ur_rna.StructureEditor.services.fileIO

Class DrawingFileIO

java.lang.Object

ur_rna.StructureEditor.services.fileIO.DrawingFileIO

public class DrawingFileIO
extends java.lang.Object

There are two types of native drawing file formats. CTE "Extended CT File" - Similar to CT, but with additional columns. NSD "Nucleotide Structure Drawing" - Hierarchical Structured Object-based format that stores Nucleotides, Bonds, and Styles in a format that is richer and more extensible than CTE

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static interface	DrawingFileIO.CTE Constants for CTE File IO
private static class	DrawingFileIO.CTEWriter
private static interface	DrawingFileIO.NSD Constants for Nucleotide Structure Drawing (NSD) File IO
private static class	DrawingFileIO.SimpleScanner This replacement for Scanner automatically skips whitespace, but does NOT skip over newlines unless DrawingFileIO.SimpleScanner.nextLine() is called.
static class	DrawingFileIO.TextWriter Simplifies writing tabular text data in which the table formatting is achieved by padding values with spaces.

Field Summary

Fields

Modifier and Type	Field and Description
private static java.text.DecimalFormat	_dblFormat

Constructor Summary

Constructors

Constructor and Description
DrawingFileIO()

Method Summary

Modifier and Type	Method and Description
private static java.awt.Color	decodeColor(java.lang.Object oColor, java.awt.Color defaultValue)
private static java.awt.Font	decodeFont(java.lang.Object oFont, java.awt.Font defaultValue)
private static SimpleDataSerializer.SSONList	expectList(java.lang.Object o, java.lang.String errorMessage)
private static SimpleDataSerializer.SSONMap	expectMap(java.lang.Object o, java.lang.String errorMessage)
private static java.lang.String	fmtNumber(double value)
private static java.io.Writer	newUTF8Writer(java.lang.String path, boolean append) Simplified version of Files.newBufferedWriter(Path, Charset, OpenOption...) that uses StandardCharsets.UTF_8 as the charset and accepts a boolean "append" instead of an OpenOption argument list.
private static SyntaxErrorException	parseError(DrawingFileIO.SimpleScanner scanner, java.lang.String message, java.lang.Object... args)
private static SyntaxErrorException	parseError(int line, int column, java.lang.String message, java.lang.Object... args)
static RnaSceneGroup	readCteDrawingFile(java.io.Reader input)
static RnaSceneGroup	readCteDrawingFile(java.lang.String path)
private static RnaSceneGroup	readNsdDrawingFile(java.lang.Object parsedNSDData)
static RnaSceneGroup	readNsdDrawingFile(java.io.Reader input)
static RnaSceneGroup	readNsdDrawingFile(java.lang.String path)
private static float	roundLoc(float value) round locations to the nearest 0.1
static void	writeCteDrawingFile(RnaSceneGroup scenes, java.lang.String path, boolean append) Write an Extended CT (CTE) Drawing files.
static void	writeCteDrawingFile(RnaSceneGroup scenes, java.io.Writer output, boolean includeExtendedProperties) Write an Extended CT (CTE) Drawing files.
static void	writeCtFile(RnaSceneGroup scenes, java.lang.String path, boolean append)
static void	writeNsdDrawingFile(RnaSceneGroup scenes, java.lang.String path, boolean append)
static void	writeNsdDrawingFile(RnaSceneGroup scenes, java.lang.String path, boolean append, int indent, boolean strict)
static void	writeNsdDrawingFile(RnaSceneGroup scenes, java.io.Writer out, int indent, boolean strict)

Methods inherited from class java.lang.Object

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

Field Detail

_dblFormat

private static final java.text.DecimalFormat _dblFormat

Constructor Detail

DrawingFileIO

public DrawingFileIO()

Method Detail

decodeColor

private static java.awt.Color decodeColor(java.lang.Object oColor,
                                          java.awt.Color defaultValue)

decodeFont

private static java.awt.Font decodeFont(java.lang.Object oFont,
                                        java.awt.Font defaultValue)

expectList

private static SimpleDataSerializer.SSONList expectList(java.lang.Object o,
                                                        java.lang.String errorMessage)

expectMap

private static SimpleDataSerializer.SSONMap expectMap(java.lang.Object o,
                                                      java.lang.String errorMessage)

fmtNumber

private static java.lang.String fmtNumber(double value)

newUTF8Writer

private static java.io.Writer newUTF8Writer(java.lang.String path,
                                            boolean append)
                                     throws java.io.IOException

Simplified version of Files.newBufferedWriter(Path, Charset, OpenOption...) that uses StandardCharsets.UTF_8 as the charset and accepts a boolean "append" instead of an OpenOption argument list.

Throws:

java.io.IOException

parseError

private static SyntaxErrorException parseError(DrawingFileIO.SimpleScanner scanner,
                                               java.lang.String message,
                                               java.lang.Object... args)

parseError

private static SyntaxErrorException parseError(int line,
                                               int column,
                                               java.lang.String message,
                                               java.lang.Object... args)

readCteDrawingFile

public static RnaSceneGroup readCteDrawingFile(java.io.Reader input)
                                        throws SyntaxErrorException

Throws:

SyntaxErrorException

readCteDrawingFile

public static RnaSceneGroup readCteDrawingFile(java.lang.String path)
                                        throws java.io.IOException,
                                               SyntaxErrorException

Throws:

java.io.IOException

SyntaxErrorException

readNsdDrawingFile

private static RnaSceneGroup readNsdDrawingFile(java.lang.Object parsedNSDData)
                                         throws SyntaxErrorException

Throws:

SyntaxErrorException

readNsdDrawingFile

public static RnaSceneGroup readNsdDrawingFile(java.io.Reader input)
                                        throws SyntaxErrorException,
                                               java.io.IOException

Throws:

SyntaxErrorException

java.io.IOException

readNsdDrawingFile

public static RnaSceneGroup readNsdDrawingFile(java.lang.String path)
                                        throws SyntaxErrorException,
                                               java.io.IOException

Throws:

SyntaxErrorException

java.io.IOException

roundLoc

private static float roundLoc(float value)

round locations to the nearest 0.1

writeCteDrawingFile

public static void writeCteDrawingFile(RnaSceneGroup scenes,
                                       java.lang.String path,
                                       boolean append)
                                throws java.io.IOException

Write an Extended CT (CTE) Drawing files. A CTE is a CT file with additional information encoded in the columns past those in a normal CT.

Throws:

java.io.IOException

writeCteDrawingFile

public static void writeCteDrawingFile(RnaSceneGroup scenes,
                                       java.io.Writer output,
                                       boolean includeExtendedProperties)

Write an Extended CT (CTE) Drawing files. A CTE is a CT file with additional information encoded in the columns past those in a normal CT.

writeCtFile

public static void writeCtFile(RnaSceneGroup scenes,
                               java.lang.String path,
                               boolean append)
                        throws java.io.IOException

Throws:

java.io.IOException

writeNsdDrawingFile

public static void writeNsdDrawingFile(RnaSceneGroup scenes,
                                       java.lang.String path,
                                       boolean append)
                                throws java.io.IOException,
                                       FormatterException

Throws:

java.io.IOException

FormatterException

writeNsdDrawingFile

public static void writeNsdDrawingFile(RnaSceneGroup scenes,
                                       java.lang.String path,
                                       boolean append,
                                       int indent,
                                       boolean strict)
                                throws java.io.IOException,
                                       FormatterException

Throws:

java.io.IOException

FormatterException

writeNsdDrawingFile

public static void writeNsdDrawingFile(RnaSceneGroup scenes,
                                       java.io.Writer out,
                                       int indent,
                                       boolean strict)
                                throws java.io.IOException,
                                       FormatterException

Throws:

java.io.IOException

FormatterException