info.bioinfweb.libralign.model.implementations

Class SequenceIDManager

java.lang.Object

info.bioinfweb.libralign.model.implementations.SequenceIDManager

public class SequenceIDManager
extends java.lang.Object

Manages mappings between sequence IDs and sequence names.

IDs are unique, while multiple sequences may have the same name.

Since:

0.4.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_ID_PREFIX

Constructor Summary

Constructors

Constructor and Description
SequenceIDManager()
SequenceIDManager(java.lang.String idPrefix)

Method Summary

Modifier and Type	Method and Description
java.lang.String	addSequenceName(java.lang.String sequenceName) Adds a new empty sequence to the underlying data source and generates an ID for it.
java.lang.String	renameSequence(java.lang.String sequenceID, java.lang.String newSequenceName, AlignmentModel<?> model) Renames a sequence in the underlying data source.
java.util.Set<java.lang.String>	sequenceIDsByName(java.lang.String sequenceName) Returns a set of unique sequence IDs associated with the specified name.
java.lang.String	sequenceNameByID(java.lang.String sequenceID) Returns the sequence name (that would be visible to the application user) associated with the specified unique ID.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_ID_PREFIX

public static final java.lang.String DEFAULT_ID_PREFIX

See Also:

Constant Field Values

Constructor Detail

SequenceIDManager

public SequenceIDManager()

SequenceIDManager

public SequenceIDManager(java.lang.String idPrefix)

Method Detail

addSequenceName

public java.lang.String addSequenceName(java.lang.String sequenceName)

Adds a new empty sequence to the underlying data source and generates an ID for it.

If a shared ID manager is used, a previously defined ID is used, if one exists.

Parameters:

sequenceName - the name of the new sequence

Returns:

the unique ID of the new sequence

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for sequences

renameSequence

public java.lang.String renameSequence(java.lang.String sequenceID,
                                       java.lang.String newSequenceName,
                                       AlignmentModel<?> model)
                                throws SequenceNotFoundException

Renames a sequence in the underlying data source.

Parameters:

sequenceID - the ID of the sequence to be renamed

newSequenceName - the new name the sequence shall have

model - the alignment model calling this method (This reference is only needed to set the source of a possible exceptions.)

Returns:

the name the sequence had until now

Throws:

SequenceNotFoundException - if a sequence with the specified ID is not present the underlying data source

sequenceIDsByName

public java.util.Set<java.lang.String> sequenceIDsByName(java.lang.String sequenceName)

Returns a set of unique sequence IDs associated with the specified name. (Multiple sequences with the same name are allowed to be present.)

Parameters:

sequenceName - the name of the sequence that would be visible to the application user

Returns:

the set of sequence IDs (The set maybe empty if no sequence with the specified name is contained in this model. Returns sets are not modifiable.)

sequenceNameByID

public java.lang.String sequenceNameByID(java.lang.String sequenceID)

Returns the sequence name (that would be visible to the application user) associated with the specified unique ID.

Parameters:

sequenceID - the unique unmodifiable ID the sequence is identified by

Returns:

the sequence name or null if no sequence with this ID is contained in this model