Uses of Class
org.proteinshader.structure.visitor.exceptions.VisitorException

Packages that use VisitorException

org.proteinshader.gui	Holds all of the Swing GUI components and their associated listeners, including class Renderer, which is registered as a listener for the GLCanvas object that is used a drawing surface.
org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.io.demos	Holds demo classes that were used for early testing of the io classes.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.
org.proteinshader.structure.visitor.demos	Holds demo classes that were used for early testing of the Visitor classes.
org.proteinshader.structure.visitor.exceptions	Holds exception classes needed by the Visitor classes.

Uses of VisitorException in org.proteinshader.gui

Methods in org.proteinshader.gui that throw VisitorException

void	Renderer.setVisibleDrawables(Model model, StyleEnum style) An array of opaque Segments, and array of opaque Atoms and Bonds, and an array of translucent Drawable objects will be obtained from the Model.

Uses of VisitorException in org.proteinshader.structure

Methods in org.proteinshader.structure that throw VisitorException

void	AminoAcid.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Water.accept(Visitor visitor) Accepts a Visitor and does a callback.
abstract void	Drawable.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Segment.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Structure.accept(Visitor visitor) Accepts a Visitor and does a callback.
abstract void	Residue.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Chain.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Model.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Helix.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Atom.accept(Visitor visitor) Accepts a Visitor and does a callback.
abstract void	Region.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	BetaStrand.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Loop.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Bond.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Heterogen.accept(Visitor visitor) Accepts a Visitor and does a callback.
void	Structure.calculateBounds() Sets the min and max values for x, y, and z on each Model held by the Structure.
void	Structure.calculateFrenetFrames() Before Regions objects (Helix, BetaStrand, and Loop) are added to the Structure, a rotation (the equivalent to a discrete Frenet Frame) should be calculated for each AminoAcid.
void	Structure.clearAllBonds() Clears all Bonds (AminoAcids, Heterogens, and Waters) from the Structure.
void	Structure.clearBonds(ResidueMode residueMode) Clears Bonds from the Structure.
void	Structure.generateLoopRegions() Generates Loop objects from any AminoAcids that do not already belong to a Helix or BetaStrand object.
void	Structure.generateStandardBonds() Generates standard Bonds (AminoAcids and Waters).
List<String>	Structure.getAminoAcidLabels() Returns a list of all AminoAcid residueIDs.
void	Model.updateListsOfVisibles(boolean includeAtoms, boolean includeBonds, boolean includeAminoAcids, boolean includeHeterogens, boolean includeWaters, boolean includeSegments) Finds visible Drawable objects and transfers them to a list of opaque Segments, opaque Atoms and Bonds, or a list of translucent Drawables.

Uses of VisitorException in org.proteinshader.structure.io.demos

Methods in org.proteinshader.structure.io.demos that throw VisitorException

void	PDBStructureReaderDemo.writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.
void	SegmentDemo.writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.

Uses of VisitorException in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor that throw VisitorException

void	Visitable.accept(Visitor visitor) Accepts a Vistor so that a call back can be done.
void	SFWriterVisitor.closeOutputFile() This method flushes the output buffer to make sure that all data is written before closing the output file.
void	SFWriterVisitor.flush() This method forces the writer to immediately write all data in its buffer.
void	SFWriterVisitor.openOutputFile(String outputFile) Opens a buffered writer using the filename given as an argument.
void	Visitor.visit(AminoAcid aminoAcid) Traverses all Atoms owned by the AminoAcid if AAPortionMode is set to ENTIRE_AA.
void	SFWriterVisitor.visit(AminoAcid aminoAcid) Writes all information held by an AminoAcid.
void	FrenetFrameGeneratorVisitor.visit(AminoAcid aminoAcid) The AminoAcid being visited is considered as CA(i+1), while the last two AminoAcids are considered to be CA(i) and CA(i-1).
void	LoopGeneratorVisitor.visit(AminoAcid aminoAcid) Checks whether a start AminoAcid and an end AminoAcid for a Loop have been found, and creates a new Loop as needed.
void	AminoAcidLabelVisitor.visit(AminoAcid aminoAcid) Adds a residueID to the list of labels if it has not been seen before.
void	BondGeneratorVisitor.visit(AminoAcid aminoAcid) Uses Atom distances to generate Bonds within the AminoAcid, and also uses the memory of the last carbonyl carbon seen to check for a possible peptide Bond.
void	ModifierVisitor.visit(Atom atom) If an AtomModifier has been added, it will be used to modify the Atom.
void	Visitor.visit(Atom atom) Traverses all Bonds owned by the Atom.
void	SFWriterVisitor.visit(Atom atom) Writes all information held by an Atom.
void	BoundsVisitor.visit(Atom atom) Checks xyz-coordinates to look for any new min or new max.
void	VisibilityVisitor.visit(Atom atom) Tests the visiblity of the Atom in order to determine if it should be transferred to the opaque Atoms and Bonds list or the translucent Drawables list.
void	BondDestroyerVisitor.visit(Atom atom) Removes all Bonds on the Atom.
void	BondGeneratorVisitor.visit(Atom atom) Checks if the Atom is a possible Bond destination Atom for any previously seen Atoms of the same Residue, and then adds the Atom to the list of Atoms to remember.
void	Visitor.visit(BetaStrand betaStrand) If debug is true, the betaStrandID, startResidueID, and endResidueID will be printed to standard out.
void	SFWriterVisitor.visit(BetaStrand betaStrand) Writes all information held by a BetaStrand.
void	ModifierVisitor.visit(Bond bond) If a BondModifier has been added, it will be used to modify the Bond.
void	Visitor.visit(Bond bond) If debug is true, the atomID of both the source Atom and the destination Atom will be printed to standard out.
void	SFWriterVisitor.visit(Bond bond) Writes all information held by a Bond.
void	VisibilityVisitor.visit(Bond bond) Tests the visiblity of the Bond in order to determine if it should be transferred to the opaque Atoms and Bonds or translucent Drawables list.
void	BondGeneratorVisitor.visit(Bond bond) NO OPERATION: This Visitor method is not needed by the bond generator.
void	Visitor.visit(Chain chain) Uses the current ResidueMode to determine if it should traverse the AminoAcids, Heterogens, and/or Waters owned by the Chain.
void	SFWriterVisitor.visit(Chain chain) Writes all information held by a Chain.
void	FrenetFrameGeneratorVisitor.visit(Chain chain) All AminoAcids of the Chain will be visited.
void	LoopGeneratorVisitor.visit(Chain chain) Generates Loop objects from AminoAcids that do not already belong to any Region.
void	BondGeneratorVisitor.visit(Chain chain) Generates all standard Bonds (AminoAcids and Waters) for the Chain.
void	Visitor.visit(Helix helix) If debug is true, the helixID, startResidueID, and endResidueID will be printed to standard out.
void	SFWriterVisitor.visit(Helix helix) Writes all information held by a Helix.
void	Visitor.visit(Heterogen heterogen) Traverses all Atoms owned by the Heterogen.
void	SFWriterVisitor.visit(Heterogen heterogen) Writes all information held by a Heterogen.
void	BondGeneratorVisitor.visit(Heterogen heterogen) NO OPERATION: This method is not needed because non-water heterogen bonds are given explicitly in the PDB structure entry.
void	Visitor.visit(Loop loop) If debug is true, the loopID will be printed to standard out.
void	SFWriterVisitor.visit(Loop loop) Writes all information held by a Loop.
void	Visitor.visit(Model model) Traverses all Chains owned by the Model.
void	SFWriterVisitor.visit(Model model) Writes all information held by a Model.
void	BoundsVisitor.visit(Model model) Finds the min and max values for x, y, and z of the Model and then calls setter methods on the Model so that these values are remembered.
void	LoopGeneratorVisitor.visit(Model model) Generates all Loop objects needed by the Model.
void	BondGeneratorVisitor.visit(Model model) Generates all standard Bonds (AminoAcids and Waters) for the Model.
void	ModifierVisitor.visit(Segment segment) If a SegmentModifier has been added, it will be used to modify the Segment.
void	Visitor.visit(Segment segment) If debug is true, the segmentID will be printed to standard out.
void	SFWriterVisitor.visit(Segment segment) Writes information on a Segment.
void	VisibilityVisitor.visit(Segment segment) Tests the visiblity of the Segment in order to determine if it should be transferred to the opaque Segments or translucent Drawables list.
void	Visitor.visit(Structure structure) Traverses all Models owned by the Structure.
void	SFWriterVisitor.visit(Structure structure) Writes a Structure's data to a simple text file.
void	BondGeneratorVisitor.visit(Structure structure) Generates all standard Bonds (AminoAcids and Waters) for the Structure.
void	Visitor.visit(Water water) Traverses all Atoms owned by the Water.
void	SFWriterVisitor.visit(Water water) Writes all information held by a Water.
void	BondGeneratorVisitor.visit(Water water) If the Water includes hydrogen atoms, then Bonds will be created between the oxygen and each hydrogen (after checking that the Bond lengths are reasonable).

Constructors in org.proteinshader.structure.visitor that throw VisitorException

SFWriterVisitor(String outputFile)
Constructs a SFWriterVisitor that will write to the output file given as an argument.

Uses of VisitorException in org.proteinshader.structure.visitor.demos

Methods in org.proteinshader.structure.visitor.demos that throw VisitorException

void	ModifierVisitorDemo.modify(Structure structure) The Helices of the Structure are modified by changing their shape to CYLINDER and setting all of their Atoms and Bonds to INVISIBLE.
void	VisitorDemo.testVisitor(Structure structure) Creates a Visitor and tests it by activating debug mode so that it will print the ID of each object in the Structure.
void	ModifierVisitorDemo.writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.

Uses of VisitorException in org.proteinshader.structure.visitor.exceptions

Subclasses of VisitorException in org.proteinshader.structure.visitor.exceptions

class

WriterVisitorException Used to report that an error occurred while trying to write info on a Visitable object.