      Parameters:
      nAnnotatedMostIntensePeaks - the minimal number of annotated most intense peaks

    • getMinAnnotatedPeaks

      public int getMinAnnotatedPeaks()
      Returns the minimal number of annotated peaks a peptide should have.
      Returns:
      the minimal number of annotated peaks a peptide should have

    • setMinAnnotatedPeaks

      public void setMinAnnotatedPeaks(int minAnnotatedPeaks)
      Sets the minimal number of annotated peaks a peptide should have.
      Parameters:
      minAnnotatedPeaks - the minimal number of annotated peaks a peptide should have

    • getMinPeaks

      public int getMinPeaks()
      Returns the minimal number of peaks a spectrum should contain.
      Returns:
      the minimal number of peaks a spectrum should contain

    • setMinPeaks

      public void setMinPeaks(int minPeaks)
      Sets the minimal number of peaks a spectrum should contain.
      Parameters:
      minPeaks - the minimal number of peaks a spectrum should contain

    • isCleaveNterMethionine

      public boolean isCleaveNterMethionine()
      Indicates whether N-terminal methionines should be cleaved.
      Returns:
      a boolean indicating whether N-terminal methionines should be cleaved

    • setCleaveNterMethionine

      public void setCleaveNterMethionine(boolean cleaveNterMethionine)
      Sets whether N-terminal methionines should be cleaved.
      Parameters:
      cleaveNterMethionine - whether N-terminal methionines should be cleaved

    • getMaxMzLadders

      public int getMaxMzLadders()
      Returns the maximal m/z ladder length.
      Returns:
      the maximal m/z ladder length

    • setMaxMzLadders

      public void setMaxMzLadders(int maxMzLadders)
      Sets the maximal m/z ladder length.
      Parameters:
      maxMzLadders - the maximal m/z ladder length

    • getMaxFragmentCharge

      public int getMaxFragmentCharge()
      Returns the maximal fragment charge.
      Returns:
      the maximal fragment charge

    • setMaxFragmentCharge

      public void setMaxFragmentCharge(int maxFragmentCharge)
      Sets the maximal fragment charge.
      Parameters:
      maxFragmentCharge - the maximal fragment charge

    • getFractionOfPeaksForChargeEstimation

      public double getFractionOfPeaksForChargeEstimation()
      Returns the fraction of peaks to be retained for charge >1 estimation.
      Returns:
      the fraction of peaks to be retained for charge >1 estimation

    • setFractionOfPeaksForChargeEstimation

      public void setFractionOfPeaksForChargeEstimation(double fractionOfPeaksForChargeEstimation)
      Sets the fraction of peaks to be retained for charge >1 estimation.
      Parameters:
      fractionOfPeaksForChargeEstimation - the fraction of peaks to be retained for charge >1 estimation

    • isDetermineChargePlusOneAlgorithmically

      public boolean isDetermineChargePlusOneAlgorithmically()
      Indicates whether charge plus one should be determined algorithmically.
      Returns:
      whether charge plus one should be determined algorithmically

    • setDetermineChargePlusOneAlgorithmically

      public void setDetermineChargePlusOneAlgorithmically(boolean determineChargePlusOneAlgorithmically)
      Sets whether charge plus one should be determined algorithmically.
      Parameters:
      determineChargePlusOneAlgorithmically - whether charge plus one should be determined algorithmically

    • isSearchPositiveIons

      public boolean isSearchPositiveIons()
      Indicates whether positive ions are searched. False means negative ions.
      Returns:
      a boolean indicating whether positive ions are searched

    • setSearchPositiveIons

      public void setSearchPositiveIons(boolean searchPositiveIons)
      Sets whether positive ions are searched. False means negative ions.
      Parameters:
      searchPositiveIons - a boolean indicating whether positive ions are searched

    • getMinPrecPerSpectrum

      public int getMinPrecPerSpectrum()
      Returns the minimal number of precursors per spectrum.
      Returns:
      the minimal number of precursors per spectrum

    • setMinPrecPerSpectrum

      public void setMinPrecPerSpectrum(int minPrecPerSpectrum)
      Sets the minimal number of precursors per spectrum.
      Parameters:
      minPrecPerSpectrum - the minimal number of precursors per spectrum

    • isSearchForwardFragmentFirst

      public boolean isSearchForwardFragmentFirst()
      Indicates whether forward ions (b1) should be searched first.
      Returns:
      a boolean indicating whether forward ions (b1) should be searched first

    • setSearchForwardFragmentFirst

      public void setSearchForwardFragmentFirst(boolean searchForwardFragmentFirst)
      Sets whether forward ions (b1) should be searched first.
      Parameters:
      searchForwardFragmentFirst - whether forward ions (b1) should be searched first

    • isSearchRewindFragments

      public boolean isSearchRewindFragments()
      Indicates whether C-terminal fragments should be searched.
      Returns:
      a boolean indicating whether C-terminal fragments should be searched

    • setSearchRewindFragments

      public void setSearchRewindFragments(boolean searchRewindFragments)
      Sets whether C-terminal fragments should be searched.
      Parameters:
      searchRewindFragments - whether C-terminal fragments should be searched

    • getMaxFragmentPerSeries

      public int getMaxFragmentPerSeries()
      Returns the maximal number of fragments to retain per series.
      Returns:
      the maximal number of fragments to retain per series

    • setMaxFragmentPerSeries

      public void setMaxFragmentPerSeries(int maxFragmentPerSeries)
      Sets the maximal number of fragments to retain per series.
      Parameters:
      maxFragmentPerSeries - the maximal number of fragments to retain per series

    • isUseCorrelationCorrectionScore

      public boolean isUseCorrelationCorrectionScore()
      Indicates whether the correlation correction score should be used.
      Returns:
      a boolean indicating whether the correlation correction score should be used

    • setUseCorrelationCorrectionScore

      public void setUseCorrelationCorrectionScore(boolean useCorrelationCorrectionScore)
      Sets whether the correlation correction score should be used.
      Parameters:
      useCorrelationCorrectionScore - a boolean indicating whether the correlation correction score should be used

    • getConsecutiveIonProbability

      public double getConsecutiveIonProbability()
      Returns the consecutive ion probability.
      Returns:
      the consecutive ion probability

    • setConsecutiveIonProbability

      public void setConsecutiveIonProbability(double consecutiveIonProbability)
      Set the consecutive ion probability.
      Parameters:
      consecutiveIonProbability - the consecutive ion probability

    • getIterativeSequenceEvalue

      public double getIterativeSequenceEvalue()
      Returns the e-value threshold to use to consider a sequence for the iterative search. 0.0 means all.
      Returns:
      the e-value threshold to use to consider a sequence for the iterative search

    • setIterativeSequenceEvalue

      public void setIterativeSequenceEvalue(double iterativeSequenceEvalue)
      Sets the e-value threshold to use to consider a sequence for the iterative search. 0.0 means all.
      Parameters:
      iterativeSequenceEvalue - the e-value threshold to use to consider a sequence for the iterative search

    • getIterativeReplaceEvalue

      public double getIterativeReplaceEvalue()
      Returns the e-value threshold to use to replace a hit for the iterative search. 0.0 means the best hit will be retained.
      Returns:
      the e-value threshold to use to replace a hit for the iterative search

    • setIterativeReplaceEvalue

      public void setIterativeReplaceEvalue(double iterativeReplaceEvalue)
      Sets the e-value threshold to use to replace a hit for the iterative search. 0.0 means the best hit will be retained.
      Parameters:
      iterativeReplaceEvalue - the e-value threshold to use to replace a hit for the iterative search

    • getIterativeSpectrumEvalue

      public double getIterativeSpectrumEvalue()
      Returns the e-value threshold to use consider a spectrum for the iterative search. 0.0 means all.
      Returns:
      the e-value threshold to use consider a spectrum for the iterative search

    • setIterativeSpectrumEvalue

      public void setIterativeSpectrumEvalue(double iterativeSpectrumEvalue)
      Sets the e-value threshold to use consider a spectrum for the iterative search. 0.0 means all.
      Parameters:
      iterativeSpectrumEvalue - the e-value threshold to use consider a spectrum for the iterative search

    • getNoProlineRuleSeries

      public ArrayList<Integer> getNoProlineRuleSeries()
      Returns the id numbers of ion series to apply no product ions at proline rule at.
      Returns:
      the id numbers of ion series to apply no product ions at proline rule at

    • setNoProlineRuleSeries

      public void setNoProlineRuleSeries(ArrayList<Integer> noProlineRuleSeries)
      Sets the id numbers of ion series to apply no product ions at proline rule at.
      Parameters:
      noProlineRuleSeries - the id numbers of ion series to apply no product ions at proline rule at

    • setPtmIndex

      public void setPtmIndex(String modificationName, int ptmIndex)
      Sets the index for a given modification. If another modification was already given with the same index the previous setting will be silently overwritten.
      Parameters:
      modificationName - the name of the modification
      ptmIndex - the index of the modification

    • getModificationName

      public String getModificationName(int ptmIndex)
      Returns the name of the modification indexed by the given index. Null if not found.
      Parameters:
      ptmIndex - the index of the modification to look for
      Returns:
      the name of the modification indexed by the given index

    • hasModificationIndexes

      public boolean hasModificationIndexes()
      Indicates whether the modification profile has PTM indexes.
      Returns:
      true if an PTM indexes map is set

    • getPtmIndex

      public int getPtmIndex(String modificationName)
      Returns the index of a given modification
      Parameters:
      modificationName - the name of the modification
      Returns:
      the corresponding index

    • getPtmIndexes

      public HashMap<Integer,String> getPtmIndexes()
      Returns the PTM indexes as a map.
      Returns:
      the PTM indexes

    • setPtmIndexes

      public void setPtmIndexes(ModificationParameters modificationProfile)
      Set the PTM indexes of the modifications searched.
      Parameters:
      modificationProfile - the modification profile of this search

    • getOMSSAIndexes

      public static HashMap<String,Integer> getOMSSAIndexes(File modificationsFile) throws org.xmlpull.v1.XmlPullParserException, FileNotFoundException, IOException
      Imports the OMSSA indexes from an XML file.
      Parameters:
      modificationsFile - the modification file
      Returns:
      a map of all indexes: modification name > OMSSA index
      Throws:
      org.xmlpull.v1.XmlPullParserException - if an XmlPullParserException occurs
      FileNotFoundException - if a FileNotFoundException occurs
      IOException - if an IOException occurs

    • getAlgorithm

      public Advocate getAlgorithm()
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the identification algorithm.
      Specified by:
      getAlgorithm in interface IdentificationAlgorithmParameter
      Returns:
      the identification algorithm

    • equals

      public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
      Description copied from interface: IdentificationAlgorithmParameter
      Indicates whether another identificationAlgorithmParameter has the same parameters.
      Specified by:
      equals in interface IdentificationAlgorithmParameter
      Parameters:
      identificationAlgorithmParameter - the other identificationAlgorithmParameter
      Returns:
      true if the algorithm and parameters are the same

    • toString

      public String toString(boolean html)
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the parameters as a string.
      Specified by:
      toString in interface IdentificationAlgorithmParameter
      Parameters:
      html - use HTML formatting
      Returns:
      the parameters as a string