public class SearchParameters extends ExperimentObject implements MarshallableParameter
Modifier and Type | Class and Description |
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static class |
SearchParameters.MassAccuracyType
Possible mass accuracy types.
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MarshallableParameter.Type
Modifier and Type | Field and Description |
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static String[] |
implementedForwardIons
Convenience array for forward ion type selection.
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static String[] |
implementedRewindIons
Convenience array for rewind ion type selection.
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static int |
preferredMaxVariableModifications
The preferred maximal number of variable modifications.
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static int |
preferredMinSequences
The preferred minimal number of protein sequences.
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String |
version
Version number.
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NO_KEY
Constructor and Description |
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SearchParameters()
Constructor.
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SearchParameters(SearchParameters searchParameters)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(SearchParameters otherSearchParameters)
Returns true if the search parameter objects have identical settings.
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Set<Integer> |
getAlgorithms()
Returns the algorithms for which specific parameters are stored.
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HashMap<Integer,IdentificationAlgorithmParameter> |
getAlgorithmSpecificParameters()
Returns the algorithm specific parameters in a map: algorithm as indexed
in the Advocate class > parameters.
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DigestionParameters |
getDigestionParameters()
Returns the digestion preferences.
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boolean |
getFlanking()
Return whether the flanking amino acids of a mapped peptide are to be
reported.
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ArrayList<Integer> |
getForwardIons()
Returns the forward ions searched as list of integers as indexed in the
FragmentIon class.
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SearchParameters.MassAccuracyType |
getFragmentAccuracyType()
Returns the fragment accuracy type.
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double |
getFragmentIonAccuracy()
Returns the MS2 ion m/z tolerance.
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double |
getFragmentIonAccuracyInDaltons()
Returns the absolute fragment ion tolerance in Dalton.
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double |
getFragmentIonAccuracyInDaltons(double refMass)
Returns the absolute fragment ion tolerance in Dalton.
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IdentificationAlgorithmParameter |
getIdentificationAlgorithmParameter(int algorithmID)
Returns the algorithm specific parameters, null if not found.
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static SearchParameters |
getIdentificationParameters(File searchParametersFile)
Loads the identification parameters from a file.
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static String[] |
getIons()
Getter for the list of ion symbols used.
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int |
getMaxChargeSearched()
Returns the maximal charge searched.
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int |
getMaxIsotopicCorrection()
Returns the maximal isotopic correction.
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int |
getMinChargeSearched()
Returns the minimal charge searched.
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int |
getMinIsotopicCorrection()
Returns the minimal isotopic correction.
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ModificationParameters |
getModificationParameters()
Returns the modification settings.
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double |
getPrecursorAccuracy()
Returns the precursor tolerance.
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SearchParameters.MassAccuracyType |
getPrecursorAccuracyType()
Returns the precursor accuracy type.
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double |
getRefMass()
Returns the reference mass used to convert ppm to Da.
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ArrayList<Integer> |
getRewindIons()
Returns the rewind ions searched as list of integers as indexed in the
FragmentIon class.
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String |
getShortDescription()
Returns a short description of the parameters.
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MarshallableParameter.Type |
getType()
Returns the type of marshalled parameter from an unmarshalled object.
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Boolean |
isPrecursorAccuracyTypePpm()
Returns true if the current precursor accuracy type is ppm.
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static void |
saveIdentificationParameters(SearchParameters searchParameters,
File searchParametersFile)
Saves the identification parameters to a serialized file.
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void |
saveIdentificationParametersAsTextFile(File file)
Saves the identification parameters as a human readable text file.
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void |
setDefaultAdvancedSettings()
Set the advanced settings to the default values.
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void |
setDefaultAdvancedSettings(SearchParameters searchParameters)
Set the advanced settings to the values in the given search parameters
object or to the default values of the advanced settings are not set for
a given advocate.
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void |
setDigestionParameters(DigestionParameters digestionParameters)
Sets the digestion preferences.
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void |
setFlanking(boolean flanking)
Set whether the flanking amino acids of a mapped peptide are to be
reported.
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void |
setForwardIons(ArrayList<Integer> forwardIons)
Sets the forward ions searched as list of integers as indexed in the
FragmentIon class.
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void |
setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType)
Sets the fragment accuracy type.
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void |
setFragmentIonAccuracy(double fragmentIonMZTolerance)
Sets the fragment ion m/z tolerance.
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void |
setIdentificationAlgorithmParameter(int algorithmID,
IdentificationAlgorithmParameter identificationAlgorithmParameter)
Adds identification algorithm specific parameters.
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void |
setMaxChargeSearched(int maxChargeSearched)
Sets the maximal charge searched.
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void |
setMaxIsotopicCorrection(int maxIsotopicCorrection)
Sets the maximal isotopic correction.
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void |
setMinChargeSearched(int minChargeSearched)
Sets the minimal charge searched.
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void |
setMinIsotopicCorrection(int minIsotopicCorrection)
Sets the minimal isotopic correction.
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void |
setModificationParameters(ModificationParameters modificationParameters)
Sets the modification settings.
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void |
setPrecursorAccuracy(double precursorTolerance)
Sets the precursor tolerance.
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void |
setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType)
Sets the precursor accuracy type.
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void |
setRefMass(double refMass)
Sets the reference mass used to convert ppm to Da.
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void |
setRewindIons(ArrayList<Integer> rewindIons)
Sets the rewind ions searched as list of integers as indexed in the
FragmentIon class.
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void |
setType()
Sets the parameters type.
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String |
toString() |
String |
toString(boolean html)
Returns the search parameters as a string.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public final String version
public static final String[] implementedForwardIons
public static final String[] implementedRewindIons
public static final int preferredMaxVariableModifications
public static final int preferredMinSequences
public SearchParameters()
public SearchParameters(SearchParameters searchParameters)
searchParameters
- the search parameter to base the search
parameters on.public void setDefaultAdvancedSettings()
public void setDefaultAdvancedSettings(SearchParameters searchParameters)
searchParameters
- the search parameter to extract the advanced
settings frompublic double getRefMass()
public void setRefMass(double refMass)
refMass
- the reference mass used to convert ppm to Dapublic ModificationParameters getModificationParameters()
public void setModificationParameters(ModificationParameters modificationParameters)
modificationParameters
- the modification settingspublic double getFragmentIonAccuracy()
public double getFragmentIonAccuracyInDaltons()
public double getFragmentIonAccuracyInDaltons(double refMass)
refMass
- the reference mass to use for the conversion of tolerances
in ppm.public void setFragmentIonAccuracy(double fragmentIonMZTolerance)
fragmentIonMZTolerance
- the fragment ion m/z tolerancepublic DigestionParameters getDigestionParameters()
public void setDigestionParameters(DigestionParameters digestionParameters)
digestionParameters
- the digestion preferencespublic ArrayList<Integer> getForwardIons()
public void setForwardIons(ArrayList<Integer> forwardIons)
forwardIons
- the forward ions searchedpublic ArrayList<Integer> getRewindIons()
public void setRewindIons(ArrayList<Integer> rewindIons)
rewindIons
- the rewind ions searchedpublic static String[] getIons()
public double getPrecursorAccuracy()
public void setPrecursorAccuracy(double precursorTolerance)
precursorTolerance
- 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 int getMaxChargeSearched()
public void setMaxChargeSearched(int maxChargeSearched)
maxChargeSearched
- the maximal charge searchedpublic int getMinChargeSearched()
public void setMinChargeSearched(int minChargeSearched)
minChargeSearched
- the minimal charge searchedpublic 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 int getMinIsotopicCorrection()
public void setMinIsotopicCorrection(int minIsotopicCorrection)
minIsotopicCorrection
- the minimal isotopic correctionpublic int getMaxIsotopicCorrection()
public void setMaxIsotopicCorrection(int maxIsotopicCorrection)
maxIsotopicCorrection
- the maximal isotopic correctionpublic static SearchParameters getIdentificationParameters(File searchParametersFile) throws IOException, ClassNotFoundException
searchParametersFile
- the search parameter fileIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occurspublic static void saveIdentificationParameters(SearchParameters searchParameters, File searchParametersFile) throws IOException
searchParameters
- the identification parameterssearchParametersFile
- the fileIOException
- if an IOException occurspublic void saveIdentificationParametersAsTextFile(File file) throws IOException
file
- the fileIOException
- if an IOException occurspublic String getShortDescription()
public String toString(boolean html)
html
- use HTML formattingpublic boolean equals(SearchParameters otherSearchParameters)
otherSearchParameters
- the parameters to compare topublic void setFlanking(boolean flanking)
flanking
- whether the flanking amino acids of a mapped peptide are
to be reportedpublic boolean getFlanking()
public void setType()
MarshallableParameter
setType
in interface MarshallableParameter
public MarshallableParameter.Type getType()
MarshallableParameter
getType
in interface MarshallableParameter
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