Uses of Class
com.compomics.util.exceptions.ExceptionHandler

Packages that use ExceptionHandler

Package	Description
com.compomics.util.exceptions.exception_handlers	Implementations of the ExceptionHandler interface.
com.compomics.util.experiment.biology	Experiment classes related to biological entities.
com.compomics.util.experiment.identification.protein_inference.proteintree	Protein sequence database indexing classes.
com.compomics.util.experiment.identification.protein_sequences	Protein sequence handling related classes.

Uses of ExceptionHandler in com.compomics.util.exceptions.exception_handlers

Subclasses of ExceptionHandler in com.compomics.util.exceptions.exception_handlers

Modifier and Type	Class and Description
class	CommandLineExceptionHandler Exception handler for command line processes.
class	FrameExceptionHandler Handles exception for a given application and displays warnings using dialogs.
class	WaitingDialogExceptionHandler Exception handler for processes making use of a waiting dialog.

Uses of ExceptionHandler in com.compomics.util.experiment.biology

Methods in com.compomics.util.experiment.biology with parameters of type ExceptionHandler

Modifier and Type	Method and Description
ArrayList<String>	Peptide.getParentProteinsCreateTree(SequenceMatchingPreferences sequenceMatchingPreferences, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) Returns the parent proteins and remaps the peptide to the protein if no protein mapping was set using the default protein tree of the sequence factory.

Uses of ExceptionHandler in com.compomics.util.experiment.identification.protein_inference.proteintree

Methods in com.compomics.util.experiment.identification.protein_inference.proteintree with parameters of type ExceptionHandler

Modifier and Type	Method and Description
void	ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, Enzyme enzyme, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean printExpectedImportTime, boolean displayProgress, int nThreads) Initiates the tree.
void	ProteinTree.initiateTree(int initialTagSize, int maxNodeSize, int maxPeptideSize, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean printExpectedImportTime, boolean displayProgress, int nThreads) Initiates the tree.

Uses of ExceptionHandler in com.compomics.util.experiment.identification.protein_sequences

Methods in com.compomics.util.experiment.identification.protein_sequences with parameters of type ExceptionHandler

Modifier and Type	Method and Description
boolean	SequenceFactory.deleteProteinTree(ExceptionHandler exceptionHandler) Try to delete the default protein tree.
ProteinTree	SequenceFactory.getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
ProteinTree	SequenceFactory.getDefaultProteinTree(int nThreads, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, boolean displayProgress) Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.
ProteinTree	SequenceFactory.getDefaultProteinTree(WaitingHandler waitingHandler, ExceptionHandler exceptionHandler) Returns the default protein tree corresponding to the database loaded in factory, creates a new one if none found.