Package | Description |
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com.compomics.util.experiment.biology.genes |
Classes related to genes.
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com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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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.io.identification.writers |
Writer for identification results.
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com.compomics.util.gui.genes |
Dialogs for the handling of genes.
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Modifier and Type | Method and Description |
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GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler)
Returns the gene maps for the given proteins.
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Modifier and Type | Method and Description |
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boolean |
MatchFilter.isValidated(long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider)
Tests whether a match is validated by this filter.
|
boolean |
PsmFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
boolean |
ProteinFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
boolean |
PeptideFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
abstract boolean |
MatchFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider)
Indicates whether the match designated by the match key validates the
given item using the given comparator and value threshold.
|
boolean |
AssumptionFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long spectrumMatchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
Modifier and Type | Class and Description |
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class |
FMIndex
The FM index.
|
Constructor and Description |
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SimpleMzIdentMLExporter(String softwareName,
String softwareVersion,
String softwareUrl,
File tempFolder,
File destinationFile,
ArrayList<File> spectrumFiles,
File searchEngineFile,
HashMap<String,ArrayList<String>> searchEngines,
File fastaFile,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider,
ModificationProvider modificationProvider,
FastaSummary fastaSummary,
String contactFirstName,
String contactLastName,
String contactAddress,
String contactEmail,
String contactOrganizationName,
String contactOrganizationAddress,
String contactOrganizationEmail,
boolean peptideInference)
Constructor.
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Constructor and Description |
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GeneDetailsDialog(Frame parent,
ProteinMatch proteinMatch,
GeneMaps geneMaps,
ProteinDetailsProvider proteinDetailsProvider)
Creates a new GeneDetailsDialog.
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