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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--org.biojava.bio.seq.db.HashSequenceDB
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
Constructor Summary | |
HashSequenceDB()
Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name. |
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HashSequenceDB(IDMaker idMaker)
Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name. |
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HashSequenceDB(IDMaker idMaker,
java.lang.String name)
Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name. |
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HashSequenceDB(java.lang.String name)
Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name. |
Method Summary | |
void |
addSequence(Sequence seq)
Add a sequence under its default id. |
void |
addSequence(java.lang.String id,
Sequence seq)
Add a sequence under a particular id. |
IDMaker |
getIDMaker()
Retrieve the IDMaker associated with this database. |
java.lang.String |
getName()
Get the name of this sequence database. |
Sequence |
getSequence(java.lang.String id)
Retrieve a single sequence by its id. |
java.util.Set |
ids()
Get an imutable set of all of the IDs in the database. |
SequenceIterator |
sequenceIterator()
Returns a SequenceTterator over all sequences in the database. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public HashSequenceDB()
public HashSequenceDB(IDMaker idMaker)
idMaker
- the object that will work out the default id for a sequencepublic HashSequenceDB(java.lang.String name)
name
- the name for this databasepublic HashSequenceDB(IDMaker idMaker, java.lang.String name)
idMaker
- the object that will work out the default id for a sequencename
- the name for this databaseMethod Detail |
public java.lang.String getName()
public Sequence getSequence(java.lang.String id)
the
- id to retrieve bypublic java.util.Set ids()
public SequenceIterator sequenceIterator()
public void addSequence(java.lang.String id, Sequence seq)
id
- the id to useseq
- the Sequence to addpublic IDMaker getIDMaker()
public void addSequence(Sequence seq)
seq
- the Sequence to add
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