Package pl.poznan.put.structure.formats

Class Ct.ExtendedEntry

java.lang.Object

pl.poznan.put.structure.formats.Ct.ExtendedEntry

All Implemented Interfaces:

Comparable<Ct.ExtendedEntry>

Direct Known Subclasses:

ImmutableExtendedEntry

Enclosing class:

Ct

@Immutable
public abstract static class Ct.ExtendedEntry
extends Object
implements Comparable<Ct.ExtendedEntry>

A single entry in the CT formatted structure.

Constructor Summary

Constructors

Constructor	Description
ExtendedEntry()

Method Summary

Modifier and Type	Method	Description
abstract int	after()
abstract int	before()
String	comment()
int	compareTo(Ct.ExtendedEntry t)
static Ct.ExtendedEntry	fromDotBracketSymbol(DotBracket dotBracket, List<DotBracketSymbol> symbols, int i)	Converts a dot-bracket symbol into an instance of this class.
static Ct.ExtendedEntry	fromEntry(BpSeq.Entry entry)	Converts a BPSEQ entry into an instance of this class.
static Ct.ExtendedEntry	fromEntryAndPdbResidue(BpSeq.Entry entry, ChainNumberICode residue, PdbModel model)	Converts a BPSEQ entry into an instance of this class using information from a parsed 3D data.
static Ct.ExtendedEntry	fromString(String line)	Creates an instance from a string in format: int string int int int int.
abstract int	index()
boolean	isPaired()
abstract int	original()
abstract int	pair()
abstract char	seq()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtendedEntry

public ExtendedEntry()

Method Detail

fromString

public static Ct.ExtendedEntry fromString(String line)

Creates an instance from a string in format: int string int int int int.

Parameters:

line - A line of text formatted as a CT content line.

Returns:

An instance of this class.

fromEntry

public static Ct.ExtendedEntry fromEntry(BpSeq.Entry entry)

Converts a BPSEQ entry into an instance of this class.

Parameters:

entry - A BPSEQ entry to convert.

Returns:

An instance of this class.

fromEntryAndPdbResidue

public static Ct.ExtendedEntry fromEntryAndPdbResidue(BpSeq.Entry entry,
                                                      ChainNumberICode residue,
                                                      PdbModel model)

Converts a BPSEQ entry into an instance of this class using information from a parsed 3D data.

Parameters:

entry - A BPSEQ entry to convert.

residue - A PDB residue mapped to the BPSEQ entry.

model - The PDB model that contains the residue.

Returns:

An instance of this class.

fromDotBracketSymbol

public static Ct.ExtendedEntry fromDotBracketSymbol(DotBracket dotBracket,
                                                    List<DotBracketSymbol> symbols,
                                                    int i)

Converts a dot-bracket symbol into an instance of this class.

Parameters:

dotBracket - The whole dot-bracket structure.

symbols - The list of symbols in the current strand.

i - The index of the current symbol.

Returns:

An instance of this class.

index

@Parameter(order=1)
public abstract int index()

Returns:

The value of `index` column.

seq

@Parameter(order=2)
public abstract char seq()

Returns:

The value of `seq` column.

before

@Parameter(order=3)
public abstract int before()

Returns:

The value of `before` column.

after

@Parameter(order=4)
public abstract int after()

Returns:

The value of `after` column.

pair

@Parameter(order=5)
public abstract int pair()

Returns:

The value of `pair` column.

original

@Parameter(order=6)
public abstract int original()

Returns:

The value of `original` column.

comment

@Default
public String comment()

Returns:

An optional comment.

isPaired

public boolean isPaired()

Returns:

True if `pair` column is non-zero.

toString

public String toString()

Overrides:

toString in class Object

compareTo

public int compareTo(Ct.ExtendedEntry t)

Specified by:

compareTo in interface Comparable<Ct.ExtendedEntry>