Package | Description |
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com.compomics.cli.fasta |
Command line for the handling of fasta files.
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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.experiment.identification.utils |
This package contains utilities classes to handle identification objects.
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com.compomics.util.experiment.io.biology.protein |
Experiment IO classes for biological resources.
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com.compomics.util.experiment.io.biology.protein.converters |
Fasta file converters.
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com.compomics.util.gui.parameters.identification.search |
Dialogs for search parameters.
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com.compomics.util.gui.protein |
GUI class related to protein sequence formatting.
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com.compomics.util.parameters.identification |
Identification parameters.
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Modifier and Type | Method and Description |
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FastaParameters |
FastaParametersInputBean.getFastaParameters()
Returns the FASTA parameters as parsed from the command line.
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Constructor and Description |
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FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
IdentificationParameters identificationParameters)
Constructor.
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FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsParameters peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
|
Modifier and Type | Method and Description |
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static boolean |
ProteinUtils.isDecoy(String accession,
FastaParameters fastaParameters)
Returns a boolean indicating whether the given accession corresponds to a
decoy sequence according to the given FASTA parameters.
|
Modifier and Type | Method and Description |
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static FastaParameters |
FastaParameters.inferParameters(String fastaFilePath,
WaitingHandler waitingHandler)
Infers the parameters used to parse the file.
|
Modifier and Type | Method and Description |
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boolean |
FastaParameters.equals(FastaParameters fastaParameters) |
static FastaSummary |
FastaSummary.getSummary(String fastaFile,
FastaParameters fastaParameters,
boolean alwaysCreateNew,
WaitingHandler waitingHandler)
Gathers summary data on the FASTA file content.
|
static FastaSummary |
FastaSummary.getSummary(String fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Gathers summary data on the FASTA file content.
|
boolean |
FastaParameters.isSameAs(FastaParameters fastaParameters)
Returns a boolean indicating whether the parsing parameters are the same
as the given parameters.
|
Modifier and Type | Method and Description |
---|---|
static FastaParameters |
DecoyConverter.getDecoyParameters(FastaParameters targetParameters)
Returns the FASTA parameters of the target-decoy database based on the
parameters of the target database.
|
Modifier and Type | Method and Description |
---|---|
static void |
DecoyConverter.appendDecoySequences(File fastaIn,
File fastaOut,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Appends decoy sequences to the provided FASTA file.
|
static FastaParameters |
DecoyConverter.getDecoyParameters(FastaParameters targetParameters)
Returns the FASTA parameters of the target-decoy database based on the
parameters of the target database.
|
Modifier and Type | Method and Description |
---|---|
FastaParameters |
SequenceDbDetailsDialog.getFastaParameters()
Returns the FASTA parameters.
|
Constructor and Description |
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SequenceDbDetailsDialog(Dialog owner,
Frame parent,
String selectedFastaFile,
FastaParameters fastaParameters,
LastSelectedFolder lastSelectedFolder,
boolean dbEditable,
Image normalImange,
Image waitingImage)
Creates a new SequenceDbDetailsDialog with a dialog as owner.
|
SequenceDbDetailsDialog(Frame parent,
String selectedFastaFile,
FastaParameters fastaParameters,
LastSelectedFolder lastSelectedFolder,
boolean dbEditable,
Image normalImange,
Image waitingImage)
Creates a new SequenceDbDetailsDialog.
|
Modifier and Type | Method and Description |
---|---|
FastaParameters |
FastaParametersDialog.getFastaSettings()
Returns the FASTA settings as set by the user.
|
Constructor and Description |
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FastaParametersDialog(Dialog owner,
Frame parentFrame,
FastaParameters fastaSettings,
boolean editable)
Creates a new FractionSettingsDialog with a dialog as owner.
|
FastaParametersDialog(Frame parentFrame,
FastaParameters fastaSettings,
boolean editable)
Creates a new FractionSettingsDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
FastaParameters |
IdentificationParameters.getFastaParameters()
Returns the FASTA processing parameters.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParameters.setFastaParameters(FastaParameters fastaParameters)
Sets the ASTA processing 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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