nct.service.sequences
Class DIPSequenceDatabase

java.lang.Object
  extended by nct.service.sequences.DIPSequenceDatabase
All Implemented Interfaces:
SequenceDatabase

public class DIPSequenceDatabase
extends java.lang.Object
implements SequenceDatabase

An implementation of the SequenceDatabase interface that is constructed from a DIP fasta file. The assumption is that at least all of the sequences found in the DIP XIN file will be found in the fasta file.


Field Summary
protected  java.util.Map<java.lang.String,java.lang.String> sequenceMap
           
protected  SynonymMapper synonyms
           
 
Constructor Summary
DIPSequenceDatabase(java.lang.String fastaFile, SynonymMapper synonyms)
           
 
Method Summary
 boolean contains(java.lang.String id)
          Determines whether or not the specified id points to a sequence in the database.
 java.lang.String getSequence(java.lang.String id)
          Returns the sequence associated with the specified id from the database.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

sequenceMap

protected java.util.Map<java.lang.String,java.lang.String> sequenceMap

synonyms

protected SynonymMapper synonyms
Constructor Detail

DIPSequenceDatabase

public DIPSequenceDatabase(java.lang.String fastaFile,
                           SynonymMapper synonyms)
Parameters:
fastaFile - The DIP fastaFile with which to create the database.
Method Detail

contains

public boolean contains(java.lang.String id)
Determines whether or not the specified id points to a sequence in the database.

Specified by:
contains in interface SequenceDatabase
Parameters:
id - The id to search for in the database.
Returns:
True if the id is found in the database, false otherwise.

getSequence

public java.lang.String getSequence(java.lang.String id)
Returns the sequence associated with the specified id from the database.

Specified by:
getSequence in interface SequenceDatabase
Parameters:
id - The id of the sequence to retrieve from the database.
Returns:
A String representation of the sequence found in the database.