org.biojava.nbio.structure

Class ResidueRangeAndLength

java.lang.Object

org.biojava.nbio.structure.ResidueRange

org.biojava.nbio.structure.ResidueRangeAndLength

Direct Known Subclasses:

AugmentedResidueRange

public class ResidueRangeAndLength
extends ResidueRange

A chain, a start residue, and an end residue. Also stores a length. Because of insertion codes, this length is not necessarily end − start.

Field Summary

Fields inherited from class org.biojava.nbio.structure.ResidueRange

CHAIN_REGEX, RANGE_REGEX

Constructor Summary

Constructors

Constructor and Description
ResidueRangeAndLength(String chain, ResidueNumber start, ResidueNumber end, int length)
ResidueRangeAndLength(String chain, String start, String end, int length)

Method Summary

Methods

Modifier and Type	Method and Description
static int	calcLength(List<ResidueRangeAndLength> rrs) Calculates the combined number of residues of the ResidueRanges in rrs.
boolean	equals(Object o)
int	getLength()
int	hashCode()
Iterator<ResidueNumber>	iterator(AtomPositionMap map) Returns a new Iterator over every ResidueNumber in this ResidueRange.
static ResidueRangeAndLength	parse(String s, AtomPositionMap map) Parses a residue range.
static List<ResidueRangeAndLength>	parseMultiple(List<String> ranges, AtomPositionMap map)
static List<ResidueRangeAndLength>	parseMultiple(String s, AtomPositionMap map)

Methods inherited from class org.biojava.nbio.structure.ResidueRange

contains, getChainId, getEnd, getResidue, getStart, multiIterator, multiIterator, parse, parseMultiple, parseMultiple, toString, toString, toStrings

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ResidueRangeAndLength

public ResidueRangeAndLength(String chain,
                     ResidueNumber start,
                     ResidueNumber end,
                     int length)

ResidueRangeAndLength

public ResidueRangeAndLength(String chain,
                     String start,
                     String end,
                     int length)

Method Detail

iterator

public Iterator<ResidueNumber> iterator(AtomPositionMap map)

Returns a new Iterator over every ResidueNumber in this ResidueRange. Stores the contents of map until the iterator is finished, so calling code should set the iterator to null if it did not finish.

Overrides:

iterator in class ResidueRange

calcLength

public static int calcLength(List<ResidueRangeAndLength> rrs)

Calculates the combined number of residues of the ResidueRanges in rrs. Assumes no overlap. If two or more ranges cover the same residues, will over-count the union of the residues.

Parameters:

rrs - A list of ResidueRanges

Returns:

The combined length

Throws:

IllegalArgumentException - If the length of one or more ResidueRange is null

See Also:

getLength()

parse

public static ResidueRangeAndLength parse(String s,
                          AtomPositionMap map)

Parses a residue range. The AtomPositionMap is used to calculate the length and fill in missing information, such as for whole chains ('A:'). Supports the special chain name '_' for single-chain structures. If residues are specified outside of the range given in the map, attempts to decrease the input range to valid values. In extreme cases where this process fails fails to find any valid indices, returns null. For a function which more conservatively represents the input range, without chain inference and error fixes, use ResidueRange.parse(String).

Parameters:

s - A string of the form chain_start-end. For example: A.5-100.

Returns:

The unique ResidueRange corresponding to s.

parseMultiple

public static List<ResidueRangeAndLength> parseMultiple(List<String> ranges,
                                        AtomPositionMap map)

parseMultiple

public static List<ResidueRangeAndLength> parseMultiple(String s,
                                        AtomPositionMap map)

Parameters:

s - A string of the form chain_start-end,chain_start-end, ... For example: A.5-100,R_110-190,Z_200-250.

Returns:

The unique ResidueRange corresponding to s.

getLength

public int getLength()

Returns:

The number of residues in this ResidueRange

equals

public boolean equals(Object o)

Overrides:

equals in class ResidueRange

hashCode

public int hashCode()

Overrides:

hashCode in class ResidueRange