org.proteinshader.structure.visitor
Class SFWriterVisitor

java.lang.Object
  org.proteinshader.structure.visitor.Visitor
      org.proteinshader.structure.visitor.SFWriterVisitor

public class SFWriterVisitor
extends Visitor

A simple file writer subclass of Visitor that writes to a file all of the data from each Model in a Structure. This class is intended to be useful for development and debugging.

The output is a simple object dump that announces each object, writes its attributes, and then traverses the objects associations so that they can be written.

Field Summary

static int	CHAR_PER_LINE
static int	INDENTATION_FACTOR

Constructor Summary

SFWriterVisitor()
Constructs a SFWriterVisitor.

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

Method Summary

void	closeOutputFile() This method flushes the output buffer to make sure that all data is written before closing the output file.
void	flush() This method forces the writer to immediately write all data in its buffer.
void	openOutputFile(String outputFile) Opens a buffered writer using the filename given as an argument.
void	visit(AminoAcid aminoAcid) Writes all information held by an AminoAcid.
void	visit(Atom atom) Writes all information held by an Atom.
void	visit(BetaStrand betaStrand) Writes all information held by a BetaStrand.
void	visit(Bond bond) Writes all information held by a Bond.
void	visit(Chain chain) Writes all information held by a Chain.
void	visit(Helix helix) Writes all information held by a Helix.
void	visit(Heterogen heterogen) Writes all information held by a Heterogen.
void	visit(Loop loop) Writes all information held by a Loop.
void	visit(Model model) Writes all information held by a Model.
void	visit(Segment segment) Writes information on a Segment.
void	visit(Structure structure) Writes a Structure's data to a simple text file.
void	visit(Water water) Writes all information held by a Water.
void	writeDescription(Description description) writeDescription() - writes all information on a Description.

Methods inherited from class org.proteinshader.structure.visitor.Visitor

clear, includeAAHetAndWater, setDebug, setMode, setMode, setMode, setMode, setMode, setMode, setVisitSegments

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CHAR_PER_LINE

public static final int CHAR_PER_LINE

See Also:

Constant Field Values

INDENTATION_FACTOR

public static final int INDENTATION_FACTOR

See Also:

Constant Field Values

Constructor Detail

SFWriterVisitor

public SFWriterVisitor()

Constructs a SFWriterVisitor.

If this no-arg constructor is used, then openOutputFile() will need to be called in order to specify a file to write to.

SFWriterVisitor

public SFWriterVisitor(String outputFile)
                throws VisitorException

Constructs a SFWriterVisitor that will write to the output file given as an argument.

If the output file does not exist, it will be created. If it does exist, it will be overwritten.

Parameters:

outputFile - the name of the file to write to.

Throws:

VisitorException - if an IO error occurs.

Method Detail

openOutputFile

public void openOutputFile(String outputFile)
                    throws VisitorException

Opens a buffered writer using the filename given as an argument.

If the output file does not exist, it will be created. If it does exist, it will be overwritten.

Parameters:

outputFile - the name of the file to write to.

Throws:

VisitorException - if an IO error occurs.

flush

public void flush()
           throws VisitorException

This method forces the writer to immediately write all data in its buffer.

Throws:

VisitorException - if an IO error occurs.

closeOutputFile

public void closeOutputFile()
                     throws VisitorException

This method flushes the output buffer to make sure that all data is written before closing the output file. After calling closeOutputFile(), further visit() or flush() invocations will result in a VisitorException, unless openOutputFile() has been called to open up another output file to write to.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Structure structure)
           throws VisitorException

Writes a Structure's data to a simple text file.

Overrides:

visit in class Visitor

Parameters:

structure - the Structure to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Model model)
           throws VisitorException

Writes all information held by a Model.

Overrides:

visit in class Visitor

Parameters:

model - the Model to write.

Throws:

VisitorException - if a problem occurs while writing.

visit

public void visit(Chain chain)
           throws VisitorException

Writes all information held by a Chain.

Overrides:

visit in class Visitor

Parameters:

chain - the Chain to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Loop loop)
           throws VisitorException

Writes all information held by a Loop.

Overrides:

visit in class Visitor

Parameters:

loop - the Loop to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Helix helix)
           throws VisitorException

Writes all information held by a Helix.

Overrides:

visit in class Visitor

Parameters:

helix - the Helix to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(BetaStrand betaStrand)
           throws VisitorException

Writes all information held by a BetaStrand.

Overrides:

visit in class Visitor

Parameters:

betaStrand - the BetaStrand to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Segment segment)
           throws VisitorException

Writes information on a Segment.

Overrides:

visit in class Visitor

Parameters:

segment - the Segment to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(AminoAcid aminoAcid)
           throws VisitorException

Writes all information held by an AminoAcid.

Overrides:

visit in class Visitor

Parameters:

aminoAcid - the AminoAcid to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Heterogen heterogen)
           throws VisitorException

Writes all information held by a Heterogen.

Overrides:

visit in class Visitor

Parameters:

heterogen - the Heterogen to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Water water)
           throws VisitorException

Writes all information held by a Water.

Overrides:

visit in class Visitor

Parameters:

water - the Water to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Atom atom)
           throws VisitorException

Writes all information held by an Atom.

Overrides:

visit in class Visitor

Parameters:

atom - the Atom to write.

Throws:

VisitorException - if an IO error occurs.

visit

public void visit(Bond bond)
           throws VisitorException

Writes all information held by a Bond.

Overrides:

visit in class Visitor

Parameters:

bond - the Bond to write.

Throws:

VisitorException - if an IO error occurs.

writeDescription

public void writeDescription(Description description)
                      throws WriterVisitorException

writeDescription() - writes all information on a Description.

Parameters:

description - the Description to write.

Throws:

WriterVisitorException - if an IO error occurs.