ur_rna.StructureEditor.windows

Class NewFileWindow.StructItem

java.lang.Object

ur_rna.StructureEditor.windows.NewFileWindow.StructItem

Enclosing class:

NewFileWindow

private static class NewFileWindow.StructItem
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	BP
static int	DOT
static int	ERROR
static int	HELIX
(package private) int	len
(package private) int	pos1
(package private) int	pos2
(package private) int	seq1
(package private) int	seq2
(package private) int	type

Constructor Summary

Constructors

Modifier	Constructor and Description
private	StructItem(int type, int pos1, int pos2)

Method Summary

Modifier and Type	Method and Description
boolean	containsBase(int baseIndex) Returns true if this helix element the nucleobase as the given index.
static NewFileWindow.StructItem	Dot(int seqPos, int charPos)
static NewFileWindow.StructItem	Error(int charPos)
static NewFileWindow.StructItem	Error(int charPos1, int charPos2)
int	getBase(int positionInHelix) Returns the sequence-index of the 5'-base at the 0-based position in this helix
int	getPair(int baseIndex) Returns -1 if the given index does not belong to this structure element or if it is not paired.
int	getTextRegion(int[] regions) A client calls with with an already-created array of integers.
static NewFileWindow.StructItem	Helix(int seq1, int seq2, int len, int pos1, int pos2)
(package private) boolean	isSelected(int selStart, int selEnd) Returns true if the selection falls inside the element and NOT beyond it.
static NewFileWindow.StructItem	Pair(int seq1, int seq2, int pos1, int pos2)
int	pairCount()

Methods inherited from class java.lang.Object

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

Field Detail

BP

public static final int BP

See Also:

Constant Field Values

DOT

public static final int DOT

See Also:

Constant Field Values

ERROR

public static final int ERROR

See Also:

Constant Field Values

HELIX

public static final int HELIX

See Also:

Constant Field Values

len

int len

pos1

final int pos1

pos2

final int pos2

seq1

int seq1

seq2

int seq2

type

final int type

Constructor Detail

StructItem

private StructItem(int type,
                   int pos1,
                   int pos2)

Method Detail

containsBase

public boolean containsBase(int baseIndex)

Returns true if this helix element the nucleobase as the given index.

Dot

public static NewFileWindow.StructItem Dot(int seqPos,
                                           int charPos)

Error

public static NewFileWindow.StructItem Error(int charPos)

Error

public static NewFileWindow.StructItem Error(int charPos1,
                                             int charPos2)

getBase

public int getBase(int positionInHelix)

Returns the sequence-index of the 5'-base at the 0-based position in this helix

getPair

public int getPair(int baseIndex)

Returns -1 if the given index does not belong to this structure element or if it is not paired. Otherwise, returns the index of the base that is paired with the base at the given index.

getTextRegion

public int getTextRegion(int[] regions)

A client calls with with an already-created array of integers. The StructItem must fill it with a list of text regions from which the element was created. Each region occupies two elements in the array: the start and stop positions (inclusive) in the text.

Parameters:

regions - an already-instantiated array of integers to receive the text regions.

Returns:

The number of regions that were filled.

Helix

public static NewFileWindow.StructItem Helix(int seq1,
                                             int seq2,
                                             int len,
                                             int pos1,
                                             int pos2)

isSelected

boolean isSelected(int selStart,
                   int selEnd)

Returns true if the selection falls inside the element and NOT beyond it.

Pair

public static NewFileWindow.StructItem Pair(int seq1,
                                            int seq2,
                                            int pos1,
                                            int pos2)

pairCount

public int pairCount()