Uses of Class
eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation

Packages that use ResidueAnnotation

Package	Description
eu.isas.peptideshaker.gui.protein_sequence	Protein sequence annotation.
eu.isas.peptideshaker.gui.tabpanels	Main GUI panels.
eu.isas.peptideshaker.utils	Various utilities classes.

Uses of ResidueAnnotation in eu.isas.peptideshaker.gui.protein_sequence

Method parameters in eu.isas.peptideshaker.gui.protein_sequence with type arguments of type ResidueAnnotation

Modifier and Type	Method and Description
void	ProteinSequencePanelParent.annotationClicked(ArrayList<ResidueAnnotation> allAnnotation, org.jfree.chart.ChartMouseEvent cme)
org.jfree.chart.ChartPanel	ProteinSequencePanel.getSequencePlot(ProteinSequencePanelParent aProteinSequencePanelParent, no.uib.jsparklines.data.JSparklinesDataset sparklineDataset, HashMap<Integer,ArrayList<ResidueAnnotation>> proteinAnnotations, boolean addReferenceLine, boolean allowZooming) Returns a sequence plot as a ChartPanel.

Constructor parameters in eu.isas.peptideshaker.gui.protein_sequence with type arguments of type ResidueAnnotation

Constructor and Description
ProteinAnnotations(HashMap<Integer,ArrayList<ResidueAnnotation>> proteinAnnotations) Create a new ProteinAnnotations object.

Uses of ResidueAnnotation in eu.isas.peptideshaker.gui.tabpanels

Method parameters in eu.isas.peptideshaker.gui.tabpanels with type arguments of type ResidueAnnotation

Modifier and Type	Method and Description
void	ProteinFractionsPanel.annotationClicked(ArrayList<ResidueAnnotation> allAnnotation, org.jfree.chart.ChartMouseEvent cme)
void	OverviewPanel.annotationClicked(ArrayList<ResidueAnnotation> allAnnotation, org.jfree.chart.ChartMouseEvent cme)

Uses of ResidueAnnotation in eu.isas.peptideshaker.utils

Methods in eu.isas.peptideshaker.utils that return types with arguments of type ResidueAnnotation

Modifier and Type

Method and Description

HashMap<Integer,ArrayList<ResidueAnnotation>>

DisplayFeaturesGenerator.getResidueAnnotation(long proteinMatchKey, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.identification.Identification identification, boolean allPeptides, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, boolean enzymatic) Returns the residue annotation for a given protein in a map for enzymatic or not enzymatic peptides only.