Package | Description |
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com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
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com.compomics.util.gui.parameters.identification.advanced |
Dialogs for advanced identification parameters.
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com.compomics.util.parameters.identification |
Identification parameters.
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com.compomics.util.parameters.identification.advanced |
Advanced Identification parameters.
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Constructor and Description |
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FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsParameters peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
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Modifier and Type | Method and Description |
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PeptideVariantsParameters |
PeptideVariantsParametersDialog.getPeptideVariantsPreferences()
Returns the peptide variants settings as set by the user.
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Constructor and Description |
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PeptideVariantsParametersDialog(Dialog owner,
Frame parentFrame,
PeptideVariantsParameters peptideVariantPreferences,
boolean editable)
Creates a new FractionSettingsDialog with a dialog as owner.
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PeptideVariantsParametersDialog(Frame parentFrame,
PeptideVariantsParameters peptideVariantPreferences,
boolean editable)
Creates a new FractionSettingsDialog with a frame as owner.
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Modifier and Type | Method and Description |
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PeptideVariantsParameters |
IdentificationParameters.getPeptideVariantsParameters()
Returns the peptide variant parameters.
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Modifier and Type | Method and Description |
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void |
IdentificationParameters.setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)
Sets the peptide variant parameters.
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Constructor and Description |
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationParameters annotationParameters,
SequenceMatchingParameters sequenceMatchingParameters,
PeptideVariantsParameters peptideVariantsParameters,
GeneParameters geneParameters,
PsmScoringParameters psmScoringParameters,
PeptideAssumptionFilter peptideAssumptionFilter,
ModificationLocalizationParameters ModificationLocalizationParameters,
ProteinInferenceParameters proteinInferenceParameters,
IdMatchValidationParameters idValidationParameters,
FractionParameters fractionParameters,
FastaParameters fastaParameters)
Constructor.
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Modifier and Type | Method and Description |
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static PeptideVariantsParameters |
PeptideVariantsParameters.getNoVariantPreferences()
Returns the preferences corresponding to no variants allowed.
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Modifier and Type | Method and Description |
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boolean |
PeptideVariantsParameters.isSameAs(PeptideVariantsParameters peptideVariantsPreferences)
Indicates whether another peptide variant preferences is the same as this
one.
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