htsjdk.samtools

Class SAMSequenceDictionary

java.lang.Object

htsjdk.samtools.SAMSequenceDictionary

All Implemented Interfaces:

java.io.Serializable

public class SAMSequenceDictionary
extends java.lang.Object
implements java.io.Serializable

Collection of SAMSequenceRecords.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static long	serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMSequenceDictionary()
SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSequence(SAMSequenceRecord sequenceRecord)
void	assertSameDictionary(SAMSequenceDictionary that) Non-comprehensive equals(Object)-assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord).
boolean	equals(java.lang.Object o)
long	getReferenceLength()
SAMSequenceRecord	getSequence(int sequenceIndex)
SAMSequenceRecord	getSequence(java.lang.String name)
int	getSequenceIndex(java.lang.String sequenceName)
java.util.List<SAMSequenceRecord>	getSequences()
int	hashCode()
boolean	isEmpty()
void	setSequences(java.util.List<SAMSequenceRecord> list) Replaces the existing list of SAMSequenceRecords with the given list.
int	size()

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

SAMSequenceDictionary

public SAMSequenceDictionary()

SAMSequenceDictionary

public SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list)

Method Detail

getSequences

public java.util.List<SAMSequenceRecord> getSequences()

getSequence

public SAMSequenceRecord getSequence(java.lang.String name)

setSequences

public void setSequences(java.util.List<SAMSequenceRecord> list)

Replaces the existing list of SAMSequenceRecords with the given list.

Parameters:

list - This value is used directly, rather than being copied.

addSequence

public void addSequence(SAMSequenceRecord sequenceRecord)

getSequence

public SAMSequenceRecord getSequence(int sequenceIndex)

Returns:

The SAMSequenceRecord with the given index, or null if index is out of range.

getSequenceIndex

public int getSequenceIndex(java.lang.String sequenceName)

Returns:

The index for the given sequence name, or -1 if the name is not found.

size

public int size()

getReferenceLength

public long getReferenceLength()

Returns:

The sum of the lengths of the sequences in this dictionary

isEmpty

public boolean isEmpty()

assertSameDictionary

public void assertSameDictionary(SAMSequenceDictionary that)

Non-comprehensive equals(Object)-assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord).

Throws:

java.lang.AssertionError - When the dictionaries are not the same, with some human-readable information as to why

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object