ur_rna.StructureEditor.services.fileIO

Class RnaFileIO

java.lang.Object

ur_rna.StructureEditor.services.fileIO.RnaFileIO

public class RnaFileIO
extends java.lang.Object

RnaFileIO is used to load and save RNA files (CT, SEQ etc)

This is a further abstraction of the RNA Backend class. It is a mixture of backend (c++) and Java-based functions. Ideally, we would go the opposite route--integrate the backend classes into the java program to make the distinction as seamless as possible, but unfortunately the backend c++ is too brittle, and adding the necessary features to the c++ classes might have a performance impact for the command-line interfaces.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	RnaFileIO.AsyncTask<TResult>
static class	RnaFileIO.BackendCalc<TResult> A task that is run in the RNAstructure Backend (JNI).
static class	RnaFileIO.BackgroundWork<TResult>
(package private) static class	RnaFileIO.NucIndexConverter The backend uses "III" (or some other character in extended nucleobase alphabets) to indicate an inter-molecular linker.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALPHABET_RNA
private static java.lang.String	DATA_PATH
static char	InterMolecularBreakChar
static int	InterMolecularBreakLength
static java.lang.String	InterMolecularBreakStr
private static AppLog	log
static int	MAX_SEQUENCE_LENGTH
static int	SEQUENCE_FMT_FASTA
static int	SEQUENCE_FMT_SEQ
static int	SEQUENCE_FMT_TEXT
(package private) static java.util.regex.Pattern	stripEnergyTitleRegex

Constructor Summary

Constructors

Constructor and Description
RnaFileIO()

Method Summary

Modifier and Type	Method and Description
private static int	backendPairIndex(Nuc n)
static void	breakBackendPseudoknots(RnaScene scene, RNA rna, int structureNumber)
static double	calculateEnergy(RnaScene scene) Calculates the free energy of the structure in kcal/mol
private static void	checkErrors(RNA rna, java.lang.String operation)
static void	checkForErrors(RNA rna)
static RNA	createRNAfromScene(RnaScene scene, boolean includePairs, boolean allowUnknownBases, boolean skipThermo)
static RnaScene	createSceneFromRNA(RNA rna, int structureIndex, boolean includeBonds) Create new RnaScene from an RNA structure.
private static int	defaultWindowSize(RNA rna)
static RnaFileIO.BackendCalc<RnaSceneGroup>	foldSeq(java.lang.String sequence, int maxStructures)
static boolean	getBestOrientation(double[] oldVals, double[] newVals, double[] params, double allowedError)
private static java.lang.String	getDataPath()
static java.lang.String	getInterStrandLinker()
static java.lang.String	getRNASequence(RnaScene scene)
static RnaSceneGroup	getRNAstructureGroup(RNA rna)
static int	getRNAType(FileType type)
static java.lang.String	getStructureTitle(RNA rna, int structureIndex)
static void	identifyPseudoKnotsBackend(RnaScene scene)
static boolean	isInterStrandLinker(char c)
static RnaSceneGroup	readFileAsScene(java.lang.String path, FileType type)
static void	setStructureTitle(RNA rna, int structureIndex, java.lang.String title)
static void	splitStrandsAtLinkers(RnaScene scene)
static java.lang.String	stripEnergyTitle(java.lang.String title)
protected static void	updateBackendBonds(RnaScene scene, RNA rna, int structureIndex) Clear the RNA structure's bonds and re-read them from the RnaScene.
protected static void	updateSceneBonds(RnaScene scene, RNA rna, int structureIndex) Clear the RnaScene's bonds and re-write them from the RNA structure.
private static boolean	verifyDataFiles(java.lang.String path)
private static void	verifyDataPath()
static RNA	writeRNAstructureGroup(RnaSceneGroup scenes, boolean allowUnknownBases, boolean skipThermo)
static boolean	writeSequenceFile(RnaScene scene, java.lang.String path, FileType type, boolean append)
static boolean	writeStructureFile(RnaSceneGroup scenes, java.lang.String path, FileType type, boolean append)

Methods inherited from class java.lang.Object

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

Field Detail

ALPHABET_RNA

public static final java.lang.String ALPHABET_RNA

See Also:

Constant Field Values

DATA_PATH

private static java.lang.String DATA_PATH

InterMolecularBreakChar

public static final char InterMolecularBreakChar

See Also:

Constant Field Values

InterMolecularBreakLength

public static final int InterMolecularBreakLength

InterMolecularBreakStr

public static final java.lang.String InterMolecularBreakStr

See Also:

Constant Field Values

log

private static final AppLog log

MAX_SEQUENCE_LENGTH

public static final int MAX_SEQUENCE_LENGTH

See Also:

Constant Field Values

SEQUENCE_FMT_FASTA

public static final int SEQUENCE_FMT_FASTA

See Also:

Constant Field Values

SEQUENCE_FMT_SEQ

public static final int SEQUENCE_FMT_SEQ

See Also:

Constant Field Values

SEQUENCE_FMT_TEXT

public static final int SEQUENCE_FMT_TEXT

See Also:

Constant Field Values

stripEnergyTitleRegex

static java.util.regex.Pattern stripEnergyTitleRegex

Constructor Detail

RnaFileIO

public RnaFileIO()

Method Detail

backendPairIndex

private static int backendPairIndex(Nuc n)

breakBackendPseudoknots

public static void breakBackendPseudoknots(RnaScene scene,
                                           RNA rna,
                                           int structureNumber)

calculateEnergy

public static double calculateEnergy(RnaScene scene)
                              throws RnaBackendException

Calculates the free energy of the structure in kcal/mol

Throws:

RnaBackendException

checkErrors

private static void checkErrors(RNA rna,
                                java.lang.String operation)
                         throws RnaBackendException

Throws:

RnaBackendException

checkForErrors

public static void checkForErrors(RNA rna)
                           throws RnaBackendException

Throws:

RnaBackendException

createRNAfromScene

public static RNA createRNAfromScene(RnaScene scene,
                                     boolean includePairs,
                                     boolean allowUnknownBases,
                                     boolean skipThermo)
                              throws RnaBackendException

Throws:

RnaBackendException

createSceneFromRNA

public static RnaScene createSceneFromRNA(RNA rna,
                                          int structureIndex,
                                          boolean includeBonds)
                                   throws RnaBackendException

Create new RnaScene from an RNA structure.

Throws:

RnaBackendException

defaultWindowSize

private static int defaultWindowSize(RNA rna)

foldSeq

public static RnaFileIO.BackendCalc<RnaSceneGroup> foldSeq(java.lang.String sequence,
                                                           int maxStructures)

getBestOrientation

public static boolean getBestOrientation(double[] oldVals,
                                         double[] newVals,
                                         double[] params,
                                         double allowedError)

getDataPath

private static java.lang.String getDataPath()

getInterStrandLinker

public static java.lang.String getInterStrandLinker()

getRNASequence

public static java.lang.String getRNASequence(RnaScene scene)

getRNAstructureGroup

public static RnaSceneGroup getRNAstructureGroup(RNA rna)
                                          throws RnaBackendException

Throws:

RnaBackendException

getRNAType

public static int getRNAType(FileType type)

getStructureTitle

public static java.lang.String getStructureTitle(RNA rna,
                                                 int structureIndex)

identifyPseudoKnotsBackend

public static void identifyPseudoKnotsBackend(RnaScene scene)
                                       throws RnaBackendException

Throws:

RnaBackendException

isInterStrandLinker

public static boolean isInterStrandLinker(char c)

readFileAsScene

public static RnaSceneGroup readFileAsScene(java.lang.String path,
                                            FileType type)
                                     throws RnaBackendException

Throws:

RnaBackendException

setStructureTitle

public static void setStructureTitle(RNA rna,
                                     int structureIndex,
                                     java.lang.String title)

splitStrandsAtLinkers

public static void splitStrandsAtLinkers(RnaScene scene)

stripEnergyTitle

public static java.lang.String stripEnergyTitle(java.lang.String title)

updateBackendBonds

protected static void updateBackendBonds(RnaScene scene,
                                         RNA rna,
                                         int structureIndex)

Clear the RNA structure's bonds and re-read them from the RnaScene.

updateSceneBonds

protected static void updateSceneBonds(RnaScene scene,
                                       RNA rna,
                                       int structureIndex)

Clear the RnaScene's bonds and re-write them from the RNA structure.

verifyDataFiles

private static boolean verifyDataFiles(java.lang.String path)

verifyDataPath

private static void verifyDataPath()
                            throws RnaBackendException

Throws:

RnaBackendException

writeRNAstructureGroup

public static RNA writeRNAstructureGroup(RnaSceneGroup scenes,
                                         boolean allowUnknownBases,
                                         boolean skipThermo)
                                  throws RnaBackendException

Throws:

RnaBackendException

writeSequenceFile

public static boolean writeSequenceFile(RnaScene scene,
                                        java.lang.String path,
                                        FileType type,
                                        boolean append)
                                 throws RnaBackendException,
                                        java.io.IOException

Throws:

RnaBackendException

java.io.IOException

writeStructureFile

public static boolean writeStructureFile(RnaSceneGroup scenes,
                                         java.lang.String path,
                                         FileType type,
                                         boolean append)
                                  throws java.io.IOException,
                                         RnaBackendException

Throws:

java.io.IOException

RnaBackendException